Latest News

Talia's paper on Pseudomonas population structure published

Posted on July 11, 2018

A single Pseudomonas lineage dominates local Arabidopsis populations read more

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.

Danelle's paper on transmission ratio distortion published

Posted on June 28, 2018

Over 500 segregating F2 populations analyzed read more

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.

Pangenome analysis tool for Pseudomonas online

Posted on June 26, 2018

panX website for 1,524 Pseudomonas genomes read more

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 presentation GRC

Posted on June 14, 2018

Presentation on figshare read more

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.

PANX output of Karasov et al. online

Posted on June 14, 2018

PANX lets you explore 1,524 Pseudomonas genomes read more

The 1,524 genomes, based on a collection of local Pseudomonas isolated from A. thaliana, are described in this article by Karasov et al.

PANX lets you explore their gene content.

Spiegel Online interview with Detlef

Posted on May 31, 2018

Advocating for leaving genome edited plants unregulated read more

Why Detlef is not afraid of genetically modified plants (in German).

And why it is at the same time nonsense that we will all die of hunger without GMO or genome editing.

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