Genome Informatics

We use both phenotype-first and genotype-first approaches to understand how plants adapt to their environment. The most extensively investigated species remains Arabidopsis thaliana. To enable the rapid discovery of functionally relevant variation, we have spearheaded for almost a decade now, extensive genome sequencing using Illumina technology. The resulting 1001 Genomes Project for A. thaliana has been setting the stage for improved genome-wide association studies, but also revealed a much more fine-grained picture of the evolutionary past of the species. Because few computational tools were available when we started to use short read sequencing, we produced the SHORE pipeline for the analysis of such data.

While the early focus was on re-sequencing, we are now focusing on assembling genomes de novo using both short and long-read technologies. This work is complemented by assembling high-quality genomes of related species for pan-genome analyses, as well as studies of spontaneous mutation rates and of epigenomic variation.

Intra- and interspecific genome and methylome variation
Graph-based methods for comparative sequence analyses
Resource and tool development for genomics

People

Detlef Weigel

Director

I started out as a developmental biologist, but over the past two decades years, my lab has come to focus more and more on questions of evolution. We investigate these both from a genomic perspective and starting from phenotypes, primarily, but not exclusively in Arabidopsis thaliana.

Fernando Rabanal

Postdoctoral Researcher

Ribosome heterogeneity. Evolution of regulation of ribosomal RNA genes. Population genomics of herbicide resistance

Haim Ashkenazy

Postdoctoral Researcher

Plant evolutionary genomics. Evolutionary dynamics of gene content in bacterial and plant genomes. Co-evolution of plant-microbe interactions. Comparative genomics and phylogenomics

Ilja Bezrukov

Staff Scientist

Sebastian Vorbrugg

Doctoral Researcher

Application of genome graphs

Wenfei Xian

Doctoral Researcher

Population genomics

Yueqi Tao

Doctoral Researcher

Evolutionary genomics

Zhigui Bao

Doctoral Researcher

Complex structural variants. Pangenome graphs.

Collaboration Partners

Claude Becker

Ludwig Maximilian University Munich, Germany

Ian Henderson

Cambridge University, UK

Magnus Nordborg

Gregor Mendel Institute, Vienna, Austria

Selected References

Koenig, D., Hagmann, J., Li, R., Bemm, F., Slotte, T., Neuffer, B., Wright, S. I., and Weigel, D. (2019) Long-term balancing selection drives evolution of immunity genes in Capsella. eLife 8, e43606.

The 1001 Genomes Consortium (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481-491. (D. Weigel & M. Nordborg, corresponding authors).

Van de Weyer, A.-L., Monteiro, F., Furzer, O. J., Nishimura, M. T., Cevik, V., Witek, K., Jones, J. D. G., Dangl, J. L., Weigel, D.*, and Bemm, F. (2019) A species-wide inventory of NLR genes and alleles in Arabidopsis thaliana. Cell 178, 1260-1272.e14. *Lead contact.

Voichek, Y., and Weigel, D. (2020) Finding genetic variants underlying phenotypic variation in plants without complete genomes. Nat. Genet. 52, 534-540.