the Department of Human Evolutionary Biology, Graduate School of Art and Science, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138.
J Hered. 2014 May-Jun;105(3):436-43. doi: 10.1093/jhered/est097. Epub 2014 Jan 7.
It has been revealed that gene content changes, or gene gains or losses, have played an important role in the evolution of modern humans. As one of the major players accounting for gene content changes, gene pseudogenization is abundant in mammalian genomes, and approximately 20000 pseudogenes have been identified in ape genomes. Therefore, it is an interesting question how to exploit rich information embedded in pseudogenes. Here, I present a bioinformatic pipeline that utilizes a pseudogene database to identify both lineage-specific genes and pseudogenes in humans and chimpanzees. I found 6 human-specific gene gains (HSGs), 1 chimpanzee-specific gene gain, and 4 chimpanzee-specific pseudogenes, most not discovered in previous studies. Further analysis showed that HSGs have been evolving under strong purifying selection and are broadly expressed, indicating strong functional constraint. This study demonstrates the usage of pseudogene information in comparative genomics and suggests that new genes during primate evolution may acquire essential functions in a short time. The pipeline developed here could also be applied to other species.
研究表明，基因内容的改变，即基因的获得或缺失，在现代人的进化过程中发挥了重要作用。基因假基因化作为导致基因内容改变的主要因素之一，在哺乳动物基因组中大量存在，在猿类基因组中已鉴定出约 20000 个假基因。因此，如何利用假基因中嵌入的丰富信息是一个有趣的问题。在这里，我提出了一个生物信息学流程，该流程利用假基因数据库来鉴定人类和黑猩猩中的谱系特异性基因和假基因。我发现了 6 个人类特异性基因获得（HSGs）、1 个黑猩猩特异性基因获得和 4 个黑猩猩特异性假基因，其中大多数在以前的研究中未被发现。进一步的分析表明，HSGs 一直受到强烈的纯化选择而进化，并广泛表达，表明其受到强烈的功能约束。这项研究展示了假基因信息在比较基因组学中的应用，并表明灵长类动物进化过程中的新基因可能在短时间内获得重要功能。这里开发的流程也可应用于其他物种。
