The Genomes of Oryza sativa: a history of duplications.
The Genomes of Oryza sativa: a history of duplications.
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DOI：
10.1371/journal.pbio.0030038
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发表时间：
2005-02
期刊：
影响因子：
9.8
通讯作者：
Yang H
中科院分区：
文献类型：
--
作者：
Yu J;Wang J;Lin W;Li S;Li H;Zhou J;Ni P;Dong W;Hu S;Zeng C;Zhang J;Zhang Y;Li R;Xu Z;Li S;Li X;Zheng H;Cong L;Lin L;Yin J;Geng J;Li G;Shi J;Liu J;Lv H;Li J;Wang J;Deng Y;Ran L;Shi X;Wang X;Wu Q;Li C;Ren X;Wang J;Wang X;Li D;Liu D;Zhang X;Ji Z;Zhao W;Sun Y;Zhang Z;Bao J;Han Y;Dong L;Ji J;Chen P;Wu S;Liu J;Xiao Y;Bu D;Tan J;Yang L;Ye C;Zhang J;Xu J;Zhou Y;Yu Y;Zhang B;Zhuang S;Wei H;Liu B;Lei M;Yu H;Li Y;Xu H;Wei S;He X;Fang L;Zhang Z;Zhang Y;Huang X;Su Z;Tong W;Li J;Tong Z;Li S;Ye J;Wang L;Fang L;Lei T;Chen C;Chen H;Xu Z;Li H;Huang H;Zhang F;Xu H;Li N;Zhao C;Li S;Dong L;Huang Y;Li L;Xi Y;Qi Q;Li W;Zhang B;Hu W;Zhang Y;Tian X;Jiao Y;Liang X;Jin J;Gao L;Zheng W;Hao B;Liu S;Wang W;Yuan L;Cao M;McDermott J;Samudrala R;Wang J;Wong GK;Yang H
我们报告了改进的籼稻和粳稻基因组全基因组鸟枪测序，两者都具有多兆连续性，或者说比2002年的草案改进了近1,000倍。对19，079个全长cDNA的非冗余集合进行测试，97.7%的基因与一个或另一个基因组的映射超级支架对齐，没有片段化。我们介绍了一个基因识别程序的植物，不依赖于已知基因的相似性，以消除错误的预测转座因子。使用可用的EST数据来调整预测中的残余误差，估计的基因计数至少为38，000 - 40，000。只有2%-3%的基因是任何一个亚种所独有的，与可能仍然缺失的序列数量相当。尽管基因内容缺乏变异，但基因间区域存在巨大变异。两个序列中至少有四分之一不能比对，而在它们可以比对的地方，单核苷酸多态性（SNP）率从编码区的3.0 SNP/kb到转座因子的27.6 SNP/kb不等。这里介绍了一种更具包容性的分析重复历史的新方法。它揭示了一个古老的全基因组复制，最近在11号和12号染色体上的片段复制，以及大量正在进行的个体基因复制。我们发现了18对不同的重复片段，覆盖了65.7%的基因组;其中17对可以追溯到禾本科植物分化之前的共同时间。更重要的是，持续的个体基因复制为基因发生提供了永无止境的原材料来源，并且是禾本科成员之间差异的主要贡献者。籼稻和粳稻基因组的比较测序揭示了基因和基因组区域的重复在禾本科植物基因组的进化中起着重要作用
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family. Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes
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DOI：
10.1073/pnas.94.13.6809
发表时间：
1997-06-24
影响因子：
11.1
作者：
Gaut, BS;Doebley, JF
通讯作者：
Doebley, JF
影响因子：
7
作者：
Camon, E;Magrane, M;Apweiler, R
通讯作者：
Apweiler, R
影响因子：
64.8
作者：
Altshuler, D;Pollara, VJ;Lander, ES
通讯作者：
Lander, ES
影响因子：
13.8
作者：
Dominguez, I;Graziano, E;Barnes, S
通讯作者：
Barnes, S
影响因子：
4.2
作者：
Feuillet, C;Keller, B
通讯作者：
Keller, B