Sequence and structure of Brassica rapa chromosome A3

Genome Biology, Sep 2010

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.

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Sequence and structure of Brassica rapa chromosome A3

Mun et al. Genome Biology Sequence and structure of Brassica rapa chromosome A3 Jeong-Hwan Mun 0 Soo-Jin Kwon 0 Young-Joo Seol 0 Jin A Kim 0 Mina Jin 0 Jung Sun Kim 0 Myung-Ho Lim 0 Soo-In Lee 0 Joon Ki Hong 0 Tae-Ho Park 0 Sang-Choon Lee 0 Beom-Jin Kim 0 Mi-Suk Seo 0 Seunghoon Baek 0 Min-Jee Lee 0 Ja Young Shin 0 Jang-Ho Hahn 0 Yoon-Jung Hwang Ki-Byung Lim Jee Young Park Jonghoon 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 AP Parkin Jacqueline Batley Dave Edwards Beom-Seok Park 0 0 Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration , 150 Suin-ro, Gwonseon-gu, Suwon 441-707 , Korea 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. - Background The Brassicaceae family includes approximately 3,700 species in 338 genera. The species, which include the widely studied Arabidopsis thaliana, have diverse characteristics and many are of agronomic importance as vegetables, condiments, fodder, and oil crops [1]. Economically, Brassica species contribute to approximately 10% of the worlds vegetable crop produce and approximately 12% of the worldwide edible oil supplies [2]. The tribe Brassiceae, which is one of 25 tribes in the Brassicaceae, consists of approximately 240 species and contains the genus Brassica. The cultivated Brassica species are B. rapa (which contains the Brassica A genome) and B. oleracea (C genome), which are grown mostly as vegetable cole crops, B. nigra (B genome) as a source of mustard condiment, and oil crops, mainly B. napus (a recently formed allotetraploid containing both A and C genomes), B. juncea (A and B genomes), and B. carinata (B and C genomes) as sources of canola oil. These genome relationships between the three diploid species and their pairwise allopolyploid derivative species have long been known, and are described by Us triangle [3]. B. rapa is a major vegetable or oil crop in Asia and Europe, and has recently become a widely used model for the study of polyploid genome structure and evolution because it has the smallest genome (529 Mb) of the Brassica genus and, like all members of the tribe Brassiceae, has evolved from a hexaploid ancestor [4-6]. Our previous comparative genomic study revealed conserved linkage arrangements and collinear chromosome segments between B. rapa and A. thaliana, which diverged from a common ancestor approximately 13 to 17 million years ago. The B. rapa genome contains triplicated homoeologous counterparts of the corresponding segments of the A. thaliana genome due to triplication of the entire genome (whole genome triplication), which occurred approximately 11 to 12 million years ago [6]. Furthermore, studies in B. napus, which was generated in the last 10,000 years, have demonstrated that overall genome structure is highly conserved compared to its progenitor species, B. rapa and B. oleracea, which diverged approximately 8 million years ago, but significantly diverged relative to A. thaliana at the sequence level [7,8]. Thus, investigation of the B. rapa genome provides substantial opportunities to study the divergence of gene function and genome evolution associated with polyploidy (...truncated)


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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 Park, Jonghoon 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 AP Parkin, Jacqueline Batley, Dave Edwards, Beom-Seok Park. Sequence and structure of Brassica rapa chromosome A3, Genome Biology, 2010, pp. R94, 11, DOI: 10.1186/gb-2010-11-9-r94