Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water.
Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water.
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DOI：
10.1371/journal.ppat.1009730
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发表时间：
2021-07
期刊：
影响因子：
6.7
通讯作者：
Han GZ
中科院分区：
文献类型：
--
作者：
Zheng J;Wang J;Gong Z;Han GZ
鲸目动物的祖先在五千万年前的始新世早期经历了从陆地到水的宏观进化转变。然而，人们对多种逆转录病毒在从陆地环境到水生环境的转变过程中如何进化知之甚少。逆转录病毒是否会伴随宿主转移到水中？鲸目动物入侵水生环境后，逆转录病毒是否通过跨物种传播感染了鲸目动物？内源性逆转录病毒（ERV）为追踪逆转录病毒在这一宏观进化转变过程中的进化提供了重要的分子化石。在这里，我们使用系统发育学方法来研究鲸类动物 ERV 的起源和进化。我们在 25 种鲸目动物的基因组中总共鉴定出了 8,724 个 ERV，系统发育分析表明这些 ERV 聚类成 315 个独立的谱系，每个谱系代表一个或多个独立的内源化事件。我们发现鲸类 ERV 起源于两种可能的途径。 298 ERV谱系可能源自鲸目动物从陆地向水体过渡之前或期间发生的逆转录病毒内源化，并且这些鲸目动物ERV中的大多数已达到进化的死胡同。 17 ERV谱系很可能源自须鲸类和齿鲸类分裂后发生的独立逆转录病毒内源化事件，表明多种逆转录病毒在从非鲸类哺乳动物过渡到水生生物后，通过跨物种传播感染了鲸类动物。整合时间和同线性分析都支持鲸目动物中多个逆转录病毒谱系最近或正在进行的活动，其中一些在宿主基因组内增殖成数百个拷贝。尽管ERV仅记录了过去逆转录病毒感染的一部分，但我们的研究结果阐明了逆转录病毒在脊椎动物历史上最显着的宏观进化转变之一期间的复杂进化。鲸目动物的祖先在 5000 万年前入侵了水生环境。最近的比较基因组研究已经开始揭示鲸目动物形态和生态转变的分子机制。然而，在从陆地到水的转变过程中，逆转录病毒是如何进化的，目前还不清楚。内源性逆转录病毒（ERV）记录了过去的逆转录病毒感染。在这里，我们系统地挖掘和分析了 25 种鲸目动物基因组中的 ERV，发现鲸目动物 ERV 聚集成 315 个不同的谱系。在这些鲸目动物ERV谱系中，298个谱系可能起源于鲸目动物在水生环境定植之前或期间的逆转录病毒内源化，17个谱系可能源于在鲸目动物过渡到水生生物后，通过非鲸目哺乳动物跨物种传播感染鲸目动物的逆转录病毒内源化。总而言之，我们的研究提供了逆转录病毒在重大宏观进化转变期间进化的独特快照。
The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history. The ancestor of cetaceans invaded the aquatic environments >50 million years ago. Recent comparative genomic studies have begun to reveal the molecular mechanisms underlying the morphological and ecological transformation of cetaceans. However, it has been largely obscure how retroviruses evolved during this land-to-water transition. Endogenous retroviruses (ERVs) recorded past retroviral infections. Here, we systematically mined and analyzed ERVs in the genomes of 25 cetaceans, and found that cetacean ERVs clustered into 315 distinct lineages. Among these cetacean ERV lineages, 298 lineages may originate through retrovirus endogenization before or during the colonization of aquatic environments by cetaceans, and 17 lineages may arise from endogenization of retroviruses that infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Taken together, our study provides a unique snapshot of the evolution of retroviruses during a major macroevolutionary transition.
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DOI：
10.1073/pnas.0307800101
发表时间：
2004-04-06
影响因子：
11.1
作者：
Belshaw, R;Pereira, V;Tristem, M
通讯作者：
Tristem, M