LEGACY information on Genome Sequencing
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.
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 |
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. |
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 lines![]() |
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 |