Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

Rabanal et al. (2022) Nucleic Acids Res, published online Dec 1, 2022

Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Eyach15-2 to HiFi assemblies of the same sample. The use of five different assemblers starting from subsampled data allowed us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of >85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between the Eyach15-2 accession and the reference accession Col-0.

It is entitled "Characterization of a natural Arabidopsis thaliana - Pseudomonas viridiflava pathosystem"

Congratulations, Alejandra!

MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data

Hüther et al. (2022) Quant. Plant Biol. 3, e9

Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype–epigenotype associations.

Jiawei Wang, a postdoc in the lab from 2005 to 2011 supported by EMBO, is one of this year's Xplorer Prize awardees, recognizing his fundamental contributions to plant developmental biology, including having been a pioneer in scRNA-seq analyses of plants. Congratulations, Jiawei!

(Translated from German)

Tübingen Children's University

Max Planck researcher Detlef Weigel at the Children's University: Big beak on demand

Max Planck researcher Detlef Weigel talked about dogs, finches and the four letters of life.

29.06.2022
By Ulla Steuernagel

Watching evolution at work takes time. At the Tübingen Children's University, it went a little faster. On Tuesday, biology professor Detlef Weigel explained to the young students how biodiversity develops and why a sheepdog is a sheepdog and not a dachshund. About 180 young and old listeners followed the lecture of the renowned and award-winning plant geneticist in the Kupferbau lecture hall.

When most people think of evolution, they think of dinosaurs. After all, they are considered the losers of evolution, having become extinct about 60 million years ago. Or are there still relatives, Weigel asked the children. And they knew that lizards and crocodiles are indeed related to the dinos, and birds even their descendants.

As an evolutionary scientist, you're dealing with very large periods of time and tiny little changes. But sometimes change can happen quickly and be highly visible. Here, "Sam" took the lecture hall stage, a mongrel of Australian shepherd and poodle. This friendly-looking animal with fuzzy fur and floppy ears could no longer be seen that dogs originally descended from wolves. With dogs, breeders mixed and mix, depending on the speed of long legs (sheepdog) or assistance in hunting (dachshund).

However, the development of living creatures usually happens entirely without human intervention. Nature creates the diversity and adapts the species to the environmental conditions. Even Charles Darwin, who was born more than two hundred years ago, observed how the beaks of finches on the Galapagos Islands changed depending on which seeds they had to pick.

However, the research couple Rosemary and Peter Grant found out long after him that large beaks were not advantageous for all times. Beaks evolved according to the weather and the size of the seeds. "Evolution," the professor said, "doesn't just go in one direction." The causes of such changes play out entirely in secret: in the tiny nucleus of each cell. This is where the genetic material, the genes, sit. "Not everything is inherited," Weigel explained. No matter how much the parents go to the gym - the muscles trained here do not transfer to the next generation.

Genes are part of DNA (the deoxyribonucleic acid or English: acid for acid), two spiral-shaped strands. DNA is composed of four elements, each designated by a letter: A, T, G, C. These elements cannot combine at will: G can only combine with C, A can only combine with T, and vice versa. The DNA also does not always remain the same: "Mutations, i.e. changes, occur all the time," says Weigel. If something goes wrong, the body can often repair it itself, but not always. For example, you can get sick from too much exposure to the sun.

Incidentally, the DNA was discovered in Tübingen. Weigel recommended taking a look at Friedrich Miescher's laboratory in the castle. And as far as evolution is concerned, Weigel summarized for the children: It creates changes in genes, it can be fast or slow, it doesn't run in just one direction, and it always takes place.

Wikipedia is often a good source
For his lecture, Detlef Weigel revealed, he had to look up some things, and he did so in a place that tends to be frowned upon in schools: "I find Wikipedia quite a good source," Weigel said. His real area of research is not dogs, but inconspicuous plants. The thale cress (scientific name: Arabidopsis) is very suitable for evolutionary observers; it reproduces quickly and is extremely adaptable, coping with a wide variety of climates in Europe, as well as in Asia, Africa and even Patagonia, just outside the South Pole. It is not obvious that it is also related to wild cabbage, which in turn was once related to wild mustard. But that was a while ago: "Ten million years," said Weigel.

Detlef Weigel with Sam, a family-friendly mix of Australian Shepherd dog and poodle. Picture: Ulrich Metz

Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Derek S. Lundberg et al. (2022) bioRxiv 438366 https://doi.org/10.1101/2021.04.06.438366

Sphingomonas is one of the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana, but relative to Pseudomonas, the ecology of Sphingomonas and its interaction with plants remains elusive. We analyzed the genomic features of over 400 Sphingomonas isolates collected from local A. thaliana populations, which revealed high intergenomic diversity, in contrast to genetically much more uniform Pseudomonas isolates found in the same host populations. Variation in Sphingomonas plasmid complements and additional genomic features suggest high adaptability of this genus, and the widespread presence of protein secretion systems hints at frequent biotic interactions. While some of the isolates showed plant-protective properties in lab tests, this was a rare trait. To begin to understand the extent of strain sharing across alternate hosts, we employed amplicon sequencing and a novel bulk-culturing metagenomics approach on both A. thaliana and neighboring plants. Our data reveal that Sphingomonas and Pseudomonas both thrive on other diverse plant hosts, but that Sphingomonas is a poor competitor in dying or dead leaves.

Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing

Sonja Kersten et al. (2022) bioRxiv 496946 doi.org/10.1101/2022.06.22.496946

Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potential to manifest resistance in the course of only a few generations. Target-site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio's long-read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons is both costly and time consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool-based approaches overcome these limitations and provide reliable allele frequencies, albeit at the expense of not preserving haplotype information. In this proof-of-concept study, we sequenced with PacBio High Fidelity (HiFi) reads long-range amplicons (13.2 kb) encompassing the entire ACCase gene in pools of over hundred individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools and for plants. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analyzed new pools from a Germany-wide collection of A. myosuroides populations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward-in-time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, pointing to the importance of accurate measurement of TSR haplotype prevalence for weed management.

PICLN modulates alternative splicing and ensures adaptation to light and temperature changes in plants

Julieta L. Mateos et al. (2022) bioRxiv 496170 doi.org/10.1101/2022.06.14.496170

Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the PRMT5-methylosome complex. PICLN is part of the PRMT5-methylosome complex in both humans and Arabidopsis thaliana, and we show here that the human PICLN ortholog rescues phenotypes of A. thaliana picln mutants. Altered photomorphogenic and photoperiodic responses in A. thaliana picln mutants are associated with changes in pre-mRNA splicing, which partially overlap with those in prmt5 mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5 are controlled

by A. thaliana GEMIN2. As with GEMIN2 and SME1/PCP, low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.

Monitoring rapid evolution of plant populations at scale with Pool-Sequencing

Lucas Czech et al. (2022) bioRxiv 477408 doi.org/10.1101/2022.02.02.477408

The change in allele frequencies within a population over time represents a fundamental process of evolution. By monitoring allele frequencies, we can analyze the effects of natural selection and genetic drift on populations. To efficiently track time-resolved genetic change, large experimental or wild populations can be sequenced as pools of individuals sampled over time using high-throughput genome sequencing (called the Evolve & Resequence approach, E&R). Here, we present a set of experiments using hundreds of natural genotypes of the model plant Arabidopsis thaliana to showcase the power of this approach to study rapid evolution at large scale. First, we validate that sequencing DNA directly extracted from pools of flowers from multiple plants -- organs that are relatively consistent in size and easy to sample -- produces comparable results to other, more expensive state-of-the-art approaches such as sampling and sequencing of individual leaves. Sequencing pools of flowers from 25-50 individuals at ~40X coverage recovers genome-wide frequencies in diverse populations with accuracy r?>?0.95. Secondly, to enable analyses of evolutionary adaptation using E&R approaches of plants in highly replicated environments, we provide open source tools that streamline sequencing data curation and calculate various population genetic statistics two orders of magnitude faster than current software. To directly demonstrate the usefulness of our method, we conducted a two-year outdoor evolution experiment with A. thaliana to show signals of rapid evolution in multiple genomic regions. We demonstrate how these laboratory and computational Pool-seq-based methods can be scaled to study hundreds of populations across many climates.

Drought selection on Arabidopsis populations and their microbiomes

Talia L. Karasov (2022) bioRxiv 487684 doi.org/10.1101/2022.04.08.487684

Microbes affect plant health, stress tolerance1 and life history2. In different regions of the globe, plants are colonized by distinct pathogenic and commensal microbiomes, but the factors driving their geographic variation are largely unknown3. We identified and measured the core leaf microbiome of Arabidopsis thaliana in its native range, from almost 300 populations across Europe. Comparing the distribution of the approximately 500 major bacterial phylotypes, we discovered marked, geography-dependent differences in microbiome composition within A. thaliana and between A. thaliana and other Brassicaceae, with two distinct microbiome types segregating along a latitudinal gradient. The differences in microbiome composition mirror the spatial genetics of A. thaliana, with 52-68% of variance in the first two principal coordinates of microbiome type explained by host genotype. Microbiome composition is best predicted by drought-associated metrics that are well known to be a major selective agent on A. thaliana populations. The reproducible and predictable associations between specific microbes and water availability raise the possibility that drought not only directly shapes genetic variation in A. thaliana, but does so also indirectly through its effects on the leaf microbiome.

Predictable and stable epimutations induced during clonal propagation with embryonic transcription factors

Wibowo et al. (2022) bioRxiv 2022.03.15.484412

Read the Twitter thread here

Although clonal propagation is frequently used in commercial plant breeding and plant biotechnology programs because it minimizes genetic variation, it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have shown that epigenetic modifications induced during regeneration are associated with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes associated with it remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct tissues. We found that both the epi(genetic) status of explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic state of clonal plants. Phenotypic variation of regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. Moreover, regenerants from roots were particularly affected by the inheritance of epigenetic imprints, which resulted in increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal pathways for targeted manipulation of phenotypic variation in clonal plants.

Gal Ofir is joining us from the lab of Rotem Sorek at the Weizmann Institute, where he has helped to discover and characterize new immunity systems that bacteria use to defend themselves against phages. Check out Gal's impressive publication record on Google Scholar.

For his postdoctoral work, Gal has proposed to explore "the combinatorial space of plant immune receptors and pathogen signals". A main goal will be to establish high-throughput methods for monitoring plant immune responses to an array of viruses, and to use these to characterize not only members of known immune gene families, but also to discover potential new families.

This year's class of HFSP Fellows has been announced here.

Pervasive under-dominance in gene expression as unifying principle of biomass heterosis in Arabidopsis

Yuan et al. (2022) bioRxiv 2022.03.03.482808

Heterosis, the generally superior performance in hybrids compared to their inbred parents, is one of the most enigmatic biological phenomena. Many different explanations have been put forward for heterosis, which begs the question whether common principles underpinning it do exist at all. We performed a systematic transcriptomic study in Arabidopsis thaliana involving 141 random crosses, to search for the general principles, if any, that heterotic hybrids share. Consistent additive expression in F1 hybrids was observed for only about 300 genes enriched for roles in stress response and cell death. Regulatory rare-allele burden affects the expression level of these genes but does not correlate with heterosis. Non-additive gene expression in F1 hybrids is much more common, with the vast majority of genes (over 90%) being expressed below parental average. These include genes that are quantitatively correlated with biomass accumulation in both parents and F1 hybrids, as well as genes strongly associated with heterosis. Unlike in the additive genes, regulatory rare allele burden in this non-additive gene set is strongly correlated with growth heterosis, even though it does not covary with the expression level of these genes. Together, our study suggests that while additive complementation is an intrinsic property of F1 hybrids, the major driver of growth in hybrids derives from the quantitative nature of non-additive gene expression, especially under-dominance and thus lower expression in hybrids than predicted from the parents.

Under Aim 1 of our ERC-SyG project PATHOCOM, we are generating foundational data, by characterizing the intra- and interspecific diversity as well as abundance of pathobiota and commensal microbiota across multiple populations of A. thaliana in three regions in France, Germany and the US that provide geographic and genetic contrasts. We are doing this at a sufficient scale and with sufficient detail that it not only allows inferences about broad patterns, but also enables the detection of interactions between specific genomic variants in subsequent Aims.

We are collecting a structured sample of 3,600 wild plants (from 60 sites across six seasons), which we will genotype by whole-genome shotgun sequencing (WGS). We are planning to obtain conventional measures of microbiota diversity by bacterial 16S and eukaryotic ITS1 rDNA amplicon analyses, which we will also apply to soil samples and companion plants, both of which can be sources of infecting microbes. We will use pathogen enrichment sequencing, PEN-seq, to record in detail genetic variation in three common pathogens, Pseudomonas, Xanthomonas and Pantoea, as well as Sphingomonas. We will ascertain the presence and relative levels of different genes and genetic variants, and estimate diversity at the strain level for our focal taxa. A central question that we will address with these data is the extent of cooperation and competition within the A. thaliana pathobiota. In addition, we will learn how abiotic variables, pathogen richness and the composition of background microbiota and surrounding plants affect the success and genetic makeup of our focal microbes, at the level of individual plants, sites and seasons.

Here you see the team sampling in the Southwest of France.

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant

Or Shalev et al., Nature Ecology & Evolution (published online February 24, 2022)

The community structure in the plant-associated microbiome depends collectively on host–microbe, microbe–microbe and host–microbe–microbe interactions. The ensemble of interactions between the host and microbial consortia may lead to outcomes that are not easily predicted from pairwise interactions. Plant–microbe–microbe interactions are important to plant health but could depend on both host and microbe strain variation. Here we study interactions between groups of naturally co-existing commensal and pathogenic Pseudomonas strains in the Arabidopsis thaliana phyllosphere. We find that commensal Pseudomonas prompt a host response that leads to selective inhibition of a specific pathogenic lineage, resulting in plant protection. The extent of protection depends on plant genotype, supporting that these effects are host-mediated. Strain-specific effects are also demonstrated by one individual Pseudomonas isolate eluding the plant protection provided by commensals. Our work highlights how within-species genetic differences in both hosts and microbes can affect host–microbe–microbe dynamics.

Collaboration with Ian Henderson (Cambridge):

Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

Fernando Rabanal et al. bioRxiv 480579 doi 10.1101/2022.02.15.480579 (posted February 16, 2022)

Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of >85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two A. thaliana accessions.

Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

Julia Kreiner et al., eLife 11:e70242 (2022). doi: 10.7554/eLife.70242

Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 18 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size (Ne) estimate of 8x107. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median allele age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. The evolutionary history of TSR has also been shaped by both intra- and inter-locus allelic interactions. We report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.

Mutation bias reflects natural selection in Arabidopsis thaliana

Grey Monroe et al., Nature, published online January 12, 2022

Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r?=?0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.

Update on January 23: Altmetric score: top 7% of all Nature articles of similar age. Current Almetric score here.

Rafal Gutaker, former postdoc with Hernán Burbano and now a group leader at Kew Botanical Gardens, and Derek Lundberg, current postdoc and soon Group Leader at SLU Uppsala, won ERC Starting Grants. Rafal's project GREENrice aims to unlock the properties of pre-Green Revolution rice with focus on nitrogen economy. Derek's SPINOCULANT project has the goal of revealing the secrets to success of Sphingomonas, a versatile bacterial genus with exceptional potential as a beneficial agricultural inoculant. The full list of grantees can be found here. With these two awards, a grand total of 18 ERC grants have been awarded to current and former WeigelWorld members!

MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant WGBS data

Patrick Hüther et al. bioRxiv 475031 doi 10.1101/2022.01.06.475031 (posted January 6, 2022)

Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Many WGBS-based studies aim to identify biologically relevant loci that display differential methylation between genotypes, treatment groups, tissues, or developmental stages. Over the years, different tools have been developed to extract differentially methylated regions (DMRs) from whole-genome data. Often, such tools are built upon assumptions from mammalian data and do not consider the substantially more complex and variable nature of plant DNA methylation. Here, we present MethylScore, a pipeline to analyze WGBS data and to account for plant-specific DNA methylation properties. MethylScore processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. It uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation, substantially reducing the number of necessary statistical tests while increasing the signal-to-noise ratio and the statistical power. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1001 Genomes dataset to unveil known and unknown genotype-epigenotype associations. MethylScore is an accessible pipeline for plant WGBS data, with unprecedented features for DMR calling in small- and large-scale datasets; it is built as a Nextflow pipeline and its source code is available at https://github.com/Computomics/MethylScore.

Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms

Or Shalev et al., ISME J, published December 11, 2021

Plants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.

Current and former members of the Weigel Lab present the "Celebration of Plant Science 2021“, a free International Online Symposium with exceptional line up of speakers, on Dec 16, 2021. More information here.

Wallenberg Academy Fellows, the career program for young researchers launched by the Knut and Alice Wallenberg Foundation in 2012, provides long-term funding for young, promising Swedish and foreign researchers from all academic fields. Derek, who will start his own lab at SLU Uppsala next year, was just named a recipient of this prestigious award. Congratulation, Derek!

Congratulations, Thanvi!

Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia

Gautam Shirsekar et al., Molecular Biology and Evolution, published September 9, 2021

Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.

The EDS1–PAD4–ADR1 node mediates Arabidopsis pattern-triggered immunity

Rory N. Pruitt et al., Nature 598, 495–499 (2021)

Plants deploy cell-surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens1. LRR receptor kinases and LRR receptor proteins at the plasma membrane recognize microorganism-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR proteins detect microbial effectors inside cells to confer effector-triggered immunity (ETI). Although PTI and ETI are initiated in different host cell compartments, they rely on the transcriptional activation of similar sets of genes2, suggesting pathway convergence upstream of nuclear events. Here we report that PTI triggered by the Arabidopsis LRR receptor protein RLP23 requires signalling-competent dimers of the lipase-like proteins EDS1 and PAD4, and of ADR1 family helper nucleotide-binding LRRs, which are all components of ETI. The cell-surface LRR receptor kinase SOBIR1 links RLP23 with EDS1, PAD4 and ADR1 proteins, suggesting the formation of supramolecular complexes containing PTI receptors and transducers at the inner side of the plasma membrane. We detected similar evolutionary patterns in LRR receptor protein and nucleotide-binding LRR genes across Arabidopsis accessions; overall higher levels of variation in LRR receptor proteins than in LRR receptor kinases are consistent with distinct roles of these two receptor families in plant immunity. We propose that the EDS1–PAD4–ADR1 node is a convergence point for defence signalling cascades, activated by both surface-resident and intracellular LRR receptors, in conferring pathogen immunity.

Our contribution: Extended Data Fig. 10: Classification of LRR-RPs, LRR-RKs and NLRs according to genetic conservation in Arabidopsis accessions.
a, Reads from 80 Arabidopsis accessions were mapped to the reference genome of Col-0. Genes were categorised as being conserved, having complex patterns of variation or exhibiting presence/absence polymorphisms according to the distribution of large-scale polymorphisms across all accessions as inferred from stringent read mappings. Criteria for categorization are detailed in the Methods. The numbers of genes falling into each category are provided in the corresponding bars. b, LRR-RP genes classified as in a. Genes encoding known immune receptors are indicated in bold.

Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition
 
Derek S Lundberg et al., eLife 10:e66186 (2021)

The ratio of microbial population size relative to the amount of host tissue, or ‘microbial load’, is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.

Congratulations, Or!

Congratulations - very well deserved summa cum laude degree!

Together with Fabrice Roux from CNRS in Toulouse and Joy Bergelson from the University of Chicago, we have been awarded one of the prestigious and highly competitive Synergy Grants of the European Research Council (ERC). The PATHOCOM project, funded with 10 million Euros over six years, aims to discover how pathogens team up to cause disease.

Everybody knows that pathogens are the cause of many serious diseases in plants, animals and humans, but what is less widely known is that pathogens rarely act on their own. As one example, the majority of deaths during the 1918/1919 flu pandemic were not caused by the influenza virus, but rather by complications from bacterial pneumonia. How pathogens interact to displace other, harmless microbes and in consequence injure or even kill their hosts is thus a question with broad relevance in many systems.

The goal of  PATHOCOM  is to discover how frequent different types of interactions between microbes, especially cooperation and competition, are in complex microbial communities, and how ecology and genetics alter these interactions. In other words, what are the key drivers of pathogens success, and how do pathogens interact with each other and the environment within their host? Similar to what happens in a massive marathon race with different teams and individual competitors, PATHOCOM aims to learn who among the pathogens competes with whom, and who among them is teaming up with whom to win.

The full grant application can be found here.

Congratulations, Alba!

Congratulations, Sergio!

Moises Exposito-Alonso named a member of the 2020 class of Forbes’ 30 Under 30 Europe list in science and healthcare

Out of the thousands of nominees, the 30 finalists in each of the 10 categories comprise “the world’s most impactful community of young entrepreneurs and game-changers,” said the publication in announcing his selection.  

“Growing up in southern Spain, I saw how Mediterranean forests may be transformed by climate change into arid deserts,” said Moi. “My childhood desire to halt this destructive trend manifested in a career pursuing the answers to fundamental questions about genetics, ecology, and evolution, which I believe are key to solving the global biodiversity crisis.”

Moi received his PhD at the end of 2018 for work on plant adaptation to climate change. Today, he leads a team at the Carnegie Institution that conducts large-scale ecological and genome sequencing experiments to generate maps of a species’ genomic susceptibility to climate change that may guide policymakers and management efforts in how to respond to this global challenge.   

Atypical Resistance Protein RPW8/HR Triggers Oligomerization of the NLR Immune Receptor RPP7 and Autoimmunity

Lei Li et al., Cell Host Microbe, published Feb 26, 2020. https://doi.org/10.1016/j.chom.2020.01.012

In certain plant hybrids, immunity signaling is initiated when immune components interact in the absence of a pathogen trigger. In Arabidopsis thaliana, such autoimmunity and cell death are linked to variants of the NLR RPP7 and the RPW8 proteins involved in broad-spectrum resistance. We uncover the molecular basis for this autoimmunity and demonstrate that a homolog of RPW8, HR4 Fei-0, can trigger the assembly of a higher-order RPP7 complex, with autoimmunity signaling as a consequence. HR4 Fei-0-mediated RPP7 oligomerization occurs via the RPP7 C-terminal leucine-rich repeat (LRR) domain and ATP-binding P-loop. RPP7 forms a higher-order complex only in the presence of HR4 Fei-0 and not with the standard HR4 variant, which is distinguished from HR4 Fei-0 by length variation in C-terminal repeats. Additionally, HR4 Fei-0 can independently form self-oligomers, which directly kill cells in an RPP7-independent manner. Our work provides evidence for a plant resistosome complex and the mechanisms by which RPW8/HR proteins trigger cell death.

"The 2020 Novozymes Prize is being awarded to Professor Detlef Weigel (photo) for his outstanding research contributions that have led to groundbreaking new knowledge of the genetic structure of plants. His work has had major impact on developing innovative biotechnological solutions for crop improvement and understanding how plants adapt to the environment. The Novo Nordisk Foundation awards the Prize, which is accompanied by DKK 3 million."

The American Society of Naturalist's Young Investigator Award goes to applicants who completed their PhD three years preceding the application deadline or are in their last year of a PhD program.

International Max Planck Planck Research School (IMPRS) "From Molecules to Organisms"

Talented junior scientists are offered the opportunity to earn a doctorate under excellent research conditions in Tübingen.  Fully-funded projects are offered at the Max Planck Institute for Developmental Biology, the Friedrich Miescher Laboratory and the University of Tübingen, alongside a structured supporting program. The working language of our school is English.

WeigelWorld is currently seeking students interested in long-read assemblies and the functional analysis of plant microbes and microbiomes.

Apply now!

The Earth BioGenome project: Opportunities and Challenges for Plant Genomics and Conservation

Moises Exposito Alonso, Hajk Georg Drost, Hernán A. Burbano & Detlef Weigel
Plant Journal | 01 December 2019 https://doi.org/10.1111/tpj.14631

Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome Project (Lewin et al., 2018), which aims to produce reference genomes for all eukaryotic species within the next decade. In this Perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300,000 species. For this, we highlight four key points: (1) the unique biological insights that could be gained from studying plants, (2) their apparent underrepresentation in sequencing efforts given the number of threatened species, (3) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (4) the accounting for within?species genetic diversity and the historical aspect of conservation genetics.

AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana

Matteo Togninalli, Ümit Seren, Jan A Freudenthal, J Grey Monroe, Dazhe Meng, Magnus Nordborg, Detlef Weigel, Karsten Borgwardt, Arthur Korte, Dominik G Grimm

Nucleic Acids Research, gkz925, https://doi.org/10.1093/nar/gkz925

Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.

The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere

Karasov et al., bioRxiv 828814, posted November 3, 2019.

A central goal in microbiome research is to learn what distinguishes a healthy from a dysbiotic microbial community. Shifts in diversity and taxonomic composition are important indicators of dysbiosis, but a full understanding also requires knowledge of absolute microbial biomass. Simultaneous information on both microbiome composition and the quantity of its components can provide insight into microbiome function and disease state. Here we use shotgun metagenomics to simultaneously assess microbiome composition and microbial load in the phyllosphere of wild populations of the plant Arabidopsis thaliana. We find that wild plants vary substantially in the load of colonizing microbes, and that high loads are typically associated with the proliferation of single taxa, with only a few putatively pathogenic taxa achieving high abundances in the field. Our results suggest (i) that the inside of a plant leaf is on average sparsely colonized with an estimated two bacterial genomes per plant genome and an order of magnitude fewer eukaryotic microbial genomes, and (ii) that higher levels of microbial biomass often indicate successful colonization by pathogens. Lastly, our results show that load is a significant explanatory variable for loss of estimated Shannon diversity in phyllosphere microbiomes, implying that reduced diversity may be a significant predictor of microbial dysbiosis in a plant leaf.

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

Regalado, Lundberg et al., bioRxiv 823492, posted October 30, 2019.

Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, acquire nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of 16S rDNA and/or the internal transcribed spacer (ITS) of rDNA loci, but the decreasing cost of high-throughput sequencing has made shotgun metagenome sequencing increasingly accessible. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S rDNA and eukaryotic ITS1 amplicon data from 176 of these samples. The shotgun data were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. For shotgun and amplicon data, microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. We use the metagenome data, which captures the ratio of bacterial to plant DNA in leaves of wild plants, to scale the 16S rDNA amplicon data such that they reflect absolute bacterial abundance. We show that this cost-effective hybrid strategy overcomes compositionality problems in amplicon data and leads to fundamentally different conclusions about microbiome community assembly.

Finding genetic variants in plants without complete genomes

Voichek, Y., & Weigel, D., bioRxiv 818096, posted October 25, 2019.

Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the genetic variants detected in GWAS to include major deletions, insertions, and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we re-analyzed 2,000 traits measured in Arabidopsis thaliana, tomato, and maize populations. Associations identified with k-mers recapitulate those found with single-nucleotide polymorphisms (SNPs), however, with stronger statistical support. Moreover, we  identified new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allow detection of a wider range of genetic variants responsible for phenotypic variation.

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

Kreiner et al., PNAS, published September 30, 2019

While evolution has been thought of as playing out over millions of years, adaptation to new environments can occur very rapidly, presenting us with key opportunities to understand evolutionary dynamics. One of the most amazing examples of real-time evolution comes from agriculture, where due to the intense use of a few herbicides, many plant species have evolved herbicide resistance to become aggressive weeds. An important question has been whether herbicide resistance arises only rarely and then spreads quickly, or whether herbicide resistance arises all the time de novo. Our work with glyphosate resistance in US Midwestern and Canadian populations of Amaranthus tuberculatus reveals the answer to be, “it depends,” as we surprisingly find examples for both modes of evolution.

Congratulations, everyone!

Our 9-players team and tournament impressions:

Natural selection on the Arabidopsis thaliana genome in present and future climates

Moises Exposito-Alonso, 500 Genomes Field Experiment Team, Hernán A. Burbano, Oliver Bossdorf, Rasmus Nielsen & Detlef Weigel
Nature, published online August 28, 2019

Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. However, current assessments of the risk of biodiversity associated with climate change do not typically take into account how natural selection influences populations differently depending on their genetic makeup. Here we make use of the extensive genome information that is available for Arabidopsis thaliana and measure how manipulation of the amount of rainfall affected the fitness of 517 natural Arabidopsis lines that were grown in Spain and Germany. This allowed us to directly infer selection along the genome. Natural selection was particularly strong in the hot-dry location in Spain, where 63% of lines were killed and where natural selection substantially changed the frequency of approximately 5% of all genome-wide variants. A significant portion of this climate-driven natural selection of variants was predictable from signatures of local adaptation (R2 = 29–52%), as genetic variants that were found in geographical areas with climates more similar to the experimental sites were positively selected. Field-validated predictions across the species range indicated that Mediterranean and western Siberian populations—at the edges of the environmental limits of this species—currently experience the strongest climate-driven selection. With more frequent droughts and rising temperatures in Europe, we forecast an increase in directional natural selection moving northwards from the southern end of Europe, putting many native A. thaliana populations at evolutionary risk.

We have found issues with our article ‘Sequence and Expression Differences Underlie Functional Specialization of Arabidopsis MicroRNAs miR159 and miR319’, published in Developmental Cell in July 2007.

1. Even though it should be clear from the text, the blot in Figure S10H is the same as the right hand blot in Figure 5H; this information could have been added to the Figure S10H figure legend.

2. The sentence ‘Even the weaker expression of miR319b (which is identical to miR319a) from a 35S:miR319b construct had a pronounced effect on TCP4:GFP RNA levels (Figure 4B)’ in the main text should read ‘Even the weaker expression of miR319b (which is identical to miR319a) from a 35S:miR319b construct had a pronounced effect on TCP4:GFP RNA levels (Figure 4A)’.

3. We noticed spliced lanes in an RNA blot in Figure 4A and Figure S7 that were not mentioned in the figure legend.

We have gone back to the original data, and properly re-assembled Figure S7 with a clear indication of the spliced lanes. A correctly assembled Figure S7 is shown here. (Because spliced gels were not in violation of journal policies at the time of publication, the journal does not judge that this issue requires a formal Correction.)

4. The most serious issue affects Figure 4B. During its assembly, the same image was mistakenly used for the upper and lower left panels of Figure 4B, with one of them rotated by 180°. The two images document experiments performed in 2004, with both panels intended to show similar TCP4:GFP fluorescence signal with or without miR159a overexpression. (There are substantial levels of endogenous miR159a in this tissue, and if miR159a affected TCP4:GFP, we would have expected to see an effect already without miR159a overexpression.)

Unfortunately, the original data of this experiment are no longer available. We have therefore repeated the complete experiment depicted in Figure 4, which includes microscopy images of N benthamiana (Figure 4B) as well as RNA and small RNA blots of the same samples (Figure 4A). TCP4:GFP fluorescence signal was indeed similar with or without miR159a overexpression. A corrected Figure 4 is shown here.

We have discussed this issue with the journal and offered a retraction, since the issue could not be remedied with data available at the time of publication, and since a simple formal Correction is therefore not possible. The journal leadership was of the opinion that retraction of the entire article would go too far, and that they prefer to publish an Editorial Note of Concern regarding these issues. We published a short manuscript describing the repeated experiment with a corrected Figure 4 on bioRxiv, in order to provide a permanent link to these data, and for colleagues to be able to more fully judge the data. We will also mark the paper in our own CVs as having a linked Note of Editorial Concern.

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Van de Weyer et al. Cell 178, 1260-1272

Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes.

RPW8/HR repeats control NLR activation in Arabidopsis thaliana

Barragan et al., PLoS Genetics, published July 25, 2019

In many plant species, conflicts between divergent elements of the immune system, especially nucleotide-binding oligomerization domain-like receptors (NLR), can lead to hybrid necrosis. Here, we report deleterious allele-specific interactions between an NLR and a non-NLR gene cluster, resulting in not one, but multiple hybrid necrosis cases in Arabidopsis thaliana. The NLR cluster is RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7), which can confer strain-specific resistance to oomycetes. The non-NLR cluster is RESISTANCE TO POWDERY MILDEW 8 (RPW8) / HOMOLOG OF RPW8 (HR), which can confer broad-spectrum resistance to both fungi and oomycetes. RPW8/HR proteins contain at the N-terminus a potential transmembrane domain, followed by a specific coiled-coil (CC) domain that is similar to a domain found in pore-forming toxins MLKL and HET-S from mammals and fungi. C-terminal to the CC domain is a variable number of 21- or 14-amino acid repeats, reminiscent of regulatory 21-amino acid repeats in fungal HET-S. The number of repeats in different RPW8/HR proteins along with the sequence of a short C-terminal tail predicts their ability to activate immunity in combination with specific RPP7 partners. Whether a larger or smaller number of repeats is more dangerous depends on the specific RPW8/HR autoimmune risk variant.

After a very successful 7 years in Weigelworld, first as a Postdoc, then as a group leader, Hernán will relocate to London, and start his new lab at UCL.
We wish you all the best!

Clemens, Hernán's first grad student who just defended a very successful PhD thesis, will continue as a postdoc in Stanford. All the best!

Congratulations, Clemens!

Detlef spoke about "How common are spontaneous mutations in plants - and how do they compare to genome editing?"

Last year, the European Court of Justice decided that the EU Directive on the release of genetically modified organisms should also be applied to genome edited plants and animals. Detlef explained what mutations are all about and how the Court arrived at its decision. His slides (in German) can be accessed on figshare.

Congratulations, Julian!

Moi Exposito-Alonso received four awards for his research and dissertation at the Max Planck Institute for Developmental Biology and the Faculty of Mathematics and Natural Sciences of the Eberhard Karls University in Tübingen. Four years ago, he embarked his PhD thesis with the goal to identify genes that could help plants to survive under future climate change.

Moi was particularly interested in how the unique blends of genetic mutations allowed different individuals of the same species to resist various magnitudes of experimentally simulated climates.

In his experiments, he investigated a survival potential of genetically distinct plant specimens from over 500 different natural populations of the small thale cress under simulated extreme drought in greenhouses located in Spain and Germany. This data was then combined with models predicting how temperatures and precipitation are expected to shift geographically in the next few decades in order to understand how plant biodiversity will be affected by climate change.

“Some of these mutations could confer physiological advantages in a changing climate,” explains Moi. “So, the primary goal of my thesis was to rank the importance of all mutations for the future survival of the species.”

As precipitation decreases and temperatures rise, especially in so-called transition zones between the Mediterranean and northern Europe, his forecasts indicate that many of the continent’s predominant plant types wouldn´t have the mutations to survive.

With such information in hand, it will be possible to improve predictions of what populations of a species are at most at risk of extinction driven by climate change.

The thesis was awarded the Leopoldina Award for Young Scientists. This prestigious prize is awarded every two years to young scientists with remarkable scientific achievements. In addition, Moi received the "Reinhold und Maria Teufel-Stiftung Doctoral Award" for outstanding dissertations in the fields of biology and law. Other awards include the "Wilhelm Pfeffer Prize" of the German Botanical Society, for outstanding dissertations in the field of botany, and the Dissertation Prize of the University of Tübingen.

The origins and adaptation of European potatoes reconstructed from historical genomes

Gutaker, R.M., Weiß, C.L., Ellis, D., Anglin, N.L., Knapp, S., Fernández-Alonso, J.L., Prat, S., Burbano H.A.

Nat. Ecol. Evol. https://rdcu.be/bHBXz

Potato, one of the most important staple crops, originates from the highlands of the equatorial Andes. There, potatoes propagate vegetatively via tubers under short days, constant throughout the year. After their introduction to Europe in the sixteenth century, potatoes adapted to a shorter growing season and to tuber formation under long days. Here, we traced the demographic and adaptive history of potato introduction to Europe. To this end, we sequenced 88 individuals that comprise landraces, modern cultivars and historical herbarium samples, including specimens collected by Darwin during the voyage of the Beagle. Our findings show that European potatoes collected during the period 1650–1750 were closely related to Andean landraces. After their introduction to Europe, potatoes admixed with Chilean genotypes. We identified candidate genes putatively involved in long-day pre-adaptation, and showed that the 1650–1750 European individuals were not long-day adapted through previously described allelic variants of the CYCLING DOF FACTOR1 gene. Such allelic variants were detected in Europe during the nineteenth century. Our study highlights the power of combining contemporary and historical genomes to understand the complex evolutionary history of crop adaptation to new environments.

Over two days, we discussed strategies how to best learn the scale of local adaptation in host-pathogen interactions, and how to understand its evolutionary and molecular foundations. Central focus was our Pathodopsis project launched last year. Fun and games and hikes further stimulated our discussions!

The Tübinger Fenster für Forschung (TÜFFF) will offer insights into local cutting edge research. It's open to all members of the public, and all ages. We'll participate with hands-on demonstrations and a public lecture on genome editing in plants.

More information here.

Moi, who obtained his PhD from WeigelWorld last year, will join the Department of Plant Biology of the Carnegie Institution as a staff associate in the summer of 2019. Moi will continue to investigate whether and how plants will evolve to keep pace with climate change by conducting large-scale ecological and genome sequencing experiments. He also develops computational methods to derive fundamental principles of evolution, such as how fast natural populations acquire new mutations and how past climates shaped continental-scale biodiversity patterns. His goal is to use these first principles and computational approaches to forecast evolutionary outcomes of populations under climate change to anticipate potential future biodiversity losses. Moi will also be an assistant professor by courtesy at the Department of Biology at Stanford. For more information see his lab page.

Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

François Vasseur , Louise Fouqueau, Dominique de Vienne, Thibault Nidelet, Cyrille Violle, Detlef Weigel 

PLoS Biology https://doi.org/10.1371/journal.pbio.3000214

Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright’s model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain phenotypic variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright’s model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of major components of crop productivity and yield.

Heterosis primer by Diddahally R. Govindaraju

Detlef has been elected to the American Academy of Arts and Sciences. This year, more than 200 individuals with compelling achievements in academia, business, government, and public affairs have been elected to the Academy.

The Academy was founded in 1780 by John Adams, James Bowdoin, and others who believed the new republic should honor exceptionally accomplished individuals and engage them in advancing the public good. The Academy’s dual mission remains essentially the same 239 years later with honorees from increasingly diverse fields and with the work now focused on the arts, democracy, education, global affairs, and science.

The 2019 class includes poet and foundation president Elizabeth Alexander (Andrew W. Mellon Foundation), gender theorist Judith Butler (University of California, Berkeley), author Jonathan Franzen, and author and former First Lady Michelle L. R. Obama. The 239th class of new members is available at this link.

“While the work of this class includes work never imagined in 1780 – such as cultural studies, cybersecurity, disease ecology, nanotechnology, paleoclimatology, and superconductivity – these members embody the founders’ vision of cultivating knowledge that advances, in their words, a ‘free, virtuous, and independent people,’” said Nancy C. Andrews, the Chair of the Board of the American Academy.

The new class will be inducted at a ceremony in October 2019 in Cambridge, Massachusetts, and join the Academy members who came before them, including Benjamin Franklin and Alexander Hamilton in the eighteenth century; Ralph Waldo Emerson, Maria Mitchell, and Charles Darwin in the nineteenth; Albert Einstein, Margaret Mead, and Martin Luther King, Jr., in the twentieth. Other notable living members are Daniel Barenboim, Judith Dench, Norman Foster, Bill Gates, Ruth Bader Ginsburg. Herbie Hancock, Yo-Yo Ma, Toni Morrison, Anne-Sophie Mutter, Barack Obama, Martin Scorsese, Twyla Tharp, and Denzel Washington.

Congratulations to Patricia Lang, who will work on "Evolutionary genetics of stomata-related climate change-adaptation through space and time", and Giovanna Capovilla, who will work on "Prochlorococcus cyanophage: lysogenic potential and development of a genetic system".

Both Anna-Lena and Darya investigated the amazing diversity of NLR genes in Arabidopsis thaliana:

Anan-Lena's PhD thesis is entitled "The pan-NLR’ome of Arabidopsis thalianaGenome-Wide Analysis of Nucleotide-Binding Domain Leucine-Rich Repeat (NLR) Variation Patterns in Arabidopsis thaliana." Anna-Lena used NLR sequence enrichment combined with PacBio long reads to reconstruct the NLR complement in 65 accessions. 

Darya's PhD thesis is entitled "Genome-Wide Analysis of Nucleotide-Binding Domain Leucine-Rich Repeat (NLR) Variation Patterns in Arabidopsis thaliana". Darya used short reads from the 1001 Genomes Project as well as short reads from A. lyrata and C. rubella accessions to examine within- and between- species conservation of NLR genes.

Phloem companion cell-specific transcriptomic and epigenomic analyses identify MRF1, a novel regulator of flowering

You et al. Plant Cell DOI: https://doi.org/10.1105/tpc.17.00714

The phloem plays essential roles in source-to-sink relationship and in long-distance communication to coordinate growth and development throughout the plant. Here we employed INTACT coupled with low-input, high-throughput sequencing approaches to analyze the changes of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with gene expression in the phloem companion cells (PCCs) of Arabidopsis thaliana shoots in response to changes in photoperiod. We observed a positive correlation between changes in expression and H3K4me3 levels of genes that are involved in essential PCC functions, including regulation of metabolism, circadian rhythm, development and epigenetic modifications. In contrast, changes in H3K27me3 signal appeared to contribute little to gene expression changes. These genomic data illustrate the complex gene-regulatory networks that integrate plant developmental and physiological processes in the PCCs. Emphasizing the importance of cell-specific analyses, we identified a previously uncharacterized MORN-motif repeat protein, MRF1, that was strongly upregulated in the PCCs in response to inductive photoperiod. mrf1 mutation delayed flowering whereas overexpression had the opposite effect, indicating that MRF1 acts as a floral promoter.

Long-term balancing selection drives evolution of immunity genes in Capsella

Koenig et al., eLife 2019;8:e43606 DOI: 10.7554/eLife.43606

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

RPW8/HR Repeats Predict NLR-dependent Hybrid Performance

Barragan et al., bioRxiv, posted Feb 24, 2019 

Hybrid offspring can look very different from their parents, including having greatly increased or decreased fitness. In many plant species, conflicts between divergent elements of the immune system can cause hybrids to express autoimmunity, a generally deleterious syndrome known as hybrid necrosis. We are investigating multiple hybrid necrosis cases in Arabidopsis thaliana that are caused by allele-specific interactions between different variants at two unlinked resistance (R) gene clusters. One is the RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7) cluster, which encodes an intracellular nucleotide binding site-leucine rich repeat (NLR) immune receptors that confer strain-specific resistance to oomycetes. The other is the RESISTANCE TO POWDERY MILDEW 8 (RPW8)/HOMOLOG OF RPW8 (HR) locus, which encodes atypical resistance proteins that can confer broad-spectrum resistance to filamentous pathogens. There is extensive structural variation in the RPW8/HR cluster, both at the level of gene copy number and at the level of C-terminal protein repeats of unknown function. We demonstrate that the number of RPW8/HR repeats correlate, albeit in a complex manner, with the severity of hybrid necrosis when these alleles are combined with specific RPP7 variants. This observation suggests that gross structural differences, rather than individual amino acid polymorphisms, guide the genetic interaction between RPW8/HR and RPP7 alleles. We discuss these findings in light of the similarity of RPW8/HR proteins with pore-forming toxins, MLKL and HET-S, from mammals and fungi.

The Arabidopsis thaliana pan-NLRome

Van de Weyer et al., bioRxiv 537001, posted January 31, 2019

Disease is both among the most important selection pressures in nature and among the main causes of yield loss in agriculture. In plants, resistance to disease is often conferred by Nucleotide-binding Leucine-rich Repeat (NLR) proteins. These proteins function as intracellular immune receptors that recognize pathogen proteins and their effects on the plant. Consistent with evolutionarily dynamic interactions between plants and pathogens, NLRs are known to be encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define the majority of the Arabidopsis thaliana species-wide 'NLRome'. From NLR sequence enrichment and long-read sequencing of 65 diverse A. thaliana accessions, we infer that the pan-NLRome saturates with approximately 40 accessions. Despite the high diversity of NLRs, half of the pan-NLRome is present in most accessions. We chart the architectural diversity of NLR proteins, identify novel architectures, and quantify the selective forces that act on specific NLRs, domains, and positions. Our study provides a blueprint for defining the pan-NLRome of plant species.

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

Julia M. Kreiner, Darci Giacomini, Felix Bemm, Bridgit Waithaka, Julian Regalado, Christa Lanz, Julia Hildebrandt, Peter H. Sikkema, Patrick J. Tranel, Detlef Weigel, John R. Stinchcombe, Stephen I. Wright

bioRxiv 498519, posted December 17, 2018

The selection pressure exerted by herbicides has led to the repeated evolution of resistance in weeds. The evolution of herbicide resistance on contemporary timescales provides an outstanding opportunity to investigate key open questions about the genetics of adaptation, in particular the relative importance of adaptation from new mutations, standing genetic variation, and geographic spread of adaptive alleles through gene flow. Glyphosate-resistant Amaranthus tuberculatus poses one of the most significant threats to crop yields in the midwestern United States, with both agricultural populations and resistance only recently emerging in Canada. To understand the evolutionary mechanisms driving the spread of resistance, we sequenced and assembled the A. tuberculatus genome and investigated the origins and population genomics of 163 resequenced glyphosate-resistant and susceptible individuals in Canada and the USA. In Canada, we discovered multiple modes of convergent evolution: in one locality, resistance appears to have evolved through introductions of preadapted US genotypes, while in another, there is evidence for the independent evolution of resistance on genomic backgrounds that are historically non-agricultural. Moreover, resistance on these local, non-agricultural backgrounds appears to have occurred predominantly through the partial sweep of a single amplification haplotype. In contrast, US genotypes and those in Canada introduced from the US show multiple amplification haplotypes segregating both between and within populations. Therefore, while the remarkable diversity of A. tuberculatus has facilitated geographic parallel adaptation of glyphosate resistance, different timescales of selection have favored either adaptation from standing variation or de novo mutation in certain parts of the range.

Long-term balancing selection drives evolution of immunity genes in Capsella

Daniel Koenig et al. bioRxiv https://doi.org/10.1101/477612

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

Leading German plant scientists agree that the gene technology law, which has been interpreted by the European Court of Justice to include genome edited organisms, is outdated and must be changed. They appeal to the Federal ministers of research and science and of agriculture to lead the charge in this matter.

Debate about genome editing and gene technology on October 29, 2018, at DAI Heidelberg.

Public discussion on chances and opportunities for women in STEM professions. With Prof. Katharina Foerster, Dr. Brigit Buschmann, Prof. Corinna Salander and Detlef

November 28, 7 pm, Frauenprojektehaus Tübingen

On November 6 and 7, we spent two days at Kloster Kirchberg to discuss the past, present and future of plant microbiome studies with the labs of Julia Vorholt at ETH and Eric Kemen at University of Tübingen. We generated lots of new ideas, and we are all looking forward to the next installment!

Anita Bollmann from the John Innes Centre received an EMBO Short Term Fellowship for her project "Studying plant-associated interactions of Pseudomonas and Sphingomonas in the A.thaliana phyllosphere".

Reporter criticizes Renate Künast for not addressing genetic modification, but mostly discussing other topics of agricultural relevance. Summary: A win for science based on points.

"Frau Künast meets the enemy"

(C) Filip Fehrmann

Moi defended his thesis on climate change and genetic evolution in Arabidopsis thaliana yesterday. For his effort, he was awarded a 'summa cum laude' -- with distinction. The examiners agreed that the work 'advances our knowledge on how and whether different populations of a species will genetically adapt to the changing climate.'

The thesis touches on many important topics from polygenic adaptation to climate change, to the potential of new mutations contributing to rapid adaptation in colonizing populations, and machine learning methods that combine field experiments, genetic and climate data to predict which populations can adapt to climate change and which ones are most at risk from climate change.

Effie defended her thesis 'Studying salicylic acid function in natural accessions of Arabidopsis thaliana using CRISPR/Cas technology'. She applied CRISPR/Cas9 genome editing of the same gene (ICS1) to multiple accessions, developed with Julian Regalado a versatile amplicon pipeline for rapid detection of genome edits ('CRISPR-finder'), and ascertained that off-target mutations are very rare.

Congratulations, Effie!

European scientists unite to safeguard precision breeding for sustainable agriculture

Detlef will debate Member of Parliament and former Federal Minister for Consumer Protection, Food and Agriculture Renate Künast (Green Party) on genome editing.

Im grünen Bereich?

Monday, October 29, 2018, 8 pm

German American Institute Heidelberg

EFFECTOR OF TRANSCRIPTION factors are novel plant?specific regulators associated with genomic DNA methylation in Arabidopsis

Tedeschi et al., New Pyhtologist, online September 25, 2018

Plant-specific EFFECTORS OF TRANSCRIPTION (ET) are characterised by a variable number of highly conserved ET repeats, which are involved in zinc and DNA binding. In addition, ETs share a GIY-YIG domain, involved in DNA nicking activity. It was hypothesised that ETs might act as epigenetic regulators. Here, methylome, transcriptome and phenotypic analyses were performed to investigate the role of ET factors and their involvement in DNA methylation in Arabidopsis thaliana. Comparative DNA methylation and transcriptome analyses in flowers and seedlings of et mutants revealed ET-specific differentially expressed genes and mostly independently characteristic, ET-specific differentially methylated regions. Loss of ET function results in pleiotropic developmental defects. The accumulation of cyclobutane pyrimidine dimers after ultraviolet stress in et mutants suggests an ET function in DNA repair.

Congratulations, Leily!

Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene

Zhu W, Zaidem M, et al.

PLoS Genet. 2018 Sep 20;14(9):e1007628. doi: 10.1371/journal.pgen.1007628. 

Plants defend themselves against pathogens by activating immune responses. Unfortunately, these can cause unintended collateral damage to the plant itself. Nevertheless, some wild plants have genetic variants that confer a low threshold for the activation of immunity. While these enable a plant to respond particularly quickly to pathogen attack, such variants might be potentially dangerous. We are investigating one such variant of the immune gene ACCELERATED CELL DEATH 6 (ACD6) in the plant Arabidopsis thaliana. We discovered that there are variants at other genetic loci that can mask the effects of an overly active ACD6 gene. One of these genes, SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1), codes for a known immune receptor. The SNC1 variant that attenuates ACD6 activity is rather common in A. thaliana populations, suggesting that new combinations of the hyperactive ACD6 variant and this antagonistic SNC1 variant will often arise by natural crosses. Similarly, because the two genes are unlinked, outcrossing will often lead to the hyperactive ACD6 variants being unmasked again. We propose that allelic diversity at SNC1 contributes to the maintenance of the hyperactive ACD6 variant in natural A. thaliana populations.

Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation

Wibowo, Becker et al.

PNAS, published online September 10, 2018 

While clonally propagated individuals should share identical genomes, there is often substantial phenotypic variation among them. Both genetic and epigenetic modifications induced during regeneration have been associated with this phenomenon. Here we investigated the fate of the epigenome after asexual propagation by generating clonal individuals from differentiated somatic cells through the manipulation of a zygotic transcription factor. We found that phenotypic novelty in clonal progeny was linked to epigenetic imprints that reflect the organ used for regeneration. Some of these organ-specific imprints can be maintained during the cloning process and subsequent rounds of meiosis. Our findings are fundamental for understanding the significance of epigenetic variability arising from asexual reproduction and have significant implications for future biotechnological applications.

Deutschlandfunk radio: Detlef debates Felix Prinz zu Löwenstein, Chairman of the Board of the Organisation of Organic Farmers (Bund Ökologische Lebensmittelwirtschaft BÖLW). You can listen to the debate here.

(Or download the .mp file here.)

An efficient CRISPR vector toolbox for engineering large deletions in Arabidopsis thaliana

Rui Wu et al Plant Methods 14:65

Vectors available at Addgene

Our knowledge of natural genetic variation is increasing at an extremely rapid pace, affording an opportunity to come to a much richer understanding of how effects of specific genes are dependent on the genetic background. To achieve a systematic understanding of such GxG interactions, it is desirable to develop genome editing tools that can be rapidly deployed across many different genetic varieties. We present an efficient CRISPR/Cas9 toolbox of super module (SM) vectors. These vectors are based on a previously described fluorescence protein marker expressed in seeds allowing identification of transgene-free mutants. We have used this vector series to delete genomic regions ranging from 1.7 to 13 kb in different natural accessions of the wild plant Arabidopsis thaliana. Based on results from 53 pairs of sgRNAs targeting individual nucleotide binding site leucine-rich repeat (NLR) genes, we provide a comprehensive overview of obtaining heritable deletions. The SM series of CRISPR/Cas9 vectors enables the rapid generation of transgene-free, genome edited plants for a diversity of functional studies.

Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana

Exposito-Alonso et al., Evolution (2018)

The evolutionary response of organisms to global climate change is expected to be strongly conditioned by preexisting standing genetic variation. In addition, natural selection imposed by global climate change on fitness-related traits can be heterogeneous over time. We estimated selection of life-history traits of an entire genetic lineage of the plant Arabidopsis thaliana occurring in north-western Iberian Peninsula that were transplanted over multiple years into two environmentally contrasting field sites in southern Spain, as southern environments are expected to move progressively northwards with climate change in the Iberian Peninsula. The results indicated that natural selection on flowering time prevailed over that on recruitment. Selection favored early flowering in six of eight experiments and late flowering in the other two. Such heterogeneity of selection for flowering time might be a powerful mechanism for maintaining genetic diversity in the long run. We also found that north-western A. thaliana accessions from warmer environments exhibited higher fitness and higher phenotypic plasticity for flowering time in southern experimental facilities. Overall, our transplant experiments suggested that north-western Iberian A. thaliana has the means to cope with increasingly warmer environments in the region as predicted by trends in global climate change models.

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales

Karaso. Almario, Friedemann et al.

Cell Host & Microbe, Volume 24, Issue 1, 11 July 2018, Pages 155-167.e5

Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.

Transmission ratio distortion is frequent in Arabidopsis thaliana controlled crosses

Seymour et al., Heredity (2018), published online June 28

bioRxiv version with a slightly different title: The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana

The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. The preferential transmission of alleles or genotypes is termed transmission ratio distortion (TRD). Examples of TRD have been identified in many species, implying that they are universal, but the resolution of species-wide studies of TRD are limited. We have performed a species-wide screen for TRD in over 500 segregating F2 populations of Arabidopsis thaliana using pooled reduced-representation genome sequencing. TRD was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the biological basis of TRD in this species.

panX is a software package for comprehensive pan-genome analysis, web-based interactive visualization and dynamic exploration, developed by Wei Ding and Richard Neher. 

We have recently assembled the genomes of 1,524 Pseudomonas genomes collected from Arabidopsis thaliana around Tübingen. Our web tool allows exploration of these genomes, described in this paper.

Detlef's presentation at the recent Gordon Research Conference on Plant Molecular Biology – Plant Dynamic Systems, focusing on aspects of epigenetic and genetic adaptation to the abiotic environment and advertising our new Pathodopsis project.

Incomplete reprogramming of cell-specific epigenetic marks during asexual reproduction leads to heritable phenotypic variation in plants

Wibowo et al. bioRxiv 2018/02/19/267955

Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. However, it is not currently known if this developmental reprogramming is coupled to a global epigenomic resetting, or what impact it has on the phenotype of the clonal progeny. Here we show that plants asexually propagated via induction of a zygotic developmental program do not fully reset cell-specific epigenetic imprints. These imprints are instead inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the founder cell used. Our results demonstrate how novel phenotypic variation in plants can be unlocked through the incomplete reprogramming of cell-specific epigenetic marks during asexual propagation.

Arabidopsis thaliana populations support long-term maintenance and parallel expansions of related Pseudomonas pathogens

Talia L Karasov, Juliana Almario, Claudia Friedemann, Wei Ding, Michael Giolai, Darren Heavens, Sonja Kersten, Derek S Lundberg, Manuela Neumann, Julian Regalado, Richard A Neher, Eric Kemen, Detlef Weigel

Crop disease outbreaks are commonly associated with the clonal expansion of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site 16S rDNA survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct pathogenic sublineages. The coexistence of diverse sublineages suggests that in contrast to crop systems, no single strain has been able to overtake these A. thaliana populations in the recent past. An important question for the future is how the maintenance of pathogenic diversity is influenced by host genetic variation versus an environment with more microbial and abiotic heterogeneity than in agricultural systems.

Seminar at UC San Diego at the Minisymposium of the "Food & Fuel for the 21st Century" group.

Detlef discussed collaborative work with Pepe Gutierrez-Marcos, led by Anjar Wibowo and Claude Becker, on epigenetics and transgenerational inheritance of stress resilience, as well as work led by Moises Exposito, on predicting future adaptation to climate change (also a recent bioRxiv preprint).

Life on the edge prepares plants for climate change

In the first study to predict whether different populations of the same plant species can adapt to climate change, we found that central European populations of A. thaliana are most at risk.

We investigated A. thaliana because it grows across a very wide geographic range. Surprisingly, Scandinavian plants can cope with extreme drought as well as those from Mediterranean countries, according to our study research just published in Nature Ecology and Evolution. This could be because water in the Scandinavian soil is frozen for many months, making it inaccessible to plants and effectively creating drought conditions.

We planted seeds collected from over two hundred locations as diverse as North Africa, Spain, central Europe and northern Sweden. After they had germinated under optimal conditions,  we challenged them with severe drought, and recorded their ability to survive this stress. Using large-scale genome sequencing information, specific genetic variants could be linked to the plants’ ability to survive longer. Combined with climate predictions from the Intergovernmental Panel on Climate Change, we could generate maps showing the location of genetic variants key to the species’ future survival.

Over the next 50 to 100 years, extreme drought events are predicted to become more and more widespread. This is one of the most challenging consequences of global warming for plants and animals. A steady increase in temperatures is already underway, but this and other studies show that reduced rainfall, which will affect plants and humans alike in a less linear way, is likely to have an even greater effect on survival. By 2070, Central Europe is likely to have much less rainfall than today. Our new research shows that plants in this region do not have the gene variants needed to adapt.  

Previous predictions for the distribution of plants or animals in response to climate change have largely ignored the fact that there is often a tremendous amount of genetic variation in a species. For the first time, knowledge about the geographic distribution of genetic variation has been used to map a species’ ability to adapt by natural selection.

A role for the F-box protein HAWAIIAN SKIRT in plant microRNA function

Lang PLM, Christie MD, Dogan ES, Schwab R, Hagmann J, Van de Weyer AL, Scacchi E, Weigel D.

Plant Physiol. 2017 Nov 7. doi.org/10.1104/pp.17.01313

As regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. While a plethora of factors involved in their biogenesis and action in Arabidopsis thaliana has been described, these processes and their fine-tuning are not fully understood. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156. We identified a new mutant allele of the F-box gene HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes. In hws plants, levels of some endogenous miRNAs are increased and their mRNA targets decreased. Plants constitutively expressing full-length HWS - but not a truncated version lacking the F-box domain - display morphological and molecular phenotypes resembling those of mutants defective in miRNA biogenesis and activity. In combination with such mutants, hws loses its delayed floral organ abscission ('skirt') phenotype, suggesting epistasis. Also, the hws transcriptome profile partially resembles those of well-known miRNA mutants hyl1-2, se-3 and ago1-27, pointing to a role in a common pathway. We thus propose HWS as a novel, F-box dependent factor involved in miRNA function.

Congratulations, Giovanna!

As big fans of Die Maus, we participated in this year's open house event and showed how DNA can be extracted, read and sequenced. 

Big thanks to all kids for a fun day!

Wangsheng Zhu et al., Genome Biology 2017 18:157, doi.org/10.1186/s13059-017-1281-4

Background: The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation. In addition, many agricultural and horticultural species are derived from interspecific hybridization. However, the detailed mechanisms responsible for non-additive phenotypic novelty in hybrids remain elusive.

Results: In an interspecific hybrid between Arabidopsis thaliana and A. lyrata, the vast majority of genes that become upregulated or downregulated relative to the parents originate from A. thaliana. Among all differentially expressed A. thaliana genes, the majority is downregulated in the hybrid. To understand why parental origin affects gene expression in this system, we compare chromatin packing patterns and epigenomic landscapes in the hybrid and parents. We find that the chromatin of A. thaliana, but not that of A. lyrata, becomes more compact in the hybrid. Parental patterns of DNA methylation and H3K27me3 deposition are mostly unaltered in the hybrid, with the exception of higher CHH DNA methylation in transposon-rich regions. However, A. thaliana genes enriched for the H3K27me3 mark are particularly likely to differ in expression between the hybrid and parent.

Conclusions: It has long been suspected that genome-scale properties cause the differential responses of genes from one or the other parent to hybridization. Our work links global chromatin compactness and H3K27me3 histone modification to global differences in gene expression in an interspecific Arabidopsis hybrid.

Denisovans

The Elephants

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

Swarts, K., Gutaker, R. M., Benz, B., Blake, M., Bukowski, R., Holland, J., Kruse-Peeples, M., Lepak, N., Prim, L., Romay, M. C., Ross-Ibarra, J., Sanchez-Gonzalez, J. d. J., Schmidt, C., Schuenemann, V. J., Krause, J., Matson, R. G., Weigel, D., Buckler, E. S., Burbano, H. A. (2017)

People introduced maize to the southwestern US by 4,000 years ago; full agriculture was established quickly in the lowland deserts but delayed in the temperate uplands for 2,000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1,900-year old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaption.

Xin et al. (2017) SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis. Proc Natl Acad Sci USA, doi: 10.1073/pnas.1706379114

Pre-mRNA processing not only enhances the diversity encoded in the genome without the need to increase the number of genes but also provides a means to adjust cellular transcript abundance. Environmental light has a profound effect on transcript accumulation, but how this is partitioned between transcriptional and posttranscriptional processes is largely unknown. Here we describe the identification and characterization of the splicing factor for phytochrome signaling (SFPS), which directly interacts with the photoreceptor phytochrome B. sfps seedlings are hyposensitive to light and display pre-mRNA splicing defects in a large number of genes, many of which regulate light signaling and the circadian clock. Thus, light might control pre-mRNA splicing in addition to transcription of many genes through SFPS to promote photomorphogenesis.

Danelle Seymour defended her PhD thesis on "Exploring the genetics and genomics of Arabidopsis thaliana and its relatives" last year. The dissertation award of the Reinhold-und-Maria-Teufel-Stiftung, which includes a personal purse of €5,000, recognizes the outstanding quality of her work. Congratulations, Danelle!

The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana

Danelle K. Seymour, Eunyoung Chae, Burak I. Ariöz, Daniel Koenig, Detlef Weigel

doi.org/10.1101/158527

The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. Such violations limit intraspecific gene flow and can facilitate the formation of genetic barriers, a first step in speciation. Biased transmission of alleles, or segregation distortion, can result from a number of biological processes including epistatic interactions between incompatible loci, gametic selection, and meiotic drive. Examples of these phenomena have been identified in many species, implying that they are universal, but comprehensive species-wide studies of segregation distortion are lacking. We have performed a species-wide screen for distorted allele frequencies in over 500 segregating populations of Arabidopsis thaliana using reduced-representation genome sequencing. Biased transmission of alleles was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the basis of intraspecific genetic barriers.

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Todd P. Michael, Florian Jupe, Felix Bemm, Stanley T. Motley, Justin P. Sandoval, Olivier Loudet, Detlef Weigel, VJoseph R. Ecker

doi.org/10.1101/149997

While many evolutionary questions can be answered by short read re-sequencing, presence/absence polymorphisms of genes and/or transposons have been largely ignored in large-scale intraspecific evolutionary studies. To enable the rigorous analysis of such variants, multiple high quality and contiguous genome assemblies are essential. Similarly, while genome assemblies based on short reads have made genomics accessible for non-reference species, these assemblies have limitations due to low contiguity. Long-read sequencers and long-read technologies have ushered in a new era of genome sequencing where the lengths of reads exceed those of most repeats. However, because these technologies are not only costly, but also time and compute intensive, it has been unclear how scalable they are. Here we demonstrate a fast and cost effective reference assembly for an Arabidopsis thaliana accession using the USB-sized Oxford Nanopore MinION sequencer and typical consumer computing hardware (4 Cores, 16Gb RAM). We assemble the accession KBS-Mac-74 into 62 contigs with an N50 length of 12.3 Mb covering 100% (119 Mb) of the non-repetitive genome. We demonstrate that the polished KBS-Mac-74 assembly is highly contiguous with BioNano optical genome maps, and of high per-base quality against a likewise polished Pacific Biosciences long-read assembly. The approach we implemented took a total of four days at a cost of less than 1,000 USD for sequencing consumables including instrument depreciation.

Check out his presentation on figshare!

A great two days in Bad Urach, discussing not only exciting science, but also how we can improve ourselves as scientists, both individually and as a team.

Neandertal and Denisovan DNA from Pleistocene sediments

Viviane Slon, Charlotte Hopfe, Clemens L. Weiß, Hernán A. Burbano, Svante Pääbo, Matthias Meyer

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found.

Article (in German) in our local newspaper

Tran, D.T.N., Chung, E.H., Habring-Müller, A., Demar, M., Schwab, R., Dangl, J.L., Weigel, D., Chae, E.

When independently evolved immune receptor variants meet in hybrid plants, they can activate immune signaling in the absence of non-self recognition. Such autoimmune risk alleles have recurrently evolved at the DANGEROUS MIX2 (DM2) nucleotide-binding domain and leucine-rich repeat (NLR)-encoding locus in A. thaliana. One of these activates signaling in the presence of a particular variant encoded at another NLR locus, DM1. We show that the risk variants of DM1 and DM2d NLRs signal through the same pathway that is activated when plant NLRs recognize non-self elicitors. This requires the P loops of each protein and Toll/interleukin-1 receptor (TIR)-domain-mediated heteromeric association of DM1 and DM2d. DM1 and DM2d each resides in a multimeric complex in the absence of signaling, with the DM1 complex shifting to higher molecular weight when heteromerizing DM2 variants are present. The activation of the DM1 complex appears to be sensitive to the conformation of the heteromerizing DM2 variant. Autoimmunity triggered by interaction of this NLR pair thus suggests that activity of heteromeric NLR signaling complexes depends on the sum of activation potentials of partner NLRs.

The Bergelson, Dean, Holm and Nordborg labs are regularly sampling Arabidopsis thaliana field sites in Sweden. Many thanks for their efforts to collect microbial samples, which we will compare to samples from Arabidopsis thaliana collected around Tübingen.

More information and the full ad is here.

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

Expósito Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H. A., Weigel, D.

Prof. Dr. Karsten M. Borgwardt (*1980), currently Associate Professor at ETH Zurich, has been appointed as Full Professor of Data Mining at ETH. Karsten is a highly renowned scientist who works on one of the key problems for the modern life sciences – efficient computer-based searches in fast-growing datasets. Congratulations, Karsten!

For more information: https://www.facebook.com/ScienceMarchTUE/ and marchforscience.com

Today, on Charles Darwin’s 208th birthday, we announce the launch of GrENE-net. A coordinated distributed global evolution experiment to study the Genomics of rapid Evolution in Novel Environments, that will give clues about plant adaptation in a rapidly changing world.

In brief, the idea is to sow seed mixtures of ca. 200 Arabidopsis thaliana ecotypes (previously sequenced in the 1001 genomes project and phenotypically characterized) in a large number of sites around the globe, starting in autumn 2017. Participants will collect plant material during subsequent flowering seasons for pool sequencing to assess allele frequency changes genome-wide. This will be used to investigate rapid evolution by natural selection across space. Combining this data with previous knowledge of phenotypes as well as with records of environmental variables will help to understand natural selection in an ecological context.

You can also find more detailed information, including the latest version of the experimental protocol, on our project website on grene-net.org.
 

Research Associate (TV-L E13 65%)
Population and quantitative genomics of heterosis in cultivated Amaranth


The three species of grain amaranth are ancient crops whose grains have a high nutritional value. Their domestication history is characterized by hybridization and gene flow. Amaranth species are annual plants with small genomes and a short generation time, which makes them attractive model organisms for lab and field experiments. Based on genomic data sets and phenotypic data from intra- and interspecific segregating populations the specific project goals are to (1) identify genomic regions with high diversity and footprints of gene flow between species (2) investigate the effects of interspecific vs. intraspecific heterosis on phenotypic traits and environmental stability a nd (3) map heterosis-associated genomic regions.
 
We are looking for a highly motivated and creative Ph. D. student with a strong background in population genetics, quantitative genetics, bioinformatics, evolutionary biology or plant breeding to work on this project. The student will be co-advised by Dr. Karl Schmid (University of Hohenheim; evoplant.uni-hohenheim.de) and Dr. Detlef Weigel (MPI of Developmental Biology; www.weigelworld.org).
 
The project is part of the Hohenheim-Tübingen Regio Alliance, which offers very good opportunities for interaction and further training. The position is available immediately and is funded for three years according to the E13 TV-L government salary scale (65% part-time). Registration for the Ph.D. program of the Faculty of Agriculture to obtain a Ph.D. degree is expected. The University of Hohenheim is an equal opportunity employer. Women and members of minority groups are strongly encouraged to apply.

Application deadline: 21.02.2017

Please attach the following documents to your application: Please upload your application material (Cover letter, CV, publications, a short letter of motivation and research interests, addresses of at least two references) as a single PDF.

The University of Hohenheim accepts applications via a secure internet site. To the application

We are offering scientists temporary bench or desk space, library access and will help with finding accommodation for US-based scientists who are stranded abroad due to the White House Executive Order 13769 "Protecting the Nation from Foreign Terrorist Entry into the United States" of 27 January, 2017.

Ove Nilsson - director of the UPSC and professor at the Swedish University of Agricultural Sciences

Catoni, M., Griffiths, J., Becker, C., Zabet N. R., Bayon, C., Dapp, M., Liebermann-Lazarovich, M., Weigel, D., Paszkowski, J.

Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss?of?function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon?derived, methylated at all cytosines, which may or may not form epialleles. We provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness of the loci predispose their susceptibility to epiallelic switching. The importance and predictive power of these genetic features were confirmed by analyses of common epialleles in natural Arabidopsis accessions, epigenetic recombinant inbred lines (epiRILs) and also verified in rice.

Grimm, D. G., Roqueiro, D., Salomé, P. A., Kleeberger, S., Greshake, B., Zhu, W., Liu, C., Lippert, C., Stegle, O., Schölkopf, B., Weigel, D., and Borgwardt, K. M. 

The ever-growing availability of high quality genotypes for a multitude of species has enabled researchers to explore the underlying genetic architecture of complex phenotypes at an unprecedented level of detail using genome-wide association studies (GWAS). The systematic comparison of results obtained from GWAS of different traits opens up new possibilities, including the analysis of pleiotropic effects. Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses. In order to facilitate the simple comparison of GWAS results, we present easyGWAS, a powerful, speciesindependent online resource for computing, storing, sharing, annotating and comparing GWAS. The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments and datasets in an interactive and user-friendly interface. easyGWAS is also a public data repository for GWAS data and summary statistics, and already includes published data and results from several major GWAS. We demonstrate the potential of easyGWAS with a case study of the model organism Arabidopsis thaliana, using flowering and growth-related traits. 

https://easygwas.ethz.ch/

Rowan, B. A., Seymour, D. K., Chae, E., Lundberg, D. S., & Weigel, D. (2017).

A major goal for biologists is to understand the connection between genes and phenotypic traits, and genetic mapping in experimental populations remains a powerful approach for discovering the causal genes underlying phenotypes. For genetic mapping, the process of genotyping was previously a major rate-limiting step. Modern sequencing technology has greatly improved the resolution and speed of genetic mapping by reducing the time, labor, and cost per genotyping marker. In addition, the ability to perform genotyping-by-sequencing (GBS) has facilitated large-scale population genetic analyses by providing a simpler way to survey segregating genetic variation in natural populations. Here we present two protocols for GBS, using the Illumina platform, that can be applied to a wide range of genotyping projects in different species. The first protocol is for genotyping a subset of marker positions genome-wide using restriction digestion, and the second is for preparing inexpensive paired-end whole-genome libraries. We discuss the suitability of each approach for different genotyping applications and provide notes for adapting these protocols for use with a liquid-handling robot.

Nam, Y. J., Herman, D., Blomme, J., Chae, E., Kojima, M., Coppens, F., Storme, V., Van Daele, T., Dhondt, S., Sakakibara, H., Weigel, D., Inzé, D., Gonzalez, N.

Although phytohormones such as gibberellins are essential for many conserved aspects of plant physiology and development, plants vary greatly in their responses to these regulatory compounds. Here, we use genetic perturbation of endogenous gibberellin levels to probe the extent of intraspecific variation in gibberellin responses in natural accessions of Arabidopsis thaliana (Arabidopsis). We find that these accessions vary greatly in their ability to buffer the effects of overexpression of GA20ox1, encoding a rate-limiting enzyme for gibberellin biosynthesis, with substantial differences in bioactive gibberellin concentrations as well as transcriptomes and growth trajectories. These findings demonstrate a surprising level of flexibility in the wiring of regulatory networks underlying hormone metabolism and signalling.

Thank you for a wonderful three years in the lab, and we hope you find the time to visit us soon!

The Genetics Society of America (GSA) Medal is awarded to an individual for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics, and exemplify the ingenuity of GSA membership. This year’s recipient was Detlef, and in this personal essay he writes about how he fell in love with Genetics, and continues to think of himself first and foremost as a geneticist.

To the article

Seren, Ü., Grimm, D. G., Fitz, J., Weigel, D., Nordborg, M., Borgwardt, K. M., and Korte, A.

Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype–phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions. Full genome sequencing data for more than 1000 different natural inbred lines are available, and this has encouraged the distributed generation of many types of phenotypic data. To leverage these data for meta analyses, AraPheno (https://arapheno.1001genomes.org) provide a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will facilitate a comparative analysis of the many different types of phenotypic data, which is the base to further enhance our understanding of the genotype–phenotype map. 

Seymour D.K., Chae E., Grimm D.G., Martín Pizarro C., Habring-Müller A., Vasseur F., Rakitsch B., Borgwardt K.M., Koenig D., Weigel D.

The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.

Congratulations, Patricia!

SLU, Uppsala, Sweden

He will soon move on to start a PhD with Claude Becker at the GMI in Vienna. 

Good luck!

Swiadek M, Proost S, Sieh D, Yu J, Todesco M, Jorzig C, Rodriguez Cubillos AE, Plötner B, Nikoloski Z, Chae E, Giavalisco P, Fischer A, Schröder F, Kim ST, Weigel D, Laitinen RA

Hybrid necrosis is a common type of hybrid incompatibility in plants. This phenomenon is caused by deleterious epistatic interactions, resulting in spontaneous activation of plant defenses associated with leaf necrosis, stunted growth and reduced fertility in hybrids. Specific combinations of alleles of ACCELERATED CELL DEATH 6 (ACD6) have been shown to be a common cause of hybrid necrosis in Arabidopsis thaliana. Increased ACD6 activity confers broad-spectrum resistance against biotrophic pathogens but reduces biomass production. We generated 996 crosses among individuals derived from a single collection area around Tübingen (Germany) and screened them for hybrid necrosis. Necrotic hybrids were further investigated by genetic linkage, amiRNA silencing, genomic complementation and metabolic profiling. Restriction site associated DNA (RAD)-sequencing was used to understand genetic diversity in the collection sites containing necrosis-inducing alleles. Novel combinations of ACD6 alleles found in neighbouring stands were found to activate the A. thaliana immune system. In contrast to what we observed in controlled conditions, necrotic hybrids did not show reduced fitness in the field. Metabolic profiling revealed changes associated with the activation of the immune system in ACD6-dependent hybrid necrosis. This study expands our current understanding of the active role of ACD6 in mediating trade-offs between defense responses and growth in A.  thaliana.

Ezgi will start a PhD with former Weigelworld postdoc Chang Liu at the ZMBP in Tübingen, and Jorge will move to Leipzig and join Barbara Treutlein’s lab at MPI-EVA as a postdoc.

We also celebrated the three freshly minted PhD graduates, Diep Tran (starting as a postdoc with Lionel Navarro at the ENS in Paris), Jorge Kageyama (starting as a postdoc with Barbara Treutlein at the MPI-EVA in Leipzig) and Cris Zaidem (starting in 2017 as a postdoc with Michael Purugganan at NYU)

Congratulations, Cris!

Polina Yu Novikova, Nora Hohmann, Viktoria Nizhynska, Takashi Tsuchimatsu, Jamshaid Ali, Graham Muir, Alessia Guggisberg, Tim Paape, Karl Schmid, Olga M Fedorenko, Svante Holm, Torbjörn Säll, Christian Schlötterer, Karol Marhold, Alex Widmer, Jun Sese, Kentaro K Shimizu, Detlef Weigel, Ute Krämer, Marcus A Koch & Magnus Nordborg

The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.

Congratulations, Jorge!

Liu, C., Wang, C., Wang, G., Becker, C., Zaidem, M., Weigel, D.

The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method, to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5' and 3' ends of genes, forming local chromatin loops. Such self-loop structures of genes are more likely to occur in more highly expressed genes, although they can also be found in silent genes. Silent genes with local chromatin loops are highly enriched for the histone variant H3.3 at their 5' and 3' ends but depleted of repressive marks such as heterochromatic histone modifications and DNA methylation in flanking regions. Our results suggest that, different from animals, a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.

Congratulations, Diep!

Kawakatsu, T., Huang, S.-S. C., Jupe, F., Sasaki, E., Schmitz, R. J., Urich, M. A., Castanon, R, Nery., J. R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C.-R., Wang, C., Bemm, F., Becker, C., O’Neil, R., O’Malley, R. C., Quarless, D. X., The 1001 Genomes Consortium, Schork, N. J., Weigel, D., Nordborg, M., Ecker, J. R. 

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Iakovidis, M., Teixeira, P. J. P. L., Exposito-Alonso, M., Cowper, M. G., Law, T. F., Liu, Q., Vu, M. C., Dang, T. M., Corwin, J. A., Weigel, D., Dangl, J. L., Grant, S. R. 

We identified loci responsible for natural variation in Arabidopsis thaliana (Arabidopsis) responses to a bacterial pathogen virulence factor, HopAM1. HopAM1 is a type III effector protein secreted by the virulent Pseudomonas syringae strain Pto DC3000. Delivery of HopAM1 from disarmed Pseudomonas strains leads to local cell death, meristem chlorosis, or both, with varying intensities in different Arabidopsis accessions. These phenotypes are not associated with differences in bacterial growth restriction. We treated the two phenotypes as quantitative traits to identify host loci controlling responses to HopAM1. Genome Wide Association (GWA) of 64 Arabidopsis accessions identified independent variants highly correlated with response to each phenotype. Quantitative Trait Locus (QTL) mapping in a recombinant inbred population between Bur-0 and Col-0 accessions revealed genetic linkage to regions distinct from the top GWA hits. Two major QTL associated with HopAM1-induced cell death were also associated with HopAM1-induced chlorosis. HopAM1-induced changes in Arabidopsis gene expression showed that rapid HopAM1- dependent cell death in Bur-0 is correlated with effector-triggered immune responses. Studies of the effect of mutations in known plant immune system genes showed, surprisingly, that both cell death and chlorosis phenotypes are enhanced by loss of EDS1, a regulatory hub in the plant immune signaling network. Our results reveal complex genetic architecture for response to this particular type III virulence effector, in contrast to the typical monogenic control of cell death and disease resistance triggered by most type III effectors. 

Absolute winner spirit - we keep practicing to become next year’s champions! 

Thanks to our numerous fans for believing in us, and thanks to the PhD reps for organizing a fun event!

Teams SWAT (Swift Weigel Attack Team) and Darwin’s Posse: 

Weiss, C. L., Schuenemann, V. J., Devos, J., Shirsekar, G., Reiter, E., Gould, B. A., Stinchcombe, J. R., Krause, J., Burbano, H. A.

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66×10^-4 per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

The 1001 Genome Consortium

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Wibowo, A., Becker, C., Marconi, G., Durr, J., Price, J., Hagmann, J., Papareddy, R., Putra, H., Kageyama, J., Becker, J., Weigel, D., Gutierrez-Marcos J.

Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal ‘short-term stress memory’ with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.

Congratulations, EunCheon!

Congratulations, Danelle!

Venturelli, S., Petersen, S., Langenecker, T., Weigel, D., Lauer, U. and Becker, C.

Plants compete with their neighbors via the release of chemical compounds into the rhizosphere. These phytotoxins originate from a series of secondary metabolites and can be processed further by soil-living microorganisms before exerting their activity on the target plant. To determine the molecular mode of action and the physiological relevance of potential phytotoxins, it is important to simulate true-to-life conditions in laboratory experiments, for example by applying physiologically relevant concentrations. Here, we report on an improved experimental setting to study the function of allelochemicals of the benzoxazolinone class. By adjusting the solvent and the application of the chemicals, we reduced by more than twenty-fold the concentration that is necessary to induce growth defects in the model plant Arabidopsis thaliana.

Rigal, M., Becker, C., Pélissier, T., Pogorelcnik, R., Devos, J., Ikeda, Z., Weigel, D., and Mathieu, O.

Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.

Chae, E., Tran, D. T. N., and Weigel, D.

Plants have a sophisticated innate immune system with which they defend themselves against a myriad of pathogens. During the past two decades, work in a range of species has advanced our knowledge of the molecular and biochemical details of plant immunity. Many of these studies have focused on the action of nucleotide-binding domain/leucine-rich repeat (NB-LRR or NLR) immune receptors. NLR genes constitute the most diverse gene family in plants, reflecting their role in perceiving a very diverse set of molecules that are released by pathogens. There has also been progress in unraveling the forces that drive diversification of NLR and non-NLR immune receptors in wild species. A major recent insight from mechanistic and evolutionary studies is that there is both cooperation and conflict in the plant immune system. Here, we propose that these two antagonistic forces are inherently entangled, and that they are potentially fundamental to our understanding of growth-defense trade-offs.

Bergelson, J., Buckler, E. S., Ecker, J. R., Nordborg, M., and Weigel, D.

Colleagues from the medical field have estimated that up to one third of cell lines are contaminated with other cell lines or are misidentified, and in addition, repeated passaging substantially changes cell line properties (reviewed in Hughes et al., 2007). The medical community has therefore begun to establish standards for verification of cell lines and genetic stocks, and NIH has announced efforts to require validation and to aid researchers in validating their biological material (Lorsch et al., 2014). Plant biologists should do the same. Even though the propagation of seed stocks cannot be directly compared to animal cell culture, contamination is a real possibility, and it is not uncommon that the same genetic stock produces different phenotypes in different laboratories. Confirming the genetic identity of research material is necessary to know whether such phenotypic differences reflect gene-by-environment (GxE) interactions, or whether they are simply due to apples being compared to oranges. 

Winds and snow threatened the success of the experiment, but we verified how tough both Arabidopsis and researchers can be. We finished in good spirits, and more than 200 plates are ready for a systematic molecular analysis. 

Thanks to all who helped!

More information and the full ad is here.

Thanks to all who helped repairing it so quickly!
Special thanks to all the members from Oliver Bossdorf's lab at Uni Tübingen for their help!

The society honors both seminar contributions to the understanding of flowering in Arabidopsis thaliana and the development of multiple community resources. 

Read the Public Release here.

And have a look at past recipients of the GSA medal here.

Huang, S., Weigel, D., Beachy, R. N., and Li, J.-y.

Crop breeding is being revolutionized by rapid progress in DNA sequencing and targeted alteration of DNA sequences by genome editing. Here we propose a regulatory framework for precision breeding with 'genome-edited crops' (GECs) so that society can fully benefit from the latest advances in plant genetics and genomics.

Listen to an Interview with Detlef by Deutschlandfunk, a German radio station [in German].

Here is where the new adventures will start: 

• CRAG in Barcelona, Spain (Nacho; now Group Leader)
• UC Riverside in California, USA (Dan; now Assistant Professor)
• UC Irvine in California, USA (Danelle; now Postdoc with Brandon Gaut)

or here.

Dominik worked with Karsten Borgwardt (now ETH Zürich) and among other things developed easyGWAS: https://easygwas.tuebingen.mpg.de

Weiss, C..L., Dannemann, M., Pruefer K., Burbano, H.A.

Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.

Read Nature News Article

Venturelli, S., Belz, R., Kämper, A., Berger, A., von Horn, K., Wegner, A.,  Böcker, A., Zabulon, G.,  Langenecker, T.,  Kohlbacher, O., Barneche, F.,  Weigel, D.,  Lauer, U., Bitzer, M, Becker, C.

To secure their access to water, light, and nutrients, many plant species have developed allelopathic strategies to suppress competitors. To this end, they release into the rhizosphere phytotoxic substances that inhibit the germination and growth of neighbors. Despite the importance of allelopathy in shaping natural plant communities and for agricultural production, the underlying molecular mechanisms are largely unknown. Here, we report that allelochemicals derived from the common class of cyclic hydroxamic acid root exudates directly affect the chromatin-modifying machinery in Arabidopsis thaliana. These allelochemicals inhibit histone deacetylases both in vitro and in vivo and exert their activity through locus-specific alterations of histone acetylation and associated gene expression. Our multilevel analysis collectively shows how plant-plant interactions interfere with a fundamental cellular process, histone acetylation, by targeting an evolutionarily highly conserved class of enzymes.

Read the Plant Cell Preview Article

Press Release

Galvão, V. C., Collani, S, Horrer, D., Schmid, M.

Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process. This article is protected by copyright. All rights reserved.

Karlsson, P., Christie, M.D., Seymour, D., Wang, H., Wang, X., Hagmann, J., Kulcheski, F.R. and Manavella, P.A.

The biogenesis of microRNAs (miRNAs), which regulate mRNA abundance through posttranscriptional silencing, comprises multiple well-orchestrated processing steps. We have identified the Arabidopsis thaliana K homology (KH) domain protein REGULATOR OF CBF GENE EXPRESSION 3 (RCF3) as a cofactor affecting miRNA biogenesis in specific plant tissues. MiRNA and miRNA-target levels were reduced in apex-enriched samples of rcf3 mutants, but not in other tissues. Mechanistically, RCF3 affects miRNA biogenesis through nuclear interactions with the phosphatases C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 and 2 (CPL1 and CPL2). These interactions are essential to regulate the phosphorylation status, and thus the activity, of the double-stranded RNA binding protein and DICER-LIKE1 (DCL1) cofactor HYPONASTIC LEAVES1 (HYL1)

Picture of Markus with Ove Nilsson (left), also former Weigelworld postdoc and now director of the Umeå Plant Science Centre. 

Its title: 'Characterizing short-term evolution of DNA methylation in A. thaliana using next-generation sequencing'
Congratulations, Jörg! 

Weigel, D., and Nordborg, M.

Darwin’s theory of evolution by natural selection is the foundation of modern biology. However, it has proven remarkably difficult to demonstrate at the genetic, genomic, and population level exactly how wild species adapt to their natural environments. We discuss how one can use large sets of multiple genome sequences from wild populations to understand adaptation, with an emphasis on the small herbaceous plant Arabidopsis thaliana. We present motivation for such studies; summarize progress in describing whole-genome, species-wide sequence variation; and then discuss what insights have emerged from these resources, either based on sequence information alone or in combination with phenotypic data. We conclude with thoughts on opportunities with other plant species and the impact of expected progress in sequencing technology and genome engineering for studying adaptation in nature.

Chang moved over to the other side of the hill, and just started his own group at the Center for Plant Molecular Biology. Silvio follows Markus to Umeå and will continue his projects very far up North. 

Good luck!

The Gordon and Betty Moore Foundation awarded $2.3M to the Two Blades Foundation (2Blades), a charitable organization that supports the development of durable disease resistance in crop plants and their deployment in agriculture. Jeff Dangl (University of North Carolina at Chapel Hill), Brian Staskawicz (University of California, Berkeley), Jonathan Jones (Sainsbury Laboratory in Norwich, UK) and Detlef Weigel (Max Planck Institute for Developmental Biology in Tübingen, Germany) will collaborate to discover the variability of immune system receptors of the nucleotide-binding, leucine-rich repeat (NLR) class. The enormous diversity of NLR proteins has made their genes difficult to study with conventional genome sequencing techniques. These hurdles have recently been overcome, and using a new highly accurate, fast, and cost-efficient technique developed in the Jones lab, the teams will reveal the diversity of NLR proteins within and across plant species.

Its title: 'Causes and Consequences of Hybrid Incompatibilities in Arabidopsis thaliana'

Congratulations, Subu!

The Leopoldina honors his outstanding achievements in the fields of developmental and evolutionary genetics. Weigel has received the Mendel Medal on September 18, 2015, at the ceremonial opening of the Leopoldina's Annual Assembly, which is also attended by German Chancellor Angela Merkel.The Mendel Medal commemorates Gregor Mendel (1822-1884), the founder of genetics. It was established on occasion of the 100th anniversary of the first public presentation of Mendel’s seminal findings in 1865. With this award, the Leopoldina honors pioneering achievements in the field of general and molecular genetics. Previous winners include the Nobel laureates Max Delbrück and Sydney Brenner, both pioneers of modern genetics, the evolutionary biologist Ernst Mayr, and the microbiologist Regine Kahmann.

Liu, C. and Weigel, D. 

Methods that use high-throughput sequencing have begun to reveal features of the three-dimensional structure of genomes at a resolution that goes far beyond that of traditional microscopy. Integration of these methods with other molecular tools has advanced our knowledge of both global and local chromatin packing in plants, and has revealed how patterns of chromatin packing correlate with the genomic and epigenomic landscapes. This update reports recent progress made in this area in plants, and suggests new research directions.

She will continue some of her work on guppy color patterns as a Postdoc in Würzburg. 

We wish her all the best for her future!

Team S.W.A.T (Scientists with(out) athletic talent)

Team 6Flats

Warren, R. L., Keeling, C. I., Yuen, M. M. S., Raymond, A., Taylor, G. A., Vandervalk, B. P., Paulino, D., Robertson, G., Yang, C., Hoffmann, M., Weigel, D., Ritland, C., Isabel, N., Jaquish, B., Yanchuk, A., Bousquet, J., Jone, S. J. M., MacKay, J., Birol, I., and Bohlmann, J.

White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

Kottler, V. A., Künstner, A., Koch, I., Flötenmeyer, M., Langenecker, T., Hoffmann, M., Sharma, E., Weigel, D., and Dreyer, C.

Guppies (Poecilia reticulata) are colorful fish that have attracted the attention of pigmentation researchers for almost a century. Here, we report that the blond phenotype of the guppy is caused by a spontaneous mutation in the guppy ortholog of adenylate cyclase 5 (adcy5). Using double digest restriction site-associated DNA sequencing (ddRADseq) and quantitative trait locus (QTL) mapping, we linked the blond phenotype to a candidate region of 118 kb, in which we subsequently identified a 2-bp deletion in adcy5 that alters splicing and leads to a premature stop codon. We show that adcy5, which affects lifespan and melanoma growth in mouse, is required for melanophore development and formation of male orange pigmentation traits in the guppy. We find that some components of the male orange pattern are particularly sensitive to loss of Adcy5 function. Our work thus reveals a function for Adcy5 in patterning of fish color ornaments.

Francisco-Mangilet A.G., Karlsson P., Kim M.H., Eo H.J., Oh S.A., Kim J.H., Kulcheski F.R., Park S.K., Manavella P.A.

The THO/TREX complex mediates the transport of nascent mRNAs from the nucleus towards the cytoplasm in animals, and it has a role in small interfering RNA-dependent processes in plants. Here we describe five mutant alleles of Arabidopsis thaliana THO2, a core subunit of the plant THO/TREX complex. tho2 mutants present strong developmental defects resembling those in plants compromised in microRNA (miRNA) activity. In agreement, not only the levels of siRNAs, but also of mature miRNAs were reduced in tho2 mutants. As a consequence a feedback mechanism is triggered, increasing the amount of miRNA precursors, finally causing accumulation of miRNA-targeted mRNAs. Yeast two hybrid experiments and confocal microscopy showed that THO2 does not seem to interact with any of the known miRNA biogenesis components, but rather with the splicing machinery, implying an indirect role of THO2 in small RNA biogenesis. Using a RIP approach we found that THO2 is able to interact with miRNA precursors and that tho2 mutants fail to recruit such precursors into the miRNA-processing complex, explaining the reduction in the miRNA production in this mutant background. We also detected alterations in the splicing pattern of genes encoding Serine/Arginine-Rich (SR) proteins in tho2 mutants, supporting a previously unappreciated role of the THO/TREX complex in alternative splicing.

Its title: 'Pigment cell organization and genetic analysis of color pattern formation in the guppy’

Congratulations, Verena!

Read more about Markus' research here. 

Link to retreat pictures.

Koenig D, Weigel D.

For decades a small number of model species have rightly occupied a privileged position in laboratory experiments, but it is becoming increasingly clear that our knowledge of biology is greatly improved when informed by a broader diversity of species and evolutionary context. Arabidopsis thaliana has been the primary model organism for plants, benefiting from a high-quality reference genome sequence and resources for reverse genetics. However, recent studies have made a group of species also in the Brassicaceae family and closely related to A. thaliana a focal point for comparative molecular, genomic, phenotypic and evolutionary studies. In this Review, we emphasize how such studies complement continued study of the model plant itself, provide an evolutionary perspective and summarize our current understanding of genetic and phenotypic diversity in plants.

Willing E. M., Rawat V., Mandáková T., Maumus F., James G. V., Nordström K., Becker C., Warthmann N., Chica C., Szarzynska B., Zytnicki M.,Albani M., Kiefer C., Bergonzi S., Castaings L., Mateos J. L., Berns M. C., Bujdoso N., Piofczyk T., de Lorenzo L., Barrero-Sicilia C., Mateos I.,Piednoël M., Hagmann J., Chen-Min-Tao R., Iglesias-Fernández R., Schuster S. C., Alonso-Blanco C., Roudier F., Carbonero P., Paz-Ares J.,Davis S. J., Pecinka A., Quesneville H., Colot V., Lysak M. A., Weigel D., Coupland G. and Schneeberger K. 

Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.

Smith LM, Burbano HA, Wang X, Fitz J, Wang G, Ural-Blimke Y, Weigel D.

MicroRNAs (miRNAs) are short RNAs involved in gene regulation through translational inhibition and transcript cleavage. After processing from imperfect fold-back structures, miRNAs are incorporated into RNA-induced silencing complexes (RISCs) before targeting transcripts with varying degrees of complementarity. Some miRNAs are evolutionarily deep-rooted, and sequence complementarity with their targets is maintained through purifying selection. Both Arabidopsis and Capsella belong to the tribe Camelineae in the Brassicaceae, with Capsella rubella serving as an outgroup to the genus Arabidopsis. The genome sequence of C. rubella has recently been released, which allows characterization of its miRNA complement in comparison with Arabidopsis thaliana and Arabidopsis lyrata. Through next-generation sequencing, we identify high-confidence miRNA candidates specific to the C. rubella lineage. Only a few lineage-specific miRNAs have been studied for evolutionary constraints, and there have been no systematic studies of miRNA target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in miRNAs and their targets within A. thaliana, and between A. thaliana, A. lyrata and C. rubella. We document a surprising amount of small-scale variation in miRNA-target pairs, where many miRNAs are predicted to have species-specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many miRNA-target pairs can be observed even on a relatively short evolutionary time-scale, with non-random occurrences of differences in miRNAs and their complements in the miRNA precursors, the miRNA* sequences.

Beth A. Rowan, Vipul Patel, Detlef Weigel, and Korbinian Schneeberger 

The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The re-assortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by short read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. While sequencing costs have dropped precipitously in recent years, the costs of library preparation for hundreds of individuals have remained high. To enable rapid and inexpensive CO detection and QTL mapping using low-coverage whole-genome sequencing of large mapping populations, we have developed a new method for library preparation along with Trained Individual GenomE Reconstruction (TIGER), a probabilistic method for genotype and CO predictions for recombinant individuals. In an example case with hundreds of F2 individuals from two Arabidopsis thaliana accessions, we resolved most CO breakpoints to within 2 kb and reduced a major flowering time QTL to a 9-kb interval. In addition, an extended region of unusually low recombination revealed a 1.8-Mb inversion polymorphism on the long arm of chromosome 4. We observed no significant differences in the frequency and distribution of COs between F2 individuals with and without a functional copy of the DNA helicase gene RECQ4A. In summary, we present a new, cost efficient method for large-scale, high-precision genotyping-by-sequencing.

Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D.

There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale, genome-wide epigenetic changes that are maintained over many generations. In the model plant Arabidopsis thaliana, numerous heritable DNA methylation differences have been identified in greenhouse-grown isogenic lines, but it remains unknown how natural, highly variable environments affect the rate and spectrum of such changes. Here we present detailed methylome analyses in a geographically dispersed A. thaliana population that constitutes a collection of near-isogenic lines, diverged for at least a century from a common ancestor. Methylome variation largely reflected genetic distance, and was in many aspects similar to that of lines raised in uniform conditions. Thus, even when plants are grown in varying and diverse natural sites, genome-wide epigenetic variation accumulates mostly in a clock-like manner, and epigenetic divergence thus parallels the pattern of genome-wide DNA sequence divergence.

Patrice A. Salomé and Detlef Weigel

The circadian oscillator is astonishingly robust, to changes in the environment, but also to genomic changes that alter the copy number of its components through genome duplication, gene duplication and homeologous gene loss. While studying the potential effect of aneuploidy on the Arabidopsis thaliana circadian clock, we discovered that a line thought to be trisomic for chromosome 3 also bears the gi-1 mutation, resulting in a short period and late flowering. With the help of whole genome sequencing, we uncovered the unexpected complexity of this trisomic stock's history, as its genome shows evidence of past outcrossing with another A. thaliana accession. Our study indicates that while historical aneuploidy lines exist and are available, it might be safer to generate new individuals and confirm their genomes and karyotypes by sequencing.

Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature

Rubén Alcázar,  Marcel von Reth, Jaqueline Bautor, Eunyoung Chae, Detlef Weigel, Maarten Koornneef, Jane E. Parker

PLoS Genetics
Published: December 11, 2014DOI: 10.1371/journal.pgen.1004848


Mechanisms underlying speciation in plants include detrimental (incompatible) genetic interactions between parental alleles that incur a fitness cost in hybrids. We reported on recessive hybrid incompatibility between an Arabidopsis thaliana strain from Poland, Landsberg erecta (Ler), and many Central Asian A. thaliana strains. The incompatible interaction is determined by a polymorphic cluster of Toll/interleukin-1 receptor-nucleotide binding-leucine rich repeat (TNL) RPP1 (Recognition of Peronospora parasitica1)-like genes in Ler and alleles of the receptor-like kinase Strubbelig Receptor Family 3 (SRF3) in Central Asian strains Kas-2 or Kond, causing temperature-dependent autoimmunity and loss of growth and reproductive fitness. Here, we genetically dissected the RPP1-like Ler locus to determine contributions of individual RPP1-like Ler (R1–R8) genes to the incompatibility. In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance. Incompatibility involves increased R3 expression and engineered R3 overexpression in a neutral background induces dwarfism and sterility. However, no individual RPP1-like Ler gene is sufficient for incompatibility between Ler and Kas-2 or Kond, suggesting that co-action of at least two RPP1-like members underlies this epistatic interaction. We find that the RPP1-like Ler haplotype is frequent and occurs with other Ler RPP1-like alleles in a local population in Gorzów Wielkopolski (Poland). Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible. Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.

Temporal Control of Leaf Complexity by miRNA-Regulated Licensing of Protein Complexes

Ignacio Rubio-Somoza, Chuan-Miao Zhou, Ana Confraria, Claudia Martinho, Patrick von Born, Elena Baena-Gonzalez, Jia-Wei Wang, Detlef Weigel

Current Biology 24, 2714–2719

Highlights

•miR319-targeted TCPs regulate the activity of miR164-(in)dependent CUC proteins
•miR156-targeted SPLs license active transcription factor complexes
•Changes in protein complex composition control age-dependent leaf shape

Summary

The tremendous diversity of leaf shapes has caught the attention of naturalists for centuries. In addition to interspecific and intraspecific differences, leaf morphologies may differ in single plants according to age, a phenomenon known as heteroblasty [ 1 ]. In Arabidopsis thaliana, the progression from the juvenile to the adult phase is characterized by increased leaf serration. A similar trend is seen in species with more complex leaves, such as the A. thaliana relative Cardamine hirsuta, in which the number of leaflets per leaf increases with age. Although the genetic changes that led to the overall simpler leaf architecture in A. thaliana are increasingly well understood [ 2–4 ], less is known about the events underlying age-dependent changes within single plants, in either A. thaliana or C. hirsuta. Here, we describe a conserved miRNA transcription factor regulon responsible for an age-dependent increase in leaf complexity. In early leaves, miR319-targeted TCP transcription factors interfere with the function of miR164-dependent and miR164-independent CUC proteins, preventing the formation of serrations in A. thaliana and of leaflets in C. hirsuta. As plants age, accumulation of miR156-regulated SPLs acts as a timing cue that destabilizes TCP-CUC interactions. The destabilization licenses activation of CUC protein complexes and thereby the gradual increase of leaf complexity in the newly formed organs. These findings point to posttranslational interaction between unrelated miRNA-targeted transcription factors as a core feature of these regulatory circuits.

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

Eunyoung Chae, Kirsten Bomblies, Sang-Tae Kim, Darya Karelina, Maricris Zaidem, Stephan Ossowski, Carmen Martín-Pizarro, Roosa A.E. Laitinen, Beth A. Rowan, Hezi Tenenboim, Sarah Lechner, Monika Demar, Anette Habring-Müller, Christa Lanz, Gunnar Rätsch, Detlef Weigel

Cell, published online November 20, 2014

Highlights

• A species-wide genetic analysis identifies incompatibility hot spots in the genome
• Antagonistic epistasis involving plant NLR immune receptors is a common cause
• Polymorphic NLR tandem arrays can generate multiple incompatibility alleles
• Deleterious epistasis limits the accessible space of immune receptor combinations

Summary
Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hot spots in the genome, often in regions densely populated by nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DM2, which causes multiple independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors limit the combinations of favorable disease resistance alleles accessible to plant genomes.

Danelle K. Seymour, Daniel Koenig, Jörg Hagmann, Claude Becker, Detlef Weigel

PLoS Genetics Published: November 13, 2014; DOI: 10.1371/journal.pgen.1004785

DNA methylation is an ancient molecular modification found in most eukaryotes. In plants, DNA methylation is not only critical for transcriptionally silencing transposons, but can also affect phenotype by altering expression of protein coding genes. The extent of its contribution to phenotypic diversity over evolutionary time is, however, unclear, because of limited stability of epialleles that are not linked to DNA mutations. To dissect the relative contribution of DNA methylation to transposon surveillance and host gene regulation, we leveraged information from three species in the Brassicaceae that vary in genome architecture, Capsella rubella, Arabidopsis lyrata, and Arabidopsis thaliana. We found that the lineage-specific expansion and contraction of transposon and repeat sequences is the main driver of interspecific differences in DNA methylation. The most heavily methylated portions of the genome are thus not conserved at the sequence level. Outside of repeat-associated methylation, there is a surprising degree of conservation in methylation at single nucleotides located in gene bodies. Finally, dynamic DNA methylation is affected more by tissue type than by environmental differences in all species, but these responses are not conserved. The majority of DNA methylation variation between species resides in hypervariable genomic regions, and thus, in the context of macroevolution, is of limited phenotypic consequence.

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.

Wang C, Liu C, Roqueiro D, Grimm D, Schwab R, Becker C, Lanz C, Weigel D.

Genome Res. 2014 Nov 3. pii: gr.170332.113.

The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks, and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.

Dissection of miRNA pathways using Arabidopsis mesophyll protoplasts.

Martinho C, Confraria A, Elias CA, Crozet P, Rubio-Somoza I, Weigel D, Baena-González E.

microRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this paper, we describe a transient expression system in Arabidopsis mesophyll protoplasts that is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, either by overexpression or by the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo.

One on variation in Capsella, with Magnus Nordborg and Barbara Neuffer, and one on adaptation of various Brassicaceae along a steep rainfall cline in Israel, with Katja Tielbörger and Christian Schlötterer.

Read more here:

Starting from scratch: adaptation to variable environments after an extreme bottleneck

Phenotypic and genetic variation in Biscutella didyma and adaptation to environmental change - a combined ecological-genomic approach

Weßling R et al.: Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life.
Cell Host Microbe. 2014 Sep 10;16(3):364-75. doi: 10.1016/j.chom.2014.08.004.

While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.

Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D.
Bioinformatics. 2014 Jul 29. pii: btu513. [Epub ahead of print]

MOTIVATION:
The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections.

RESULT:
We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k-mer spectrum. With high-quality k-mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at trowel-ec.sourceforge.net.

CONTACT:
euncheon.lim@tue.mpg.de or weigel@tue.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Anthony Bolger, … , Christa Lanz, … , Korbinian Schneeberger, … Daniel Koenig, … , Detlef Weigel, Björn Usadel & Alisdair R Fernie

Nature Genetics (2014) doi:10.1038/ng.3046

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.

We'll give you a glimpse of what our lab does, what we are excited about, and what new initiatives we are thinking about. Follow us under #elifetakeover.

This is part of a project where we are following a lineage of A. thaliana that was introduced in historic times in the US. We are interested in adaptation to pathogens as well as epigenetic diversification. In addition, we are using herbarium specimens to look at local evolution and study genome-wide mutation rates in ecological time.

Read more about this work here.

William Wing Ho Ho and Detlef Weigel:

Structural Features Determining Flower-Promoting Activity of Arabidopsis FLOWERING LOCUS T

Open access in Plant Cell.



Modeling surface charge in FT, its antagonist TFL1, and in FT mutant proteins.

François Parcy (who left the lab in 1997), on the evolution of LEAFY DNA binding specificity. This is sort of a follow-up study on a paper by Alexis Maizel, published 2005, also in Science.

In eLife, with the Schneeberger, Keurentjes and Koornneef labs

After a very productive time in WeigelWorld, Lisa Smith left at the end of October to start as a Lecturer/Research Fellow at the University of Sheffield - good luck, Lisa!

He now won a grant that will support his new lab in Santa Fe, Argentina, as a Max Planck Partner Group. Congratulations, Pablo!

Markus Schmid's group, with help from Detlef Weigel's PhD student Felix Ott (who was responsible for the bioinformatic analyses), in collaboration with Richard Immink and Gerco Angenent from Wageningen, show how two splice forms of the FLM transcription factor antagonize each other to control temperature dependent flowering.

Temperature-dependent regulation of flowering by antagonistic FLM variants

David Posé, Leonie Verhage, Felix Ott, Levi Yant, Johannes Mathieu, Gerco C. Angenent, Richard G. H. Immink & Markus Schmid

Nature (2013) doi:10.1038/nature12633
   
The appropriate timing of flowering is crucial for plant reproductive success. It is therefore not surprising that intricate genetic networks have evolved to perceive and integrate both endogenous and environmental signals, such as carbohydrate and hormonal status, photoperiod and temperature1, 2. In contrast to our detailed understanding of the vernalization pathway, little is known about how flowering time is controlled in response to changes in the ambient growth temperature. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process3, 4. FLM is subject to temperature-dependent alternative splicing3. Here we report that the two main FLM protein splice variants, FLM-? and FLM-?, compete for interaction with the floral repressor SVP. The SVP–FLM-? complex is predominately formed at low temperatures and prevents precocious flowering. By contrast, the competing SVP–FLM-? complex is impaired in DNA binding and acts as a dominant-negative activator of flowering at higher temperatures. Our results show a new mechanism that controls the timing of the floral transition in response to changes in ambient temperature. A better understanding of how temperature controls the molecular mechanisms of flowering will be important to cope with current changes in global climate5, 6.

Follow this link to see photos from our retreat in June.

The Laborjournal has released its ranking of developmental biologists active in one of the German speaking countries (Germany, Switzerland, Austria). We lead the list, with almost 5000 citations for articles published in 2007 to 2010. Notably, our h-index for these papers, 41, is 7 points higher than of the colleague with the second highest ranking. We are proud to do so well, especially with the heavy competition from the mammalian stem cell and microRNA fields.

it's official: our ERC Advanced Grant proposal IMMUNEMESIS is funded. The proposal text is here.

IMMUNEMESIS: The Plant Immune System: Epistasis and Fitness-Tradeoffs

A fundamental question in biology is how multicellular organisms distinguish self and non-self. The requirement to specifically recognize only foreign cells and molecules constrains the diversification of the immune system, resulting in conflicts between effective detection of enemies, adaptive changes in the cellular machinery and mating with divergent genotypes from the same species. In plants, there is generally a trade-off between immunity and growth, and immune system activation is often associated with impaired development. There are many examples of autoimmunity in hybrids, caused by a gene product from one parent erroneously interpreting a gene product from the other parent as foreign. This is not surprising, given the extraordinary diversity of many immune genes. On the other hand, hybrid vigor, or heterosis, is commonly observed in F₁ progeny from two inbred parents, and this is widely exploited in breeding. Thus, it is also of practical importance to understand how outcrossing affects the plant immune system. We hypothesize that overt hybrid autoimmunity represents only the tip of the iceberg, and that there are many more subtle non-additive genetic interactions that affect both the plant immune system and growth. We therefore propose a comprehensive research program to dissect epistatic interactions with effects on plant growth and health. Specifically, we will conduct genomics-enabled, systematic forward genetic studies with natural genotypes of the model plant Arabidopsis thaliana and its outcrossing sister species A. lyrata. This will be complemented by experiments that will link diversity of microbial communities with that of the immune system in natural plant populations. The systematic understanding of forces that shape the distribution of immune gene alleles in the wild will have important implications for engineering disease resistance in crops, by helping to chose the best ensembles of resistance genes.

Published today in Science.

Coordination of Flower Maturation by a Regulatory Circuit of Three MicroRNAs.

PLoS Genet 9(3): e1003374. doi:10.1371/journal.pgen.1003374

The development of multicellular organisms relies on interconnected genetic programs that control progression through their life cycle. MicroRNAs (miRNAs) and transcription factors (TFs) play key roles in such regulatory circuits. Here, we describe how three evolutionary conserved miRNA-TF pairs interact to form multiple checkpoints during reproductive development of Arabidopsis thaliana. Genetic, cellular, and physiological experiments show that miR159- and miR319-regulated MYB and TCP transcription factors pattern the expression of miR167 family members and their ARF6/8 targets. Coordinated action of these miRNA-TF pairs is crucial for the execution of consecutive hormone-dependent transitions during flower maturation. Cross-regulation includes both cis- and trans-regulatory interactions between these miRNAs and their targets. Our observations reveal how different miRNA-TF pairs can be organized into modules that coordinate successive steps in the plant life cycle.

of "Structural and Functional Analysis of FLOWERING LOCUS T in Arabidopsis thaliana"

An important contributor was our gene expression atlas paper published in 2005.Click  here for more details

Marco Todesco, Sang-Tae Kim, Eunyoung Chae, Kirsten Bomblies, Maricris Zaidem, Lisa M. Smith, Detlef Weigel, Roosa A. E. Laitinen

PLoS Genet 10, e1004459

A fundamental question in biology is how multicellular organisms distinguish self and non-self. The ability to make this distinction allows animals and plants to detect and respond to pathogens without triggering immune reactions directed against their own cells. In plants, inappropriate self-recognition results in the autonomous activation of the immune system, causing affected individuals to grow less well. These plants also suffer from spontaneous cell death, but are at the same time more resistant to pathogens. Known causes for such autonomous activation of the immune system are hyperactive alleles of immune regulators, or epistatic interactions between immune regulators and unlinked genes. We have discovered a third class, in which the Arabidopsis thaliana immune system is activated by interactions between natural alleles at a single locus, ACCELERATED CELL DEATH 6 (ACD6). There are two main types of these interacting alleles, one of which has evolved recently by partial resurrection of a pseudogene, and each type includes multiple functional variants. Most previously studies hybrid necrosis cases involve rare alleles found in geographically unrelated populations. These two types of ACD6 alleles instead occur at low frequency throughout the range of the species, and have risen to high frequency in the Northeast of Spain, suggesting a role in local adaptation. In addition, such hybrids occur in these populations in the wild. The extensive functional variation among ACD6 alleles points to a central role of this locus in fine-tuning pathogen defenses in natural populations.

User guide for mapping-by-sequencing in Arabidopsis

Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel and Korbinian Schneeberger

Genome Biology 2013, 14:R61 doi:10.1186/gb-2013-14-6-r61

Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.

Just out in Nature Genetics:

Slotte et al.

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

The shift from outcrossing to selfing is common in flowering plants1, 2, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.

Thirteen members of Genome Biology's Editorial Board, including Detlef Weigel, comment in Genome Biology on key advances in the field of genome biology subsequent to that discovery.

Organized by D. Tautz & D. Weigel

EMBL Heidelberg, Germany
Wednesday 1 May - Saturday 4 May 2013

Online program.

A major obstacle in linking evolution and ecology has been that for many of the preferred models for genetic and genomic research, ecological information has been lacking. Conversely, the preferred models for evolutionary ecology have generally not been amenable to genetic experiments and have had poorly developed genomic resources. The ongoing revolution in sequencing technologies is rapidly changing this. Large-scale sequencing-based studies have become affordable for individual labs and support population genomics, investigation of regulatory landscapes of the genomes as well as in situ genetics in a wide range of species. Importantly, such analyses can now be performed with hundreds or even thousands of individuals.

This meeting will present the latest advances with satellite systems, that is, species that are closely related to conventional genetic model organisms, and with entirely new models for evolutionary and ecological genetics and genomics. Special emphasis will be placed on the interaction between organisms as a basis for understanding ecological adaptation. If you want to bring a new species into the genomic era, this meeting is for you.

According to a just published publication analysis in the Laborjournal, WeigelWorld is by the far the most highly cited plant biology lab in German speaking countries. 74 articles published in 2007-2010 were cited a total of 4,440 times, with an h-index of 39 (39 articles that were cited at least 39 times).

It is the first time scientists have decoded the genome of a plant pathogen and its plant host from dried herbarium samples. This opens up a new area of research to understand how pathogens evolve and how human activity impacts the spread of plant disease.

Phytophthora infestans changed the course of history. Even today, the Irish population has still not recovered to pre-famine levels. “We have finally discovered the identity of the exact strain that caused all this havoc”, says Hernán Burbano from the Max Planck Institute for Developmental Biology.

For research to be published in eLife, a team of molecular biologists from Europe and the US reconstructed the spread of the potato blight pathogen from dried plants. Although these were 170 to 120 years old, they were found to have many intact pieces of DNA.

"Herbaria represent a rich and untapped source from which we can learn a tremendous amount about the historical distribution of plants and their pests - and also about the history of the people who grew these plants," according to Kentaro Yoshida from The Sainsbury Laboratory in Norwich.

The researchers examined the historical spread of the fungus-like oomycete Phytophthora infestans, known as the Irish potato famine pathogen. A strain called US-1 was long thought to have been the cause of the fatal outbreak. The current study concludes that a strain new to science was responsible. While more closely related to the US-1 strain than to other modern strains, it is unique. "Both strains seem to have separated from each other only years before the first major outbreak in Europe," says Burbano.

The researchers compared the historic samples with modern strains from Europe, Africa and the Americas as well as two closely related Phytophthora species. The scientists were able to estimate with confidence when the various Phytophthora strains diverged from each other during evolutionary time. The HERB-1 strain of Phytophthora infestans likely emerged in the early 1800s and continued its global conquest throughout the 19^th century. Only in the twentieth century, after new potato varieties were introduced, was HERB-1 replaced by another Phytophthora infestans strain, US-1.

The scientists found several connections with historic events. The first contact between Europeans and Americans in Mexico in the sixteenth century coincides with a remarkable increase in the genetic diversity of Phytophthora. The social upheaval during that time may have led to a spread of the pathogen from its center of origin in Toluca Valley, Mexico. This in turn would have accelerated its evolution.

The international team came to these conclusions after deciphering the entire genomes of 11 historical samples of Phytophthora infestans from potato leaves collected over more than 50 years. These came from Ireland, the UK, Europe and North America and had been preserved in the herbaria of the Botanical State Collection Munich and the Kew Gardens in London.

"Both herbaria placed a great deal of confidence in our abilities and were very generous in providing the dried plants," said Marco Thines from the Senckenberg Museum and Goethe University in Frankfurt, one of the co-authors of this study. "The degree of DNA preservation in the herbarium samples really surprised us," adds Johannes Krause from the University of Tübingen, another co-author. Because of the remarkable DNA quality and quantity in the herbarium samples, the research team could evaluate the entire genome of Phytophthora infestans and its host, the potato, within just a few weeks.

Crop breeding methods may impact on the evolution of pathogens. This study directly documents the effect of plant breeding on the genetic makeup of a pathogen. "Perhaps this strain became extinct when the first resistant potato varieties were bred at the beginning of the twentieth century," speculates Yoshida. “What is for certain is that these findings will greatly help us to understand the dynamics of emerging pathogens. This type of work paves the way for the discovery of many more treasures of knowledge hidden in herbaria.”


The following authors contributed to the publication: Kentaro Yoshida, Liliana M. Cano, Marina Pais and Sophien Kamoun of the Sainsbury Laboratory in Norwich (UK); Verena J. Schuenemann and Johannes of the University of Tuebingen (Germany); Bagdevi Mishra, Rahul Sharma and Marco Thines of the Goethe University and Senckenberg Museum in Frankfurt (Germany); Frank N. Martin of the U.S. Department of Agriculture in California (US); Christa Lanz, Detlef Weigel and Hernán A. Burbano of the Max Planck Institute for Developmental Biology in Tuebingen (Germany).

The study was funded by the European Research Council, the Gatsby Charitable Foundation, the Biotechnology and Biological Sciences Research Council of the UK, the Campaign for the Development of Scientific and Economic Excellence in Hesse (LOEWE), the Deutsche Forschungsgemeinschaft and the Max- Planck Society.


Source:
Kentaro Yoshida et al.

Rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

eLife 2:e00731 doi 10.7554/elife.00731e

The Plant Immune System at the Nexus of Trade-offs Affecting Fitness and Gene Flow

We are investigating three main questions of evolution: (i) How, and how frequently, do new genetic variants arise? (ii) Why do some variants increase in frequency? (iii) And why are some combinations of variants incompatible with each other? Through research directed at answering the third question we have become interested in the analysis of fitness tradeoffs in immunity. A while ago, we developed Arabidopsis thaliana as a model for hybrid necrosis, a syndrome that is characterized by inappropriate activation of the immune system due to self-recognition (Bomblies et al., PLoS Biol 5:e236  [2007]). We have identified dozens of hybrid necrosis cases in A. thaliana and have cloned the causal loci underlying four genetically distinct interactions. Most encode highly polymorphic immune receptors, and I will report on our efforts to describe species- and genome-wide variation at NB-LRR immune receptor genes.

While most hybrid necrosis systems involve two loci, autoimmunity can also be caused by inter-allelic interactions at a single locus, ACCELERATED CELL DEATH 6 (ACD6). We have previously shown that ACD6 is involved in a major fitness tradeoff between growth and pathogen resistance in inbred strains (Todesco et al., Nature 465:632 [2010]). The ACD6 case is particularly interesting, because necrosis is relatively mild, and naturally occurring hybrids survive in the field. Thus, while divergence of pathogen recognition systems can potentially result in reproductive isolation, hyperactivation of the immune system in hybrids may in other cases promote outcrossing in a species that is otherwise predominantly selfing.

Supported by the Max Planck Society and a Gottfried Wilhelm Leibniz Award of the DFG.

Wahl et al. Regulation of Flowering by Trehalose-6-Phosphate Signaling in Arabidopsis thaliana. Science 339, 704-707.

Accompanied by a Perspective by Jonas Danielson and Wolf Frommer.

By Xi Wang, Detlef Weigel and Lisa Smith: Transposon Variants and Their Effects on Gene Expression in Arabidopsis

Abstract

Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants.

In EMBO Journal (Open Access)

Circadian clock adjustment to plant iron status depends on chloroplast and phytochrome function

Patrice A Salomé, Michele Oliva, Detlef Weigel and Ute Krämer

Plant chloroplasts are not only the main cellular location for storage of elemental iron (Fe), but also the main site for Fe, which is incorporated into chlorophyll, haem and the photosynthetic machinery. How plants measure internal Fe levels is unknown. We describe here a new Fe-depen- dent response, a change in the period of the circadian clock. In Arabidopsis, the period lengthens when Fe becomes limiting, and gradually shortens as external Fe levels increase. Etiolated seedlings or light-grown plants treated with plastid translation inhibitors do not respond to changes in Fe supply, pointing to developed chloroplasts as central hubs for circadian Fe sensing. Phytochrome- deficient mutants maintain a short period even under Fe deficiency, stressing the role of early light signalling in coupling the clock to Fe responses. Further mutant and pharmacological analyses suggest that known players in plastid-to-nucleus signalling do not directly participate in Fe sensing. We propose that the sensor governing circa- dian Fe responses defines a new retrograde pathway that involves a plastid-encoded protein that depends on phyto- chromes and the functional state of chloroplasts.

In Plant Physiology:

Tissue-specific silencing of Arabidopsis thaliana SUVH8 by miR171a star

Pablo Manavella, Daniel Koenig, Ignacio Rubio-Somoza, Hernán A Burbano, Claude Becker, and Detlef Weigel

MicroRNAs (miRNAs) are produced from double stranded precursors, from which a short duplex is excised. The strand of the duplex that remains more abundant is usually the active form, the miRNA, while steady-state levels of the other strand, the miRNA*, are generally lower. The executive engines of miRNA-directed gene silencing are RNA-induced silencing complexes (RISCs). During RISC maturation, the miRNA/miRNA* duplex associates with the catalytic subunit, an AGO protein. Subsequently, the guide strand, which directs gene silencing, is retained, while the passenger strand is degraded. Under certain circumstances, the miRNA*s can be retained as guide strands. MiR170 and miR171 are prototypical miRNAs in Arabidopsis thaliana, with well-defined targets. We found that the corresponding star molecules, the sequence-identical miR170* and miR171a* have several features of active miRNAs, such as sequence conservation and AGO1 association. We confirmed that active AGO1-miR171a* complexes are common in A. thaliana and that they trigger silencing of SUVH8, a new miR171a* target that was acquired very recently in the A. thaliana lineage. Our study demonstrates that each miR171a strand can be loaded onto RISC, with separate regulatory outcomes.

Organized by D. Tautz & D. Weigel

EMBL Heidelberg, Germany
Wednesday 1 May - Saturday 4 May 2013

Registration for this event is now live.

A major obstacle in linking evolution and ecology has been that for many of the preferred models for genetic and genomic research, ecological information has been lacking. Conversely, the preferred models for evolutionary ecology have generally not been amenable to genetic experiments and have had poorly developed genomic resources. The ongoing revolution in sequencing technologies is rapidly changing this. Large-scale sequencing-based studies have become affordable for individual labs and support population genomics, investigation of regulatory landscapes of the genomes as well as in situ genetics in a wide range of species. Importantly, such analyses can now be performed with hundreds or even thousands of individuals.

This meeting will present the latest advances with satellite systems, that is, species that are closely related to conventional genetic model organisms, and with entirely new models for evolutionary and ecological genetics and genomics. Special emphasis will be placed on the interaction between organisms as a basis for understanding ecological adaptation. If you want to bring a new species into the genomic era, this meeting is for you.

Plant epialleles

Detlef Weigel and Vincent Colot review the role of epialleles in plant biology and evolution

Genome Biology 2012, 13:249

Manavella et al.: Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

Detlef Weigel is giving a plenary lecture at the International Plant Molecular Biology (IPMB) Congress 2012 in Jeju, Korea, today.

He passed with a magna cum laude. Congratulations, Norman!

In Current Opinion in Plant Biology

Epigenetic variation: origin and transgenerational inheritance.

Recent studies have revealed that epigenetic variation in plant populations exceeds genetic diversity and that it is influenced by the environment. Nevertheless, epigenetic differences are not entirely independent of shared ancestry. Epigenetic modifications have gained increasing attention, because one can now study their patterns across the entire genome and in many different individuals. Not only do epigenetic phenomena modulate the activity of the genome in response to environmental stimuli, but they also constitute a potential source of natural variation. Understanding the emergence and heritability of epigenetic variants is critical for understanding how they might become subject to natural selection and thus affect genetic diversity. Here we review progress in characterizing natural epigenetic variants in model and nonmodel plant species and how this work is helping to delineate the role of epigenetic changes in evolution.

Anusha Srikanth, PhD student in the Schmid group, today defended her thesis, "Dissection of the role of FT and FD in the regulation of flowering in Arabidopsis thaliana". Congratulations, Anusha!

Read our editorial in new top-flight journal eLife, on publishing our first articles.

Independent FLC Mutations as Causes of Flowering Time Variation in Arabidopsis thaliana and Capsella rubella.

Guo YL, Todesco M, Hagmann J, Das S, Weigel D.

This is what he will discuss:

We are investigating three main questions of evolution: (i) How, and how frequently, do new genetic variants arise? (ii) Why do some variants increase in frequency? (iii) And why are some combinations of variants incompatible with each other? To this end, we are employing bottom-up and top-down approaches that rely heavily on large-scale sequencing. Whole-genome sequencing supports a detailed description of the pan-genome of A. thaliana (http://1001genomes.org; Schneeberger et al., PNAS 108:10249 [2011]; Cao et al., Nat Genet 43:956 [2011]), it reveals mutational biases shaping the genome (Ossowski et al. Science 327:92 [2010]), and it allows for rapid mapping of genes with major phenotypic effects (Schneeberger et al., Nat Methods 6:550 [2009]). We have also investigated spontaneous epigenetic variation. Our results suggest that most epialleles are unlikely to contribute to long-term evolution (Becker et al., Nature 480:245).

A major interest in the lab is the analysis of fitness tradeoffs in immunity. Arabidopsis thaliana is an excellent model for hybrid necrosis, a widespread syndrome of hybrid failure in plants (Bomblies et al., PLoS Biol 5:e236  [2007]). Several causal loci encode highly polymorphic immune receptors. While most hybrid necrosis systems involve two loci, autoimmunity can also be caused by inter-allelic interactions at a single locus that is involved in a major fitness tradeoff between growth and pathogen resistance in inbred strains (Todesco et al., Nature 465:632 [2010]). Thus, divergence of pathogen recognition systems can potentially result in reproductive isolation and subsequent speciation.

Physicist Congmao Wang from Shanghai Jiao Tong University joined the Weigel group, and plant biologist Silvio Collani from the University of Padua joined the Schmid group. In addition, informatician Euncheon Lim from Seoul joined us as a potential graduate student.

See full announcement at http://www.elifesciences.org/call-for-submissions/

eLife is a researcher-driven initiative for the very best in science and science communication. eLife promotes rapid, fair, and more constructive review. It will use digital media and open access to increase the influence of published works. eLife is committed to serving authors and advancing careers in science.

eLife will launch at the end of this year; you can follow news and announcements at the eLife website.

Current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms, however, do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. As a proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, which has a genome with several large scale rearrangements relative to A. thaliana. Our approach outlines an alternative roadmap for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available.

See our paper in Plant Journal.

Out in PNAS by Manavella and colleagues: Plant secondary siRNA production determined by microRNA-duplex structure. In plants, miRNA-mediated cleavage of a target triggers in some cases the production of secondary small interfering RNAs (siRNAs), which in turn can silence other genes in trans, a phenomenon called transitivity. Several groups reported in 2010 that 22-nt miRNAs are sufficient, but not essential for generating secondary siRNAs. In this paper, we show that transitivity can be triggered when the small RNA that is not retained in AGO is 22-nt long. Moreover, we demonstrate that asymmetrically positioned bulged bases in the miRNA:miRNA* duplex, regardless of miRNA or miRNA* length, are sufficient for the initiation of transitivity. We propose that the RNA-induced silencing complex reprogramming occurs during the early steps of miRNA loading, before the miRNA duplex is disassembled and the guide strand is selected.

Just out in PNAS: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata, by Hollister, Smith, Guo, Ott, Weigel & Gaut.

However, all three approaches have limitations. In a paper published in Plant Journal, we introduce miRNA-induced gene silencing (MIGS). This method exploits a special 22-nucleotide miRNA of Arabidopsis thaliana, miR173, which can trigger production of another class of small RNAs called trans-acting small interfering RNAs (tasiRNAs). We show that fusion of gene fragments to an upstream miR173 target site is sufficient for effective silencing of the corresponding endogenous gene. MIGS can be reliably used for the knockdown of a single gene or of multiple unrelated genes. In addition, we show that MIGS can be applied to other species by co-expression of miR173.

Just published online in Current Biology

In this paper, we demonstrate that a naturally occurring polymorphism in the MIR164A gene affects leaf shape and shoot architecture in Arabidopsis thaliana, with the effects being modified by additional loci in the genome. A single base pair substitution in the miRNA complementary sequence alters the predicted stability of the miRNA:miRNA(?) duplex. It thereby greatly reduces miRNA accumulation, probably because it interferes with precursor processing. We demonstrate that this is not a rare exception and that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA biogenesis resulting from cis mutations is a common contributor to phenotypic variation in plants.

By Felippe Felippes, Felix Ott and Detlef Weigel, published online December 5, in Nucleic Acids Research.

A Founders Review covering the history of natural variation research in Arabidopsis thaliana, an overview of genetic and genomic tools, current challenges and research directions, and opportunities for future research.

Now in Heredity by Salomé et al.: The recombination landscape in Arabidopsis thaliana F₂ populations Recombination partitions alleles segregating in the progeny of hybrids, and thus has important consequences for the distribution of phenotypic variation in a population. We examined genome-wide recombination events in over 7000 plants from 17 F2 populations derived from crosses between 18 Arabidopsis thaliana accessions. We observed segregation distortion between parental alleles in over half of our populations. Most plants carry only one or two XOs per chromosome pair, and therefore inherit very large, non-recombined genomic fragments from each parent. Recombination frequencies vary between populations but consistently increase adjacent to the centromeres.

On S-locus evolution in A. thaliana and relatives and genome wide comparison of NB-LRR genes in A. thaliana and A. lyrata.

Finally -- after several previous papers in which we developed the tools and vision for the A. thaliana 1001 Genomes project, we just published its first major phase, based on 80 accessions representing much of the native range of the species. Among the major findings are that regions differ substantially in the numbers of sequence variants and deleterious mutations. In addition, we find that the mutation spectrum in the wild differs the more from the one in the laboratory, the older the mutations are. Find out more here.

This paper complements the publicaton of whole-genome assemblies by others and by us.

Beth Rowan, Detlef Weigel and Dan Koenig are discussing how next-generation sequencing is leveling the playing field for forward genetics in many different species. Read more here.

Out in PLoS Genetics. Our work provides insights into how tandem arrays, which are particularly prone to frequent, complex rearrangements, can produce genetic novelty.

In PNAS, we just published genome assemblies for four strains, including the popular Ler (Landsberg erecta) and C24 strains.

They share this year's State Research Prize of Baden Württemberg, the highest such award given out by any of the 16 German states. The award ceremony was held in Tübingen on July 6. Detlef Weigel will use the prize money of 100,000 Euros to create a stipend for the training of Asian or African PhD students in modern genetic technology.

Just out in Plant Cell: MiR156-controlled SPL transcription factors not only regulate leaf size, speed of leaf initiation, phase change, flowering and trichome formation, but also anthocyanin biosynthesis. Stay tuned, there will likely be more biological processes revealed to be under miR156 control.

If you want to find out how one can lost a major part of its genome in just 10 million years or so, and to live to tell the tale, read more here.

Marco Todesco will receive the Otto Hahn Medal of the Max Planck Society for this PhD dissertation. It comes with the medal shown below and a cash prize, and will be awarded at the Annual Meeting of the Max Planck Society in Berlin on June 8, 2011.

These networks in turn have important roles in the control of development. Read more here.

In this review, we discuss the implications of next-generation sequencing enabled genetic approaches for plant biology and plant breeding.

In contrast, we report in this paper here that a large portion of flowering-time variation in A. thaliana can be explained by large-effect loci, but that these tend to map to only a small number of regions in the genome, which include the locations of the entire clade of FLC/MAF transcription factor genes.

Out in PLoS Genetics: MiRNA-mediated control of vegetative phase change in trees -- collaboration across three continents (Asia, Europe, North America)!

http://www.haw.uni-heidelberg.de/index.en.html

An honor accorded to distinguished members of the Association, the world's largest scientific society and publisher of Science magazine. Fellows are elected annually by the AAAS Council. The Association has awarded fellowships since 1874.

Marco Todesco received the dissertation prize of the Reinhold-und-Maria-Teufel-Stiftung today.

He is also first author on the last paper of 2010 published by the department (out of 34 total!):

Comparative analysis of non-autonomous effects of tasiRNAs in miRNAs in Arabidopsis thaliana. By Felippe Felippes, Felix Ott and Detlef Weigel, published online December 5, in Nucleic Acids Research.

Ten years of genetics and genomics: what have we achieved and where are we heading?

Laubinger, S., Zeller, S., Henz, S. R., Buechel, S., Sachsenberg, T., Wang, J.-W., Rätsch, G., and Weigel, D.

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome.

Published online September 21, 2010

Wollmann H, Mica E, Todesco M, Long JA, Weigel D.Development. 2010 Sep 28. [Epub ahead of print]

This has been achieved using artificial miRNA target mimics, a recently developed technique fashioned on an endogenous mechanism of miRNA regulation. Morphological defects in the aerial part were observed for about 20% of analyzed families, all of which are deeply conserved in land plants. In addition, we find that non-cleavable mimic sites can confer translational regulation in cis.

The target mimic constructs have all been submitted to the European Arabidopsis Stock Centre, and should be available from there soon.

This work was published today in Nature. An allele at the ACD6 locus that slows plant growth but at the same time makes plants resistant to a raft of pathogens is found in aobut 20% of all individuals throughout the world. Because it is so ubiquitous, it is easily picked up by genome wide association, as shown in the companion paper, also published in Nature.

The Royal Society was founded in 1660 and is the oldest continuously existing scientific academy in the world. Among its Foreign Members is a small circle of German scientists, which apart from several Nobel laureates such as Christiane Nüsslein-Volhard includes only the former president of the Max Planck Society, Hubert Markl.

Each of the accessions is an inbred line that can be ordered as an individual line or as a set (CS76427). These stocks can be found using the ABRC catalog. For more details, please go to the 1001 Genomes Project homepage.

However, this was for mutations induced in the Col-0 reference background, for which a very high-quality reference genome is available.

In a paper that just appeared online in Plant Physiology, we now show that we can reliably distinguish even rare new mutations from a sea of background SNPs in non-reference lines. Find the paper here.

The data can be found here. The results from performing genome-wide association scans (GWAS) with the first set of lines have just been published in Nature, including several phenotypes analyzed at the Max Planck Institute.

Atwell, S, Huang, YS, Vilhjalmsson, BJ, Willems, G, Horton, M, Li, Y, Meng, D, Platt, A, Tarone, AM, Hu, TT, Jiang, R, Muliyati, NW, Zhang, X, Amer, MA, Baxter, I, Brachi, B, Chory, J, Dean, C, Debieu, M, de, Me, Ecker, JR, Faure, N, Kniskern, JM, Jones, JD, Michael, T, Nemri, A, Roux, F, Salt, DE, Tang, C, Todesco, M, Traw, MB, Weigel, D, Marjoram, P, Borevitz, JO, Bergelson, J, and Nordborg, M (2010).
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.
Nature, published online March 24, 2010.

See the project homepage for details.

Dan Koenig has won one of the highly competitive Long-Term Fellowships from the Human Frontier Science Program Organization (HFSPO). Dan is finishing his PhD work with Neelima Sinha at UC Davis and join Team Natural Variation in the Weigel lab in summer of this year. Congratulations, Dan!


See this link for a list of the company

Present were, among others, the chairman of the board of Bayer, Dr. Manfred Schneider, the CEO of Bayer, Werner Wenning, Dr. Wolfgang Plischke, member of the Management Board responsible for innovation and technology, as well as high-level colleagues from other companies active in plant science such as KWS and BASF. The event was attended by in the Weigel lab, many academic colleagues from Tübingen and elsewhere, the extended Weigel family and many friends of the family.

Stephan Ossowski designed artificial miRNAs, which turned out to provide a small, but useful piece of the puzzle.

The paper provides important information for understanding the longer-term effects of mutation and selection on the evolution of plant genomes. It also highlights the power of short read sequencing, as we were able to find 1 mutation in 5 million base pairs--harder than finding a needle in a haystack.

Read the original paper here.

The award, one of the most important scientific prizes  in the German speaking countries, will be presented by the CEO of Bayer, Werner Wenning, in Berlin on February 12, 2010. Weigel is being cited both for his efforts to understand how plants adapt to the environment, and for his work on microRNAs. The entire Weigel lab will participate in the award ceremony!

For more information, visit this website.

Her work was selected from 1105 articles submitted at NIPS, the premier conference in Machine Learning. In her paper, Nino presents a novel algorithm for efficiently comparing large networks. This was not possible before with current state-of-the-art methods (reference: Shervashidze, Borgwardt: Fast subtree kernels on graphs, NIPS 2009).

Across publications that appeared from 2003 to 2006, Detlef Weigel ranked first, by a considerable margin, among both plant biologists (as of 5/2009) and developmental biologists (as of 10/09).

In addition to Weigel, 7 current or former members of the department are among the 50 most highly cited developmental biologists!

See

Developmental biology ranking (10/2009)

Plant biology ranking (05/2009)

We have developed a graph mapping approach, that allows simultaneous mapping against all known variants, and thereby greatly increases the number of polymorphisms discovered.Simultaneous alignment of short reads against multiple genomes.

Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.

Genome Biol. 2009 Sep 17;10(9):R98. [Epub ahead of print]

Back to back with a paper from the Poethig lab, on which Jia-wei is also a co-author and which reports additional roles for miR156-regulated SPL transcription factors.

Wang, J, Czech, B, and Weigel, D (2009).
miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana.
Cell, 138(4):738-49.

Wu, G, Park, MY, Conway, SR, Wang, J, Weigel, D, and Poethig, RS (2009).
The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis.
Cell, 138(4):750-9.

To dramatically speed up identification of causative point mutations and small deletions, we provide the software package SHOREmap (http://1001genomes.org/downloads/shore.html), an extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants.

Schneeberger, K, Ossowski, S, Lanz, C, Juul, T, Petersen, AH, Nielsen, KL, Jorgensen, J, Weigel, D, and Andersen, SU (2009).
SHOREmap: simultaneous mapping and mutation identification by deep sequencing.
Nat Methods, 6(8):550-1.

Professor Rod Wing, Director of the Arizona Genomics Institute at the University of Arizona, has won a prestigious Humboldt Research Award from the Alexander von Humboldt Foundation. The award is granted to academics whose fundamental discoveries, new theories, or insights have had a significant impact on their own discipline and who are expected to continue producing cutting-edge achievements in future.

This work resulted in the first rice HapMap and laid the foundation for large-scale genetic characterization of a much larger set of rice varieties.

The EU project AENEAS--Acquired environmental epigenetics advances: from Arabidopsis to maize, and the BMBF-GABI project TRANSNET--Transcriptional networks and their evolution in the Brassicaceae.

AENEAS is led by Serena Varotto (Padova), and includes Vincenzo Rossi (Milano), José Gutierrez-Marcos (Warwick), Jurek Paszkowski (Geneva), Caroline Dean (Norwich), David Baulcombe (Cambridge), and Wyatt Paul (BIOGEMMA).

TRANSNET is led by George Coupland (Cologne), and includes Javier Paz-Ares and Pilar Carbonero (Madrid), Vincent Colot (Evry), Alexander Kel (BIOBASE), and Hadi Quesneville (Versailles).

The National Academy of Sciences is the US' most prestigious scientific organization, and election to membership in the academy is considered one of the highest honors that can be accorded a US scientist or engineer.

Among the other scientists elected this year is Timothy Berners-Lee, credited with inventing the internet.

We have identified such a case in Arabidopsis thaliana, which provides a convenient genetic model to study the origin of such triplet expansions as well as their distribution in natural populations.

See the paper by Sridevi Sureshkumar, Marco Todesco et al. in Science.

Remarkably, we have now found, in collaboration with other groups from the ERA-PG ARelatives consortium, that C. rubella apparently originated from C. grandiflora only a few tens of thousands of years ago. Allelic diversity patterns in the two species suggest that C. rubella was probably founded by a single individual, as published in PNAS. How phenotypic diversity is distributed in this species, and how it originated, are interesting questions for future research.