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bioRxiv: Stable epimutations after regeneration

Posted on March 16, 2022

TL;DR: Method of regeneration matters! read more

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.



Prestigious HFSP Long-Term Fellowship for Gal Ofir

Posted on March 16, 2022

16th HFSP Fellowship for a WeigelWorld postdoc since 1995 read more

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.

Systematic transcriptomic study of heterosis

Posted on March 04, 2022

New insights from large number of A. thaliana crosses read more

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.

PATHOCOM sampling underway

Posted on March 01, 2022

First phase of PATHOCOM underway read more

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 can protect against pathogens

Posted on February 24, 2022

From Or Shalev et al., now in Nature Ecology and Evolution (OA) read more

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.

Assembling Arabidopsis centromeres with HiFi reads

Posted on February 16, 2022

Comparison of HiFi and CLR assemblies & assemblers read more

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.


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