Research

Plant genomics

We have been studying the genome of sugar beet (Beta vulgaris) starting with the construction of a physical map and a reference genome sequence thereafter. We adopted a whole genome shotgun sequencing approach that integrated data from several sequencing platforms, as well as data from genetic and physical mapping. The current reference assembly RefBeet-1.2 was complemented with de novo assemblies of genomes from four further additional sugar beet accessions.

Current research lines

1. improvement of the reference genome using optical mapping data and long sequencing reads
2. exploration of the variability of the genus Beta
3. analysis of the spinach and quinoa genomes, both close relatives of sugar beet
4. analysis of the genome of Nicotiana benthamiana, a popular protein expression platform in biotechnology

Genomes that we have sequenced and/or assembled

• Sugar beet (Beta vulgaris)
• Chard (Beta vulgaris)
• Wild beets (Beta patula and Beta v. maritima)
• Quinoa (Chenopodium quinoa)
• Spinach (Spinacia oleracea)
• Floating bladderwort (Utricularia gibba)
• Dinosaur ant (Dinoponera quadriceps)
• Red paper wasp (Polistes canadensis)
• Common bean (Phaseolus vulgaris)
• Megavirus CeV-01B

Technology development and implementation

Cutting-edge research in genomics and bioinformatics requires an appreciation of the rapid advancements of the field. Driven by technological innovations such as the accelerated pace at which more and longer sequencing reads can be generated, analysis strategies need to be constantly revised and adapted. Our current efforts focuses onto

1. improvement of long-range continuity of genome assemblies
2. de novo genome assembly using long-read technologies
3. gene annotation and functional classification
4. genome comparison

Machine learning and Bayesian methods

• Machine learning and Bayesian methods