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.

Assembly

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) [1].

Annotation

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 [1].

References

  1. 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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAST_PRJEB5043_v1, INSDC Assembly GCA_000751015.1, Sep 2015
Database version90.1
Base Pairs738,357,821
Golden Path Length848,200,303
Genebuild byEnsemblPlants
Genebuild methodGenerated from ENA annotation
Data sourceEuropean Nucleotide Archive

Gene counts

Coding genes101,040
Non coding genes4,236
Small non coding genes4,161
Long non coding genes75
Gene transcripts105,276

About this species