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Sequence and structure of Brassica rapa chromosome A3

Jeong-Hwan Mun1*, Soo-Jin Kwon1, Young-Joo Seol1, Jin A Kim1, Mina Jin1, Jung Sun Kim1, Myung-Ho Lim1, Soo-In Lee1, Joon Ki Hong1, Tae-Ho Park1, Sang-Choon Lee1, Beom-Jin Kim1, Mi-Suk Seo1, Seunghoon Baek1, Min-Jee Lee1, Ja Young Shin1, Jang-Ho Hahn1, Yoon-Jung Hwang2, Ki-Byung Lim2, Jee Young Park3, Jonghoon Lee3, Tae-Jin Yang3, Hee-Ju Yu4, Ik-Young Choi5, Beom-Soon Choi5, Su Ryun Choi6, Nirala Ramchiary6, Yong Pyo Lim6, Fiona Fraser7, Nizar Drou7, Eleni Soumpourou7, Martin Trick7, Ian Bancroft7, Andrew G Sharpe8, Isobel AP Parkin9, Jacqueline Batley10, Dave Edwards11 and Beom-Seok Park1*

Author Affiliations

1 Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea

2 Department of Horticulture, College of Agriculture and Life Science, Kyungpook National University, 1370 Sangyeok-dong, Buk-gu, Daegu 702-701, Korea

3 Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Korea

4 Department of Life Sciences, The Catholic University of Korea, 43-1 Yeokgok 2-dong, Wonmi-gu, Bucheon 420-743, Korea

5 National Instrumentation Center for Environmental Management, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Korea

6 Department of Horticulture, Chungnam National University, 220 Kung-dong, Yusong-gu, Daejon 305-764, Korea

7 John Innes Centre, Colney, Norwich NR4 7UH, UK

8 NRC Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada

9 Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK S7N OX2, Canada

10 ARC Centre of Excellence for Integrative Legume Research and School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4067, Australia

11 Australian Centre for Plant Functional Genomics and School of Land Crop and Food Sciences, University of Queensland, Brisbane, QLD 4067, Australia

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Genome Biology 2010, 11:R94  doi:10.1186/gb-2010-11-9-r94

Published: 27 September 2010

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.