Brassica genome sequencing

Overview

A number of projects are now ongoing, to generate 'reference' genome sequences, as well as other 're-sequencing' efforts. These are summarised below. Please let us know if and when this information may be updated.

BrGSP reference projects re-sequencing projects


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 (see PAG abstract).

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Species Genotype Crop type Aims Strategy Consortium Contact Data Availability Target Completion Date notes
B. rapa Chiifu-401 Chinese cabbage ref. 'A' BAC-ends, BACs BrGSP Ian Bancroft in public databases ? incorporated in shotgun approach 2009;
BAC annotation available via Brassica Genome Gateway and BrassEnsembl;
previous BAC-status page;
B. rapa Chiifu-401 Chinese cabbage ref. 'A' Illumina + 454 CAAS-BGI Xiaowu Wang searchable via BRAD
full release on publication
June 2010 v0.1 (scaffold) released in searchable form July 2010, with annotation and markers to B. rapa maps;
annotation etc will also be available via BrassEnsembl upon publication
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 Chiifu-401 Chinese cabbage re-seq Illumina University of Queensland, Australia Dave Edwards TAGdb Oct. 2009 35bp (2.8kbp inserts) = 0.88Gbp;
36bp (140bp inserts) = 3.18Gbp;
36bp (300bp inserts) = 0.74Gbp;
contributed to the CAAS-BGI assembly.


Additional Brassica 'reference' sequencing projects


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Species Genotype Crop type Aims Strategy Consortium Contact Data Availability Target Completion Date notes
B. oleracea TO1000 Rapid cycler ref. 'C' Illumina + 454 Canada +USA +France + UK Isobel Parkin - -  
B. oleracea O212 Cabbage ref. 'C' Illumina + 454 CAAS, Wuhan, China Shengyi Liu Bolbase from OCRI -  
B. napus DH12075 Spring oilseed ref. 'AC' Illumina + 454 Can-Seq Isobel Parkin - -  
B. napus Darmor DH Winter oilseed ref. 'AC' Illumina, 454, Sanger INRA, France Boulos Chaloub - -  
B. napus Zhongshuang 11 Spring oilseed ref. 'AC' Illumina + 454 CAAS, Wuhan, China Shengyi Liu - -  
B. rapa B3 Rapid cycling, sc ? Illumina + 454 JGI - Available on NCBI SRA Jan. 2011 Ilumina = 119Gbp ; 454 = 0.83Gbp
B3 was derived in Amasino lab (Wisconsin) from rapid cycling "Fastplant" line, Doug Friend's rapid line 'Ceres' and IMB211.


Brassica re-sequencing projects


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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 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



This Page Was Last Edited: 27-Jan-2014