Sequence and structure of Brassica rapa chromosome A3.
Sequence and structure of Brassica rapa chromosome A3.
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DOI：
10.1186/gb-2010-11-9-r94
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发表时间：
2010
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;Seol YJ;Kim JA;Jin M;Kim JS;Lim MH;Lee SI;Hong JK;Park TH;Lee SC;Kim BJ;Seo MS;Baek S;Lee MJ;Shin JY;Hahn JH;Hwang YJ;Lim KB;Park JY;Lee J;Yang TJ;Yu HJ;Choi IY;Choi BS;Choi SR;Ramchiary N;Lim YP;Fraser F;Drou N;Soumpourou E;Trick M;Bancroft I;Sharpe AG;Parkin IA;Batley J;Edwards D;Park BS
芜菁是重要的蔬菜和油料作物。由于其具有古六倍体的祖先，并且与拟南芥和其他基因组较大的芸苔属物种有着密切的进化关系，因此它也是研究多倍体相关基因组进化的一个很好的模式系统。因此，其基因组序列将用于加速基因组进化的基础研究和栽培芸苔属物种的应用研究。测定并分析了B的序列。芜菁染色体A3。我们获得了31.9 Mb的序列，组织成9个重叠群，其中包括348个重叠的BAC克隆。注释揭示了7，058个蛋白质编码基因，平均基因密度为4.6kb/基因。染色体共线性分析与A.拟南芥基因组鉴定出了包含整个B的保守同线性块。rapa染色体A3和4个A.拟南芥染色体在B中保守的基因组片段之间，基因串联重复的频率不同。rapa和A. thaliana，表明这种基因的重复拷贝的发生/保留的差异率。对“祖先核型”基因组构建块的分析使得能够开发出用于推导B的假设模型。芜菁染色体A3。我们报道了一个双子叶作物染色体的近全序列。这提供了多倍体之后基因组进化复杂性的一个例子。由逐个克隆方法提供的高度邻接性为目前在B中应用的全基因组鸟枪法的性能提供了基准。以及其他基因组复杂的物种。
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.
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影响因子：
12.3
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
通讯作者：
Park BS
DOI：
10.1073/pnas.0510791103
发表时间：
2006-03-28
影响因子：
11.1
作者：
Lysak, MA;Berr, A;Schubert, I
通讯作者：
Schubert, I
影响因子：
3.3
作者：
Kim, Jung Sun;Chung, Tae Young;Park, Beom-Seok
通讯作者：
Park, Beom-Seok
影响因子：
7.2
作者：
Lim, Ki-Byung;Yang, Tae-Jin;Park, Beom-Seok
通讯作者：
Park, Beom-Seok
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.