Pan-vertebrate comparative genomics unmasks retrovirus macroevolution
Pan-vertebrate comparative genomics unmasks retrovirus macroevolution
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DOI：
10.1073/pnas.1414980112
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发表时间：
2015-01-13
影响因子：
11.1
通讯作者：
Jern, Patric
中科院分区：
文献类型：
--
作者：
Hayward, Alexander;Cornwallis, Charlie K.;Jern, Patric
虽然广泛的研究已经证明了宿主-逆转录病毒的微进化动力学，但很难更深入地了解宿主-逆转录病毒相互作用的宏观进化模式。在这里，我们使用最新的技术进步来推断广泛的模式，逆转录病毒的多样性，进化和宿主病毒的关系，通过使用大规模的逆转录病毒基因组的方法，使用内源性逆转录病毒（ERVs）。逆转录病毒将前病毒DNA拷贝插入宿主细胞基因组以产生新病毒。ERV是生殖细胞中的前病毒插入物，其沿着宿主谱系遗传，因此呈现过去宿主-病毒关联的记录。通过从脊椎动物多样性中取样的65个宿主基因组中挖掘ERVs，我们发现了ERVs的巨大多样性，表明逆转录病毒序列在脊椎动物中比以前认识到的更为普遍和广泛。大多数ERV分支，我们恢复不包含已知的逆转录病毒，这意味着要么逆转录病毒谱系是高度短暂的进化时间或相当数量的逆转录病毒仍有待确定。通过表征ERV的分布，我们发现，没有主要的脊椎动物谱系逃脱逆转录病毒的活性，逆转录病毒是极端的主机通才，具有前所未有的能力，猖獗的主机之间切换远亲脊椎动物。此外，我们研究ERVs的分布是否可以解释预测影响病毒传播的宿主因素，并发现内部受精对宿主基因组的逆转录病毒定殖有显着影响。通过捕获逆转录病毒进化的模式和模式，并将ERV多样性与已知的逆转录病毒多样性进行对比，我们的研究提供了一个有凝聚力的框架，以更好地了解宿主-病毒协同进化。
Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host-retrovirus interactions. Here we use recent technological advances to infer broad patterns in retroviral diversity, evolution, and host-virus relationships by using a large-scale phylogenomic approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA copy into the host cell genome to produce new viruses. ERVs are provirus insertions in germline cells that are inherited down the host lineage and consequently present a record of past host-viral associations. By mining ERVs from 65 host genomes sampled across vertebrate diversity, we uncover a great diversity of ERVs, indicating that retroviral sequences are much more prevalent and widespread across vertebrates than previously appreciated. The majority of ERV clades that we recover do not contain known retroviruses, implying either that retroviral lineages are highly transient over evolutionary time or that a considerable number of retroviruses remain to be identified. By characterizing the distribution of ERVs, we show that no major vertebrate lineage has escaped retroviral activity and that retroviruses are extreme host generalists, having an unprecedented ability for rampant host switching among distantly related vertebrates. In addition, we examine whether the distribution of ERVs can be explained by host factors predicted to influence viral transmission and find that internal fertilization has a pronounced effect on retroviral colonization of host genomes. By capturing the mode and pattern of retroviral evolution and contrasting ERV diversity with known retroviral diversity, our study provides a cohesive framework to understand host-virus coevolution better.