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 |
- Additional Brassica genome information, browsers, etc.
- For information: Fort Lauderdale report on data sharing from large-scale biological research 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).- Overview of BrGSP, see also updated summary below
- Previous (to Apr 2009): status and MBrGSP BAC registry
- BrGSP update, Saskatoon, Aug 2009
- Searchable database of Chiifu-401 scaffolds and annotation (BRAD), July 2010
| 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 | Oct. 2009 | 35bp (2.8kb inserts) = 0.88Gbp; 36bp (140bp inserts) = 3.18Gbp; 36pb (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 | - | - | |
| 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. 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 | - | - | > 75Gb 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 | - | - | |
| B. oleracea | var. gongylodes (wild) ATC 94684 | Kohlrabi | re-seq | Illumina | University of Queensland, Australia | Dave Edwards | TAGdb | Oct. 2009 | 76bp (3kb inserts) = 1.16Gbp |
| B. napus | 123 lines |
various | leaf transcriptome | Illumina | JIC + TGAC | Ian Bancroft | single lane (~1Gb each) | ||
| 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; 36pb (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 |
