Research

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

Jeong-Hwan Mun¹ , Soo-Jin Kwon¹ , Tae-Jin Yang² , Young-Joo Seol¹ , Mina Jin¹ , Jin-A Kim¹ , Myung-Ho Lim¹ , Jung Sun Kim¹ , Seunghoon Baek¹ , Beom-Soon Choi³ , Hee-Ju Yu⁴ , Dae-Soo Kim⁵ , Namshin Kim⁵ , Ki-Byung Lim⁶ , Soo-In Lee¹ , Jang-Ho Hahn¹ , Yong Pyo Lim⁷ , Ian Bancroft⁸ and Beom-Seok Park¹

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 Plant Science College of Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Korea

³  National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, Korea

⁴  Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Tap-dong 540-41, Gwonseon-gu, Suwon 441-440, Korea

⁵  Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea

⁶  School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Korea

⁷  Department of Horticulture, Chungnam National University, 220 Kung-dong, Yusong-gu, Daejon 305-764, Korea

⁸  John Innes Centre, Norwich Research Centre, Colney, Norwich NR4 7UH, UK

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Genome Biology 2009, 10:R111doi:10.1186/gb-2009-10-10-r111

Published:	12 October 2009

Subject areas: Evolution, Genome studies, Model organisms, Plant biology

Abstract

Background

Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics.

Results

We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago.

Conclusions

This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.