Research

Present research activities result from the group's involvement in the German plant genome project GABI-FUTURE, and technology-driven cooperations with groups at the CRG and other institutions.

BeetSeq - A reference genome for sugar beet (Beta vulgaris)

A genome sequence for sugar beet is needed to fully exploit the species' value for evolutionary genomics and as a crop plant. Presently, the completed genomes of representatives of six different genera of flowering plants are available, i.e. from Arabidopsis, poplar, grapevine, papaya, sorghum and rice. Sequencing of other plant genomes is underway, including maize and other cereals, Solanum (potato, tomato), Lotus, and evolutionary model species such as Mimulus and Aquilegia. Since sugar beet is not a close relative to one of the mentioned taxa, its genome sequence (~800 Mbp) will provide essential information on plant genome evolution. The sequencing strategy of the BeetSeq project combines BAC pool and whole-genome shotgun approaches, using next-generation sequencing technologies. Long-range continuity of scaffolds is established by the integration of Sanger end sequences from BACs and fosmids, as well as 454 paired-end reads. Being aware of the intraspecific variation between sugar beet accessions we focus on the doubled haploid line KWS2320. In a pilot genomic sequencing project (Dohm JC et al., Plant J, 2009), sugar beet BAC sequences from two haplotypes differed in exons by 1% (nucleotide level) and in non-coding regions by 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 10% of either sequence. A large proportion of such indels could be attributed to haplotype-specific integration of transposable elements.

Previous activities

De novo contig assembly of short-read data sets using SHARCGS