Brassica napus Assembly and Gene Annotation
About Brassica napus
Oilseed rape (Brassica napus) was formed ~7,500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72-fold genome multiplication since the origin of angiosperms and high gene content. Cultivation began in Europe during the Middle Ages and spread worldwide. Diversifying selection gave rise to oilseed rape (canola), rutabaga, fodder rape, and kale morphotypes grown for oil, fodder, and food.
The homozygous B. napus genome of European winter oilseed cultivar ‘Darmor-bzh’ was assembled with long-read 454 GS-FLX+ Titanium and Sanger sequence. Correction and gap filling used 79 Gbp of Illumina HiSeq sequence. The final assembly of 849.7 Mbp was obtained using SOAP and Newbler, with 89% nongapped sequence. The assembly covers ~79% of the 1,130 Mbp genome and includes 95.6% of Brassica expressed sequence tags (ESTs) .
A total of 101,040 gene models were estimated from 35.5 Gbp of RNA-Seq data in combination with ab initio gene prediction, protein and EST alignments, and transposon masking. Of these, 91,167 were confirmed by matches with B. rapa and/or B. oleracea predicted proteomes .
- Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B et al. 2014. Science. 345:950-953.
General information about this species can be found in Wikipedia.
|Assembly||AST_PRJEB5043_v1, INSDC Assembly GCA_000751015.1, Sep 2015|
|Golden Path Length||848,200,303|
|Genebuild method||Generated from ENA annotation|
|Data source||European Nucleotide Archive|
|Non coding genes||4,236|
|Small non coding genes||4,161|
|Long non coding genes||75|