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Cell-type specific RNA-seq and ChIP-seq

Posted on March 05, 2019

Identification of new flowering time regulator, MRF1 read more

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.

Out in eLife: Balancing selection in Capsella

Posted on March 05, 2019

Long-term balancing selection at immunity genes in Capsella read more

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.

bioRxiv: Barragan et al – Predicting hybrid underperformance

Posted on February 25, 2019

RPW8/HR repeats predict NLR-dependent hybrid phenotype read more

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.

First preprint of 2019: The A. thaliana pan-NLRome

Posted on February 01, 2019

1000s of NLR genes in 65 diverse accessions read more

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.

Last preprint of 2018: Evolution of herbicide resistance

Posted on December 21, 2018

Collaboration with Pat Tranel and Stephen Wright, led by Julia Kreiner read more

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.

In Genetics: over 1,000 spontaneous mutations

Posted on December 10, 2018

New resource for understanding mutational processes in plants read more

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

Mao-Lun Weng, Claude Becker, Julia Hildebrandt, Matthew T. Rutter, Ruth G. Shaw, Detlef Weigel and Charles B. Fenster

Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the Arabidopsis thaliana reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for A. thaliana is 6.95 × 10?9 (s.e. ±2.68 × 10?10) per site per generation with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10?9 (±1.07 × 10?10) per site per generation, with deletions being more frequent and larger than insertions. Among the 1,694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that de novo mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.

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Upcoming Events

Mar
25

Anna-Lena's PhD defense

11 am
Room B9N22, Auf der Morgenstelle 9, Tübingen University

Anna-Lena will defend her PhD thesis entitled 'The pan-NLR'ome of Arabidopsis thaliana'


Mar
25

Darya's PhD defense

1:30 pm
Room B9N22, Auf der Morgenstelle 9, Tübingen University

Darya will defend her PhD thesis entitled 'Genome-Wide Analysis of Nucleotide-Binding Domain Leucine-Rich Repeat (NLR) Variation Patterns in Arabidopsis thaliana'


Mar
26

Regio Plant Science Meeting 2019

March 26
University of Hohenheim

Presentations from Uni Tübingen, Uni Hohenheim, Uni Ulm, and MPI Tübingen