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Sequence and structure of Brassica rapa chromosome A3.


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.

SUBMITTER: Mun JH 

PROVIDER: S-EPMC2965386 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Sequence and structure of Brassica rapa chromosome A3.

Mun Jeong-Hwan JH   Kwon Soo-Jin SJ   Seol Young-Joo YJ   Kim Jin A JA   Jin Mina M   Kim Jung Sun JS   Lim Myung-Ho MH   Lee Soo-In SI   Hong Joon Ki JK   Park Tae-Ho TH   Lee Sang-Choon SC   Kim Beom-Jin BJ   Seo Mi-Suk MS   Baek Seunghoon S   Lee Min-Jee MJ   Shin Ja Young JY   Hahn Jang-Ho JH   Hwang Yoon-Jung YJ   Lim Ki-Byung KB   Park Jee Young JY   Lee Jonghoon J   Yang Tae-Jin TJ   Yu Hee-Ju HJ   Choi Ik-Young IY   Choi Beom-Soon BS   Choi Su Ryun SR   Ramchiary Nirala N   Lim Yong Pyo YP   Fraser Fiona F   Drou Nizar N   Soumpourou Eleni E   Trick Martin M   Bancroft Ian I   Sharpe Andrew G AG   Parkin Isobel A P IA   Batley Jacqueline J   Edwards Dave D   Park Beom-Seok BS  

Genome biology 20100927 9


<h4>Background</h4>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.<h4>Result  ...[more]

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