Brassica napus Assembly and Gene Annotation

About Brassica napus

Oilseed rape (Brassica napus) was formed ~7,500 years ago by hybridisation between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidsations, 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, swede, 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 Gb of Illumina HiSeq sequence. The final assembly of 849.7 Mb was obtained using SOAP and Newbler, with 89% nongapped sequence. The assembly covers ~79% of the 1,130 Mb genome and includes 95.6% of Brassica expressed sequence tags (ESTs) and was produced by GSC.

Annotation

A total of 101,040 gene models were estimated from 35.5 Gb of RNA-seq data in combination with ab initio gene prediction, protein and EST alignments, and transposon masking by GSC. Of these, 91,167 were confirmed by matches with B. rapa and/or B. oleracea predicted proteomes.

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 2014
Database version96.1
Base Pairs738,357,821
Golden Path Length848,200,303
Genebuild byGSC
Genebuild methodImported from ENA
Data sourceGSC

Gene counts

Coding genes101,040
Non coding genes3,533
Small non coding genes3,458
Long non coding genes75
Gene transcripts104,573

About this species