Brassica oleracea Assembly and Gene Annotation

About Brassica oleracea

Brassica oleracea L. (n=9, C genome) is a widely cultivated vegetable species integral to human diets, with a classification of cultivar groups based on the specialized morphology of their edible structures (kales, cabbages, Brussels sprouts, broccoli, kohl rabi and cauliflower).

Assembly

The genomic sequence within this version of Ensembl includes 33,459 scaffolds (>200 bp) with an N50 of 850 kb that was assembled at NRC-Saskatoon using a hybrid approach from Illumina, Roche 454 and Sanger sequence data [1]. The assembly has been orientated and assigned to the nine pseudochromosomes using dense genotype-by-sequencing genetic maps.

Annotation

Gene prediction of the assembled genomic scaffolds was conducted by JCVI and NRC-Saskatoon using MAKER and PASA [1]. Functional annotation for the gene models is provided through similarity to Arabidopsis thaliana genes.

Links

  • http://brassica.info
    This site collates and exchanges open source information relating to Brassica genomics and genetics.
  • http://brassicadb.org
    The Brassica database (BRAD) is a web-based database of genetic data at the whole genome scale for important Brassica crops.

References

  1. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
    Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL et al. 2014. Genome Biol.. 15:R77.

Picture credit: "Fractal Broccoli" by Jon Sullivan. Licensed under Public domain via Wikimedia Commons.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

Assemblyv2.1, INSDC Assembly GCA_000695525.1, May 2014
Database version90.1
Base Pairs488,535,107
Golden Path Length488,622,507
Genebuild byCanSeq
Genebuild methodImport
Data sourceEuropean Nucleotide Archive

Gene counts

Coding genes59,225
Non coding genes1,469
Small non coding genes1,447
Long non coding genes22
Gene transcripts60,694

About this species