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

被引:171
作者
Mun, Jeong-Hwan [1 ]
Kwon, Soo-Jin [1 ]
Yang, Tae-Jin [2 ]
Seol, Young-Joo [1 ]
Jin, Mina [1 ]
Kim, Jin-A [1 ]
Lim, Myung-Ho [1 ]
Kim, Jung Sun [1 ]
Baek, Seunghoon [1 ]
Choi, Beom-Soon [3 ]
Yu, Hee-Ju [4 ]
Kim, Dae-Soo [5 ]
Kim, Namshin [5 ]
Lim, Ki-Byung [6 ]
Lee, Soo-In [1 ]
Hahn, Jang-Ho [1 ]
Lim, Yong Pyo [7 ]
Bancroft, Ian [8 ]
Park, Beom-Seok [1 ]
机构
[1] Rural Dev Adm, Dept Agr Biotechnol, Natl Acad Agr Sci, Suwon 441707, South Korea
[2] Seoul Natl Univ, Dept Plant Sci, Coll Agr & Life Sci, Seoul 151921, South Korea
[3] Seoul Natl Univ, Natl Instrumentat Ctr Environm Management, Coll Agr & Life Sci, Seoul 151921, South Korea
[4] Rural Dev Adm, Vegetable Res Div, Natl Inst Hort & Herbal Sci, Suwon 441440, South Korea
[5] Korea Res Inst Biosci & Biotechnol, Taejon 305806, South Korea
[6] Kyungpook Natl Univ, Sch Appl Biosci, Coll Agr & Life Sci, Taegu 702701, South Korea
[7] Chungnam Natl Univ, Dept Hort, Taejon 305764, South Korea
[8] Norwich Res Ctr, John Innes Ctr, Norwich NR4 7UH, Norfolk, England
来源
GENOME BIOLOGY | 2009年 / 10卷 / 10期
基金
英国生物技术与生命科学研究理事会;
关键词
ARABIDOPSIS-THALIANA; PHYLOGENETIC ANALYSIS; WEB SERVER; EVOLUTION; ANGIOSPERM; MODEL; SIZE; MAP; RETROTRANSPOSONS; POLYPLOIDY;
D O I
10.1186/gb-2009-10-10-r111
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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.
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页数:18
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