Genome Informatics

For many years, genome sequences and knowledge of sequence variation have fueled our discovery of genetic variants with measurable phenotypic impact.

For almost two decades, we have been spearheading the 1001 Genomes Project for Arabidopsis thaliana, which set the stage for genome-wide association studies in plants. We were the first to describe whole-genome sequence variation in plants, beginning with large-scale microarray studies and then followed by extensive short-read sequencing. In the course of this work, we pioneered graph approaches for understanding genome variation well over a decade ago.

What we have learned from the large-scale analysis of A. thaliana genomes, we also apply to other species, including A. thaliana relatives such as Capsella species, and to woody species, such as grapevine.

While the early focus was on genome re-sequencing, we have switched to assembling complete genomes de novo using long-read technologies. This work not only provides a much more complete inventory of sequence variants of all sizes, but it also gives us much better access to variation in the repetitive regions of the genome, including transposable elements and centromeres.

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


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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.

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