Beta vulgaris Assembly and Gene Annotation

About Beta vulgaris

Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates providing nearly 30% of the world's annual sugar production and a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n=18 chromosomes, has an estimated genome size of 714-758 Mb and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops.

Assembly

The double haploid sugar beet line KWS2320 was sequenced by Dohm et al (2014) using the Roche/454, Illumina and Sanger sequencing platforms. The initial assembly was integrated with genome-wide genetic and physical map information, resulting in 225 genetically anchored scaffolds (394.6 Mb), assigned to nine chromosomes. The final assembly comprised 566.6 Mb in 2,171 scaffolds and 38,337 unscaffolded contigs. The N50 size was 2.01 Mb and the chromosomally assigned fraction 84.7%. A total of 94% of the publicly available isogenic expressed sequence tags (ESTs) were located in the assembly, suggesting that gene-containing regions are comprehensively covered.

Annotation

Dohm et al (2014) used Illumina RNA-seq reads and other cDNAs to annotate a total of 27,421 protein-coding genes; 91% included start and stop codons. They identified ncRNAs using homology searches.

Repeated sequences were called with the Repeat Detector, which is part of the Ensembl Genomes repeat feature pipelines. Repeats length: 218713351 - Repeats content: 38.6%

References

1. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
   Dohm JC, Minoche AE, Holtgrwe D, Capella-Gutirrez S, Zakrzewski F, Tafer H, Rupp O, Srensen TR, Stracke R, Reinhardt R et al. 2014. Nature. 505:546-549.

More information

General information about this species can be found in Wikipedia.