Plant Cell Advance Online Publication
Published on April 21, 2006; 10.1105/tpc.105.040535
OPEN ACCESS ARTICLE
Received December 16, 2005
Returned for revision January 24, 2006
Accepted March 27, 2006
Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa
Tae-Jin Yang 1, Jung Sun Kim 1, Soo-Jin Kwon 1, Ki-Byung Lim 2, Beom-Soon Choi 1, Jin-A Kim 1, Mina Jin 1, Jee Young Park 1, Myung-Ho Lim 1, Ho-Il Kim 1, Yong Pyo Lim 3, Jason Jongho Kang 4, Jin-Han Hong 4, Chang-Bae Kim 5, Jong Bhak 5, Ian Bancroft 6, and Beom-Seok Park 1*
1 Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
2 Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea; School of Plant Bioscience, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Korea
3 Department of Horticulture, Chungnam National University, Daejeon 305-764, Korea
4 Macrogen 60-24, Gasan-dong, Geumcheon-gu, Seoul 153-023, Korea
5 National Genome Information Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-333, Korea
6 John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
* To whom correspondence should be addressed. E-mail: pbeom{at}rda.go.kr.
Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred  0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.
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