Latest News

Graduation and farewell party!

Posted on August 08, 2016

On July 29, we said goodbye to George Wang, who will be heading the Computomics Corporation in Davis, CA. And .... read more

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, Dr. Maricris Zaidem!

Posted on July 29, 2016

Cris successfully defended her PhD thesis entitled 'Identification of genetic modifiers of ACCELERATED CELL DEATH 6 (ACD6) in natural Arabidopsis thaliana accessions' read more

Congratulations, Cris!

Complex history of Arabidopsis speciation

Posted on July 28, 2016

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism read more

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, Dr. Jorge Kageyama!

Posted on July 26, 2016

Jorge successfully defended his PhD thesis entitled 'Genome-wide analysis of organ-specific DNA methylation patterns in Arabidopsis thaliana' read more

Congratulations, Jorge!

Chromatin loops in Arabidopsis thaliana

Posted on July 25, 2016

Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution read more

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, Dr. Diep Tran!

Posted on July 25, 2016

Diep successfully defended her PhD thesis entitled 'Biochemical Basis of Autoactivity of a Pair of Plant NLR Immune Receptors'. read more

Congratulations, Diep!

Tweets



Upcoming Events

Aug
29

Wild Plant Pathosystems

August 28-31, 2016
Helsinki, Finland

Detlef will give an overview of the plant-microbe and immunity related work of the group at the "Wild Plant Pathosystems" meeting in Helsinki


Sep
05

GfÖ - 4th Annual Meeting

Sept 5-9
in Marburg, Germany

Moisés speaking about "Adaptation Genomics to Drought"


Sep
14

MiKo Talk Charles H. Langley