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Background History of the National and International Brassica rapa Genome Sequencing Initiatives

  • Ian BancroftEmail author
  • Xiaowu WangEmail author
Chapter
  • 1.3k Downloads
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Whole genome sequencing of Brassica rapa was first launched by the multinational group of Brassica rapa Genome Sequencing Project (BrGSP). The group planned to perform the assembly using the method called “bacterial artificial chromosome (BAC) by BAC” in the initial stage. However, the progress was limited and only chromosome A03 was finished under this method. Along with the development of the second generation sequencing technology, the Chinese suggest to adopt this new sequencing method and initiative assembled the B. rapa genome in short time by SOAP-denovo, which integrated the data of pair-ends short reads generated from the Illumina sequencing platform and the data of BAC sequences from BrGSP. This well assembled whole genome sequences of B. rapa—verified by the comparison to the A03 assembled by BAC sequenced—was then serves as the genome reference for the evolution, gene mapping and function studies of B. rapa.

Keywords

Bacterial Artificial Chromosome Next Generation Sequencing Bacterial Artificial Chromosome Clone Bacterial Artificial Chromosome Library Next Generation Sequencing Data 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Cheng F, Liu S, Wu J, Fang L, Sun S et al (2011) BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 11:136PubMedCentralCrossRefPubMedGoogle Scholar
  2. Cheng F, Wu J, Fang L, Wang X (2012) Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front Plant Sci 3:198PubMedCentralCrossRefPubMedGoogle Scholar
  3. Cheung F, Trick M, Drou N, Lim YP, Park J-Y et al (2009) Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell Online 21:1912–1928CrossRefGoogle Scholar
  4. Gustafson J, Badani AG, Snowdon RJ, Wittkop B, Lipsa FD et al (2006) Colocalization of a partially dominant gene for yellow seed colour with a major QTL influencing acid detergent fibre (ADF) content in different crosses of oilseed rape (Brassica napus). Genome 49:1499–1509CrossRefGoogle Scholar
  5. Li R, Zhu H, Ruan J, Qian W, Fang X et al (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272PubMedCentralCrossRefPubMedGoogle Scholar
  6. Liu L, Stein A, Wittkop B, Sarvari P, Li J et al (2012) A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds. Theor Appl Genet 124:1573–1586CrossRefPubMedGoogle Scholar
  7. Mun J-H, Kwon S-J, Yang T-J, Kim H-S, Choi B-S et al (2008) The first generation of a BAC-based physical map of Brassica rapa. BMC Genom 9:280CrossRefGoogle Scholar
  8. Mun J-H, Kwon S-J, Yang T-J et al (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:R111PubMedCentralCrossRefPubMedGoogle Scholar
  9. Mun J-H, Kwon S-J, Seol Y-J, Kim JA, Jin M et al (2010) Sequence and structure of Brassica rapa chromosome A3. Genome Biol 11:R94PubMedCentralCrossRefPubMedGoogle Scholar
  10. O’neill CM, I Bancroft (2000) Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J 23:233–243CrossRefPubMedGoogle Scholar
  11. Tang H, Lyons E (2012) Unleashing the genome of Brassica rapa. Front Plant Sci 3:172PubMedCentralCrossRefPubMedGoogle Scholar
  12. Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS et al (2012) Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190, 1563–1574.Google Scholar
  13. Teutonico R, Osborn T (1994) Mapping of RFLP and qualitative trait loci in Brassica rapa and comparison to the linkage maps of B. napus, B. oleracea, and Arabidopsis thaliana. Theor Appl Genet 89:885–894PubMedGoogle Scholar
  14. Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ et al (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell Online 18:1348–1359CrossRefGoogle Scholar
  15. Wang X, Wang H, Wang J, Sun R, Wu J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039CrossRefPubMedGoogle Scholar
  16. Wittkop B, Snowdon R, Friedt W (2009) Status and perspectives of breeding for enhanced yield and quality of oilseed crops for Europe. Euphytica 170:131–140CrossRefGoogle Scholar
  17. Yang T-J, Kim JS, Kwon S-J, Lim K-B, Choi B-S et al (2006) Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell Online 18:1339–1347CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of BiologyUniversity of YorkYorkUK
  2. 2.Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina

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