The Sugar Beet Genome Project

Reference assembly "RefBeet"

The double haploid genotype KWS2320 was initially sequenced in a whole genome shotgun approach combining data sets generated on Illumina, Roche/454, and Sanger sequencing platforms resulting in RefBeet versions 0.9, 1.1, and 1.2. We integrated existing resources of this genotype, such as large insert genomic libraries and genetic and physical maps, to achieve long-range continuity and chromosomal assignment of scaffolds. A largely improved genome assembly RefBeet-3.0 leverages the power of long-read sequencing technologies and contains nine pseudochromosomes, equivalent to the haploid beet chromosome number.

Additional sugar beet lines, sea beet, spinach, and Beta patula

For comparative studies we sequenced additional sugar beet accessions, all double haploid, as well as sea beet, spinach, and Beta patula (Illumina sequencing data). Sea beet (Beta vulgaris ssp. maritima) is the closest wild relative of sugar beet, both are fully interbreedable. Beta patula is another wild beet closely related to sea beet and endemic to the Madeira archipelago. Spinach (Spinacia oleracea) represents another member of the Amaranthaceae family.

Gene Prediction

We optimized the gene prediction parameters for Caryophyllales taxa based on confirmed gene structures including data from PacBio full-transcript sequencing. The current gene sets are BeetSet-3 (sugar beet), SpiSet-1 (spinach), MarSet-1 (sea beet), and PatSet-1 (B. patula).

Further information

The generation of the RefBeet-3.0 assembly and BeetSet-3 is described in Dohm et al. 2025, NAR Genom Bioinform. For details on data analyses of previous RefBeet verions please refer to Dohm et al. 2014, Nature and its Supplement and to Minoche et al. 2015, Genome Biol. Sea beet and B. patula assemblies and gene sets are described in Rodríguez Del Río et al. 2019, Plant J.

Contact

Heinz Himmelbauer, Juliane Dohm