Gene family evolution across 12 Drosophila genomes.
Gene family evolution across 12 Drosophila genomes.
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DOI：
10.1371/journal.pgen.0030197
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发表时间：
2007-11
期刊：
影响因子：
4.5
通讯作者：
Han SG
中科院分区：
文献类型：
--
作者：
Hahn MW;Han MV;Han SG
全基因组的比较揭示了基因家族大小的巨大而频繁的变化。这些变化的发生是因为基因获得（通过复制）和丢失（通过缺失或假基因化）的高速率，以及全新基因的进化。在这里，我们使用12个完全测序的果蝇物种的基因组，以前所未有的分辨率研究基因的获得和丢失。我们发现了大量的增益和损失，超过40%的所有基因家族在果蝇中的大小不同。据估计，每百万年大约有17个基因被复制并固定在基因组中，这一速度与以前在酵母和哺乳动物中发现的速度相当。我们发现了许多基因家族大小极端扩张或收缩的例子，包括D.在核苷酸水平上也是在正选择下进化的。在我们的数据集中，新进化的基因家族与一类已知在许多情况下从头进化的睾丸表达基因相关。基因家族的比较也使我们能够确定一些注释的D。黑腹果蝇基因，不太可能编码功能蛋白质，以及确定几十个以前未注释的D。黑腹果蝇基因与其他果蝇的保守同源基因。总之，我们的研究结果表明，物种之间的总基因数的明显停滞掩盖了个体基因获得和丢失的快速周转。很可能，这种基因组旋转门在塑造物种之间的形态，生理和代谢差异方面发挥了重要作用。虽然比较基因组测序揭示了密切相关物种中所含基因总数的巨大相似性，但这种相似性隐藏了组成蛋白质的身份和数量的巨大复杂性。物种可以通过基因复制和丢失在基因互补方面有所不同。在这里，我们研究了12个完全测序的果蝇（果蝇）基因组中基因的获得和丢失。我们发现所有物种的基因获得和丢失率都很高，估计大约每6万年就有一个新基因获得或丢失。我们还发现了几百个基因更替极其迅速的案例，几十个基因在短短几百万年内获得或丢失。基因数量的最高周转发生在涉及性和生殖的基因中。总之，我们的研究结果表明，物种之间的总基因数的明显停滞掩盖了个体基因获得和丢失的快速周转。很可能，这种进化旋转门在塑造物种之间的形态，生理和代谢差异方面发挥了重要作用。
Comparison of whole genomes has revealed large and frequent changes in the size of gene families. These changes occur because of high rates of both gene gain (via duplication) and loss (via deletion or pseudogenization), as well as the evolution of entirely new genes. Here we use the genomes of 12 fully sequenced Drosophila species to study the gain and loss of genes at unprecedented resolution. We find large numbers of both gains and losses, with over 40% of all gene families differing in size among the Drosophila. Approximately 17 genes are estimated to be duplicated and fixed in a genome every million years, a rate on par with that previously found in both yeast and mammals. We find many instances of extreme expansions or contractions in the size of gene families, including the expansion of several sex- and spermatogenesis-related families in D. melanogaster that also evolve under positive selection at the nucleotide level. Newly evolved gene families in our dataset are associated with a class of testes-expressed genes known to have evolved de novo in a number of cases. Gene family comparisons also allow us to identify a number of annotated D. melanogaster genes that are unlikely to encode functional proteins, as well as to identify dozens of previously unannotated D. melanogaster genes with conserved homologs in the other Drosophila. Taken together, our results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this genomic revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species. Though comparative genome sequencing has revealed vast similarities in the total number of genes contained within closely related species, this similarity hides enormous complexities in the identity and number of constituent proteins. Species can differ in their complement of genes through both gene duplication and loss. Here we investigated the gain and loss of genes from the genomes of 12 fully sequenced Drosophila (fruit flies). We find high rates of gain and loss in all species and estimate that approximately one new gene is gained or lost every 60,000 years. We also find several hundred cases of extremely rapid gene turnover, with dozens of genes gained or lost in only a few million years. The highest turnover in gene number occurs in genes involved in sex and reproduction. Taken together, our results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this evolutionary revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species.
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