Broad-scale phylogenomics provides insights into retrovirus-host evolution
Broad-scale phylogenomics provides insights into retrovirus-host evolution
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DOI：
10.1073/pnas.1315419110
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发表时间：
2013-12-10
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;Grabherr, Manfred;Jern, Patric
基因组数据提供了一个很好的资源，以提高逆转录病毒的进化和病毒与其宿主之间的复杂关系的理解。结合脊椎动物基因组的大规模计算机筛选，该资源提供了一个机会，以补充过去逆转录病毒传播的演变和频率的数据，从而评估未来的风险和不同宿主物种之间的水平传播的限制。在这里，我们开发了一种方法，用于从大型内源性逆转录病毒（ERV）数据集提取系统发育信号，通过折叠信息，以促进大范围的宿主样本的大规模基因组学。从60种脊椎动物宿主基因组的近90，000个ERV开始，我们构建系统发育假说，并推断γ逆转录病毒属和相关I类ERV的名称、宿主分布、起源和传播。我们的研究结果揭示了显着的深度逆转录病毒序列的多样性，支持系统发育的背景下。这一发现表明，目前的感染性外源性逆转录病毒的多样性可能被低估，增加了可信度的可能性，许多额外的外源性逆转录病毒可能仍然被发现在脊椎动物类群。我们展示了一个历史频繁的水平interorder传输从啮齿动物水库，并建议，大鼠可能已作为重要的被忽视的促进剂的gammaretrovirus传播在不同的哺乳动物宿主。总之，这些结果表明，这里使用的方法来分析大型ERV数据集，提高对逆转录病毒进化和多样性的理解，以便在更广泛的应用中利用的前景。
Genomic data provide an excellent resource to improve understanding of retrovirus evolution and the complex relationships among viruses and their hosts. In conjunction with broad-scale in silico screening of vertebrate genomes, this resource offers an opportunity to complement data on the evolution and frequency of past retroviral spread and so evaluate future risks and limitations for horizontal transmission between different host species. Here, we develop a methodology for extracting phylogenetic signal from large endogenous retrovirus (ERV) datasets by collapsing information to facilitate broad-scale phylogenomics across a wide sample of hosts. Starting with nearly 90,000 ERVs from 60 vertebrate host genomes, we construct phylogenetic hypotheses and draw inferences regarding the designation, host distribution, origin, and transmission of the Gammaretrovirus genus and associated class I ERVs. Our results uncover remarkable depths in retroviral sequence diversity, supported within a phylogenetic context. This finding suggests that current infectious exogenous retrovirus diversity may be underestimated, adding credence to the possibility that many additional exogenous retroviruses may remain to be discovered in vertebrate taxa. We demonstrate a history of frequent horizontal interorder transmissions from a rodent reservoir and suggest that rats may have acted as important overlooked facilitators of gammaretrovirus spread across diverse mammalian hosts. Together, these results demonstrate the promise of the methodology used here to analyze large ERV datasets and improve understanding of retroviral evolution and diversity for utilization in wider applications.