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LEGACY information on Genome Sequencing

Overview

This page primarily contains information that has now been superceded. However, it is retained for historical interest and comparison.

2014 saw the culmination of a major effort worldwide to generate 'reference' Brassica genome sequences, and these are now available online. The current focus is on a range of 're-sequencing' efforts. An early summary is presented below, but as of 2015 requires update. Please let send any relevant information to Graham King so that this information may be updated.

NCBI Genbank

Type Species
Source
Public repository Brassica spp.
  B. rapa
  B. oleracea
  B. napus
  B. nigra
  B. juncea
  B. carinata
EST B. napus
Shotgun (GSS) B. oleracea
  B. oleracea


The original BrGSP : Brassica rapa Genome Sequencing Project

The MBGP selected the 'A' genome Brassica rapa line Chiifu-401 as the first species to be sequenced. The mutlinational BrGSP made significant progress with this, based on a conventional end-sequenced anchor-BAC and chromosome-specific BAC by BAC sequencing to Phase II. The strategy has been modified with the availability of high throughput sequencing (primarily 454 and Illumina), and so a project initiated by CAAS/BGI in China has incorporated the existing data into a shotgun approach. The outcome of this effort was published in Nature Genetics in 2011.



Additional Brassica 'reference' sequencing projects


Species Genotype Crop type Aims Strategy Consortium Contact Data Availability Target Completion Date notes
B. napus DH12075 Spring oilseed ref. 'AC' Illumina + 454 Can-Seq Isobel Parkin - -  
B. napus Zhongshuang 11 Spring oilseed ref. 'AC' Illumina + 454 CAAS, Wuhan, China Shengyi Liu - -  
B. rapa FPsc Rapid cycling, sc ? Illumina + 454 JGI - Phytozome Jan. 2011 FPsc(B3) was derived in Amasino lab (Wisconsin) from rapid cycling "Fastplant" line, Doug Friend's rapid line 'Ceres' and IMB211.

Brassica re-sequencing projects

Species Genotype Crop type Aims Strategy Consortium Contact Data Availability Target Completion Date notes
B. oleracea ? Cabbage re-seq. x5 Illumina CAAS, Wuhan, China Shengyi Liu - -  
B. oleracea Early Big Broccoli re-seq Illumina USA Dick McCombie Available on NCBI SRA Jan. 2011 52.7Gbp Illumina
B. oleracea var. gongylodes (wild) ATC 94684 Kohlrabi re-seq Illumina University of Queensland, Australia Dave Edwards TAGdb Oct. 2009 76bp (3kbp inserts) = 1.16Gbp
B. napus 123 linesexcel various leaf transcriptome Illumina JIC + TGAC Ian Bancroft - - single lane (~1Gbp each)
B. napus Tapidor DH Winter oilseed ref. 'AC' Illumina + 454 HAU, China + UK Jinling Meng - -  
B. napus Ningyou7 Spring oilseed ref. 'AC' Illumina + 454 HAU, China + UK Jinling Meng - -  
B. nigra wild (PI 597829)
ATC 95249 		Black mustard re-seq Illumina University of Queensland, Australia Dave Edwards TAGdb Oct. 2009 76bp (2.7kb inserts) = 1.11Gbp
B. rapa Chiifu-401 Chinese cabbage re-seq Illumina University of Queensland, Australia Dave Edwards TAGdb Oct. 2009 35bp (2.8kb inserts) = 0.88Gbp;
36bp (140bp inserts) = 3.18Gbp;
36bp (300bp inserts) = 0.74Gbp;
contributed to the CAAS-BGI assembly.
B. rapa Chiifu-401 Chinese cabbage ref. 'A' 5x 454 INRA & Genosope, France Boulos Chaloub download Jul. 2010 ? contribute to CAAS-BGI assembly
B. rapa Kenshin-402 Chinese cabbage re-seq Illumina + 454 University of Queensland, Australia Dave Edwards TAGdb Oct. 2009 36bp (410bp inserts) = 0.30Gbp;
76bp (410bp inserts) = 0.43Gbp;
used for SNP generation, to validate CAAS-BGI assembly.
B. rapa R-o-18 Yellow sarson re-seq. x12 Illumina Rothamsted Graham King BrassEnsembl ;
FTP download page		 Mar. 2010 accessible via Blast on BrassEnsembl; shortly by ftp and SRA
76bp (300bp inserts) = 5.2Gbp