Sequence and structure of Brassica rapa chromosome A3
- Equal contributors
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
Genome Biology 2010, 11:R94 doi:10.1186/gb-2010-11-9-r94Published: 27 September 2010
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.