Sequence and structure of Brassica rapa chromosome A3.

Jeong Hwan Mun, Soo Jin Kwon, Young Joo Seol, Jin A. Kim, Mina Jin, Jung Sun Kim, Myung Ho Lim, Soo In Lee, Joon Ki Hong, Tae Ho Park, Sang Choon Lee, Beom Jin Kim, Mi Suk Seo, Seunghoon Baek, Min Jee Lee, Ja Young Shin, Jang Ho Hahn, Yoon Jung Hwang, Ki Byung Lim, Jee Young ParkJonghoon Lee, Tae Jin Yang, Hee Ju Yu, Ik Young Choi, Beom Soon Choi, Su Ryun Choi, Nirala Ramchiary, Yong Pyo Lim, Fiona Fraser, Nizar Drou, Eleni Soumpourou, Martin Trick, Ian Bancroft, Andrew G. Sharpe, Isobel A.P. Parkin, Jacqueline Batley, Dave Edwards, Beom Seok Park

Research output: Contribution to journalArticlepeer-review

Abstract

The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species. We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3. We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.

Original languageEnglish (US)
Pages (from-to)R94
JournalGenome biology
Volume11
Issue number9
DOIs
StatePublished - 2010

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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