Abstract

Endogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retroviral gene co-option events have been documented. Here, we use a phylogenomic approach to analyze more than 700 vertebrate genomes to uncover retroviral gene co-option taking place during the evolution of vertebrates. We identify a total of 177 independent retroviral gene co-option events in vertebrates, a majority of which have not been reported previously. Among these retroviral gene co-option events, 93 and 84 involve gag and env genes, respectively. More than 78.0% (138 out of 177) of retroviral gene co-option occurred within mammals. The gag and env co-option events share a generally similar temporal pattern with less frequent retroviral gene co-option identified in the deep branches, suggesting that retroviral gene co-option might have not been maintained for very long time periods. Moreover, we find co-opted retroviral genes are subject to different selection pressure, implying potentially diverse cellular functionality. Our study provides a comprehensive picture of co-opted retroviral genes during the evolution of vertebrates and has implications in understanding the ancient evolution of vertebrate–retrovirus interaction.

中文翻译：

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脊椎动物进化过程中频繁的逆转录病毒基因选择。

摘要

内源性逆转录病毒在脊椎动物基因组中普遍存在。有时，宿主会募集逆转录病毒基因来介导其自身的生物学功能，这一过程被正式称为共同选择或免除。尽管已经记录了十多个逆转录病毒基因选择事件，但关于脊椎动物中逆转录病毒基因选择的程度仍不清楚。在这里，我们使用一种植物学方法来分析700多个脊椎动物基因组，以揭示在脊椎动物进化过程中发生的逆转录病毒基因共同选择。我们在脊椎动物中共确定了177个独立的逆转录病毒基因选择事件，其中大多数以前未曾报道过。在这些逆转录病毒基因选择事件中，有93和84涉及gag和env基因分别。哺乳动物中发生了超过78.0％（177个中的138个）逆转录病毒基因共选。该GAG和ENV增选活动分享在深分支机构标识不太频繁逆转录病毒基因增选一个大体相似的时间模式，表明逆转录病毒基因共选择可能没有维持很长的时间周期。此外，我们发现选出的逆转录病毒基因受到不同的选择压力，暗示潜在的细胞功能多样化。我们的研究为脊椎动物进化过程中所选择的逆转录病毒基因提供了全面的信息，并有助于理解脊椎动物与逆转录病毒相互作用的古老进化。