Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns.
Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns.
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DOI：
10.1186/1471-2164-10-271
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发表时间：
2009-06-18
期刊：
影响因子：
4.4
通讯作者：
Ogihara Y
中科院分区：
文献类型：
--
作者：
Kawaura K;Mochida K;Enju A;Totoki Y;Toyoda A;Sakaki Y;Kai C;Kawai J;Hayashizaki Y;Seki M;Shinozaki K;Ogihara Y
小麦是一种异源多倍体植物，拥有巨大而复杂的基因组。因此，小麦表达序列标签（EST）的积累对于功能基因组学和分子育种变得尤为重要。我们从小麦生命周期中发育的各种组织和遭受胁迫的组织中准备了全面的 EST 集合。我们还在计算机中检查了它们的表达谱。由于全长 cDNA 对于验证收集的 EST 和注释小麦基因组中的基因是必不可少的，因此我们对全长 cDNA 克隆进行了系统调查和测序。该序列信息是功能基因组学的宝贵遗传资源，并将有助于在谷物中进行比较基因组学。作为功能基因组学和小麦基因组资源开发的一部分，我们从普通小麦中生成了一系列全长 cDNA。通过对从全长 cDNA 文库中随机选择的重组克隆的 EST 进行分组，我们能够高精度地对 6,162 个独立克隆进行测序。大约 10% 的克隆是小麦特有的基因，在 DNA 数据库中没有任何对应物。选择与水稻表现出高度同源性的小麦克隆，以研究它们在整个小麦生命周期的各种组织中的表达模式以及对非生物胁迫处理的反应。为了评估小麦和水稻中不同进化基因的变异性，我们计算了小麦和水稻中对应基因的替代率（Ka/Ks）。在某些组织或处理中优先表达的基因比在其他组织和处理中优先表达的基因具有更高的Ka/Ks值，这表明在这些组织中表达的具有较高变异性的基因处于适应性选择之下。我们已经为普通小麦生成了高质量的全长 cDNA 资源，这对于继续进行小麦基因组的管理和注释至关重要。每个克隆在不同组织和胁迫处理中的表达数据，以及小麦和水稻由于多样化而产生的变异性，是小麦功能基因组学和谷物比较基因组学的宝贵工具。
Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs) for wheat is becoming particularly important for functional genomics and molecular breeding. We prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues subjected to stress. We also examined their expression profiles in silico. As full-length cDNAs are indispensable to certify the collected ESTs and annotate the genes in the wheat genome, we performed a systematic survey and sequencing of the full-length cDNA clones. This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals. As part of the functional genomics and development of genomic wheat resources, we have generated a collection of full-length cDNAs from common wheat. By grouping the ESTs of recombinant clones randomly selected from the full-length cDNA library, we were able to sequence 6,162 independent clones with high accuracy. About 10% of the clones were wheat-unique genes, without any counterparts within the DNA database. Wheat clones that showed high homology to those of rice were selected in order to investigate their expression patterns in various tissues throughout the wheat life cycle and in response to abiotic-stress treatments. To assess the variability of genes that have evolved differently in wheat and rice, we calculated the substitution rate (Ka/Ks) of the counterparts in wheat and rice. Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection. We have generated a high-quality full-length cDNA resource for common wheat, which is essential for continuation of the ongoing curation and annotation of the wheat genome. The data for each clone's expression in various tissues and stress treatments and its variability in wheat and rice as a result of their diversification are valuable tools for functional genomics in wheat and for comparative genomics in cereals.
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影响因子：
3.3
作者：
Gill, Bikram S.;Appels, Rudi;Sasaki, Takuji
通讯作者：
Sasaki, Takuji
影响因子：
3.3
作者：
Gu, XY;Kianian, SF;Foley, ME
通讯作者：
Foley, ME
基于PCR的地标独特基因（插头）标记有效地将同种小麦基因分配给A，B和D基因组。
影响因子：
4.4
作者：
Ishikawa, Goro;Yonemaru, Junichi;Saito, Mika;Nakamura, Toshiki
通讯作者：
Nakamura, Toshiki
影响因子：
4.3
作者：
Delseny, M;Bies-Etheve, N;Aspart, L
通讯作者：
Aspart, L
影响因子：
3.5
作者：
Minglin, L;Zhang, YX;Chai, TY
通讯作者：
Chai, TY