Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling
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DOI：
10.1073/pnas.1507669112
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发表时间：
2015-12-01
影响因子：
11.1
通讯作者：
Nishida, Mutsumi
中科院分区：
文献类型：
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作者：
Inoue, Jun;Sato, Yukuto;Nishida, Mutsumi
全基因组复制（WGD）被认为是重大进化创新的重要来源。 WGD 产生的冗余基因被认为会丢失或获得新功能。然而，全基因组测序后基因丢失的速度以及基因组重塑的时间过程仍不清楚。所有硬骨鱼（所有有颌脊椎动物的一半）所共有的全基因组测序比有颌脊椎动物起源之前发生的两个古代全基因组测序更晚，因此有助于分析基因丢失和基因组重塑。使用新开发的直系同源鉴定流程，我们从时间校准树上的九个系统发育代表性硬骨鱼基因组中推断出 6,892 个蛋白质编码基因的后硬骨鱼特异性 WGD 进化历史。我们发现，在前 60 My 中确实发生了快速的基因丢失，丢失了超过 70-80% 的重复基因，并在相对较短的时间内在硬骨鱼中产生了类似的基因组基因排列。数学模型表明，快速基因丢失主要是由涉及多个基因同时丢失的事件引起的。我们发现随后的 250 个 My 的特点是个体基因缓慢而稳定地丢失。我们的管道还鉴定了大约 1,100 个共享的单拷贝基因，这些基因被推断在鲱鱼类硬骨鱼分化之前就已经成为单基因。因此，我们的比较基因组分析表明，WGD 后的快速基因丢失在大分化之前重塑了硬骨鱼基因组，并为未来的系统发育分析提供了一组有用的标记基因。
Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post-teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70-80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.