Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication.
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication.
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DOI：
10.1186/gb-2009-10-10-r111
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发表时间：
2009
期刊：
影响因子：
12.3
通讯作者：
Park BS
中科院分区：
文献类型：
--
作者：
Mun JH;Kwon SJ;Yang TJ;Seol YJ;Jin M;Kim JA;Lim MH;Kim JS;Baek S;Choi BS;Yu HJ;Kim DS;Kim N;Lim KB;Lee SI;Hahn JH;Lim YP;Bancroft I;Park BS
对芜菁基因组的常染色质区进行测序并定位到拟南芥基因组的相应区域。芜菁是世界上最重要的经济蔬菜作物之一。由于其在农艺学上的重要性和系统发育上的地位，B. rapa为理解与多倍体相关的作物基因组进化提供了重要参考。拟南芥和芸苔属基因组之间的高度序列同一性和显著保守的基因组结构使得能够使用拟南芥序列作为参考来选择B中的对应区域的比较平铺测序成为可能。rapa，这是结构和比较作物基因组学的一个强大挑战。我们组装了B的65.8兆碱基对的非冗余常染色质序列。rapa和拟南芥基因组比较，研究染色体的关系，宏同线性块，和微同线性块内。三个B。由于基因组缩小，芜菁基因组中的基因数量大约是拟南芥的两倍。基因组比较表明，B。由于最近的全基因组三倍化以及随后独特的二倍化过程，芜菁具有祖先基因组块的独特组织。在B中缺乏最近的全基因组重复（3R）事件。与其他芸苔属植物基因组相比，rapa基因组是非典型的，这可能是B的出现原因。从大约800万年前的芸苔属祖先进化而来。这项工作表明了利用比较平铺测序进行作物物种基因组分析的潜力。通过对B. rapa序列和拟南芥基因组，看来，多倍体和染色体二倍体化是正在进行的过程，共同稳定的B。基因组，并促进其进化。
Euchromatic regions of the Brassica rapa genome were sequenced and mapped onto the corresponding regions in the Arabidopsis thaliana genome. 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. 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. 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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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
DOI：
10.1073/pnas.0402251101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Choi, HK;Mun, JH;Cook, DR
通讯作者：
Cook, DR
影响因子：
3.8
作者：
Buggs, R. J. A.;Doust, A. N.;Soltis, D. E.
通讯作者：
Soltis, D. E.
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
12.3
作者：
Haas, Brian J.;Salzberg, Steven L.;Zhu, Wei;Pertea, Mihaela;Allen, Jonathan E.;Orvis, Joshua;White, Owen;Buell, C. Robin;Wortman, Jennifer R.
通讯作者：
Wortman, Jennifer R.