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