Brassica genome sequencing

Overview

The MBGP selected the 'A' genome Brassica rapa line Chiifu-401 was the first species to be sequenced. The mutlinational BrGSP made significant progress with this based on a conventional BAC-end, anchor-BACs 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).


Ongoing sequencing projects

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.

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
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B. oleracea O212 Cabbage ref. 'C' Illumina +454 CAAS, Wuhan, China Shengyi Liu
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B. oleracea ? Broccoli re-seq. x5 Illumina CAAS, Wuhan, China Shengyi Liu
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 76bp (3kb inserts) = 1.16Gbp
B. oleracea Early Big Broccoli re-seq Illumina USA Dick McCombie
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B. oleracea     re-seq Illumina ACPFG, Australia   TAGdb
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B. napus Tapidor DH Winter oilseed ref. 'AC' Illumina +454 HAU, China + UK Jinling Meng
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B. napus Ningyou7 Spring oilseed ref. 'AC' Illumina +454 HAU, China + UK Jinling Meng
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B. napus DH12075 Spring oilseed ref. 'AC' Illumina +454 Can-Seq Isobel Parkin
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B. napus Darmor DH Winter oilseed ref. 'AC' Illumina, 454, Sanger INRA, France Boulos Chaloub
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B. napus Zhongshuang 11 Spring oilseed ref. 'AC' Illumina +454 CAAS, Wuhan, China Shengyi Liu
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B. nigra ? ? re-seq Illumina ACPFG, Australia   TAGdb
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 76bp (2.7kb inserts) = 1.11Gbp
B. rapa Chiifu-401 Chinese cabbage ref. 'A' BAC-ends, BACs BrGSP Ian Bancroft see BrGSP status page ? incorporated in shotgun approach 2009
B. rapa Chiifu-401 Chinese cabbage ref. 'A' Illumina +454 CAAS-BGI Xiaowu Wang
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 ?July 2010?  
B. rapa Chiifu-401 Chinese cabbage ref. 'A' 5x 454 INRA, France Boulos Chaloub
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 ?July 2010? contribute to CAAS-BGI assembly
B. rapa Chiifu-401 Chinese cabbage re-seq Illumina ACPFG, Australia   TAGdb
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 35bp (2.8kb inserts) = 0.88Gbp;
36bp (140bp inserts) = 3.18Gbp;
36pb (300bp inserts) = 0.74Gbp
B. rapa Kenshin-402 Chinese cabbage re-seq Illumina ACPFG, Australia   TAGdb
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 36bp (410bp inserts) = 0.30Gbp 76bp (410bp inserts) = 0.43Gbp
B. rapa R-o-18 Yellow sarson re-seq. x12 Illumina Rothamsted Graham King freely available BrassEnsembl March 2010 accessible via Blast on BrassEnsembl; shortly by ftp and SRA
76bp (300bp inserts) = 2.8Gbp
                   






This Page Was Last Edited: 11-Mar-2010