Large-scale trends in the evolution of gene structures within 11 animal genomes.
Large-scale trends in the evolution of gene structures within 11 animal genomes.
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DOI：
10.1371/journal.pcbi.0020015
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发表时间：
2006-03
影响因子：
4.3
通讯作者：
Rubin GM
中科院分区：
文献类型：
--
作者：
Yandell M;Mungall CJ;Smith C;Prochnik S;Kaminker J;Hartzell G;Lewis S;Rubin GM
我们使用了六种动物基因组(智人、小鼠、肠生动物、黑腹果蝇、冈比亚按蚊和秀丽线虫)的注释以及五种未注释的果蝇基因组的序列来研究各种时间尺度上的蛋白质序列和基因结构的变化-从仿生线虫和黑线线虫分化以来的不到500万年到寒武纪大爆发以来的5亿多年。为此，我们开发了一个新的开源软件库，名为CGL(比较基因组学库)。我们的结果表明，内含子-外显子结构的变化是渐进的，像时钟一样，并且在很大程度上独立于编码序列的进化。这意味着基因组注释可以以新的方式用于告知、证实和检验基于蛋白质和核苷酸序列相似性的比较基因组学分析得出的结论。正如蛋白质序列随着时间的推移而变化一样，基因结构也是如此。在相对较短的进化时间尺度上，内含子会延长和缩短；而在较长的时间尺度上，内含子在同源基因中的数量和位置可能会发生变化。这些事实表明，基因的内含子-外显子结构可能提供了进化信息的来源。然而，基因结构作为系统发育分析材料的效用取决于它们是否独立于推动蛋白质进化的力量。例如，如果内含子-外显子结构受到氨基酸水平的选择的强烈影响，那么使用它们进行系统发育研究在很大程度上是没有意义的，因为从蛋白质分析中可以更容易地获得相同的信息。Yandell等人使用了11个动物基因组。表明内含子长度和位置的进化在很大程度上--尽管不是完全--独立于蛋白质序列进化。这意味着，基因结构提供了一个独立于蛋白质序列相似性的关于进化历史的信息来源--作者利用这一发现来研究蛋白质时钟的准确性，并探索基因结构作为解决动物内部深层系统发育关系的手段的实用性。
We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences of five unannotated Drosophila genomes to survey changes in protein sequence and gene structure over a variety of timescales—from the less than 5 million years since the divergence of D. simulans and D. melanogaster to the more than 500 million years that have elapsed since the Cambrian explosion. To do so, we have developed a new open-source software library called CGL (for “Comparative Genomics Library”). Our results demonstrate that change in intron–exon structure is gradual, clock-like, and largely independent of coding-sequence evolution. This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities. Just as protein sequences change over time, so do gene structures. Over comparatively short evolutionary timescales, introns lengthen and shorten; and over longer timescales the number and positions of introns in homologous genes can change. These facts suggest that the intron–exon structures of genes may provide a source of evolutionary information. The utility of gene structures as materials for phylogenetic analyses, however, depends upon their independence from the forces driving protein evolution. If, for example, intron–exon structures are strongly influenced by selection at the amino acid level, then using them for phylogenetic investigations is largely pointless, as the same information could have been more easily gained from protein analyses. Using 11 animal genomes, Yandell et al. show that evolution of intron lengths and positions is largely—though not completely—independent of protein sequence evolution. This means that gene structures provide a source of information about the evolutionary past independent of protein sequence similarities—a finding the authors employ to investigate the accuracy of the protein clock and to explore the utility of gene structures as a means to resolve deep phylogenetic relationships within the animals.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
12.3
作者：
通讯作者：
--
影响因子：
14.9
作者：
Drysdale RA;Crosby MA;FlyBase Consortium
通讯作者：
FlyBase Consortium
DOI：
10.1002/cjs.5540330306
发表时间：
2005-09-01
影响因子：
0.6
作者：
Chen, XH;Fan, YQ
通讯作者：
Fan, YQ
影响因子：
14.9
作者：
Birney, E;Andrews, D;Hubbard, T
通讯作者：
Hubbard, T