title: Sequence and structure of Brassica rapa chromosome A3.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea. munjh@rda.go.kr
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Mun
authors.forename: Soo-Jin
authors.initials: SJ
authors.lastname: Kwon
authors.forename: Young-Joo
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authors.forename: Jin A
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authors.forename: Mina
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authors.forename: Myung-Ho
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authors.forename: Sang-Choon
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authors.forename: Beom-Jin
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authors.forename: Ki-Byung
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authors.forename: Jee Young
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authors.forename: Jonghoon
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authors.lastname: Lee
authors.forename: Tae-Jin
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authors.lastname: Yang
authors.forename: Hee-Ju
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authors.lastname: Yu
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.forename: Su Ryun
authors.initials: SR
authors.lastname: Choi
authors.forename: Nirala
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authors.lastname: Ramchiary
authors.forename: Yong Pyo
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authors.lastname: Lim
authors.forename: Fiona
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authors.lastname: Fraser
authors.forename: Nizar
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authors.lastname: Drou
authors.forename: Eleni
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authors.lastname: Soumpourou
authors.forename: Martin
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authors.lastname: Trick
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Andrew G
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authors.lastname: Sharpe
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
authors.forename: Jacqueline
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authors.lastname: Batley
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authors.forename: Beom-Seok
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mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics*; D002874:Chromosome Mapping; D022004:Chromosome Structures; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant; D017124:Conserved Sequence; D020451:Contig Mapping; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D015321:Gene Rearrangement; D018745:Genome, Plant; D007621:Karyotyping; D058977:Molecular Sequence Annotation; D011123:Polyploidy; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D018744:DNA, Plant