Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode of Caulimoviridae
Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode of Caulimoviridae
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真叶植物古病毒揭示了茎病毒科的隐藏多样性和宏观进化模式
DOI：
10.1128/jvi.02043-17
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发表时间：
2018-05-01
影响因子：
5.4
通讯作者：
Han, Guan-Zhu
中科院分区：
文献类型：
--
作者：
Gong, Zhen;Han, Guan-Zhu
内源性病毒元件（古病毒）为研究病毒的深层历史和宏观进化提供了“分子化石”。内源性植物副逆转录病毒（EPRV）广泛存在于被子植物中，但对早期分枝植物中EPRV的研究却很少。在这里，我们使用一个大规模的基因组学方法来研究植物副逆转录病毒（正式称为花椰菜花叶病毒科）的多样性和宏观进化。我们发现了裸子植物和蕨类植物基因组中EPRV的前所未有的和未被欣赏的多样性。已知的被子植物病毒仅构成花椰菜病毒科多样性的一小部分。通过表征EPRV的分布，我们表明，没有主要的Euphyllophyte谱系逃脱的活动的花椰菜花叶病毒，提高的可能性，许多外源花椰菜花叶病毒仍然被发现在Euphyllophyte。我们发现EPRV的拷贝数普遍较高，这表明EPRV可能定义了一组独特的重复元件，并代表了真叶植物基因组的重要组成部分。进化分析表明，在被子植物中，花椰菜花叶病毒科的一个古老的起源和至少三个独立的起源。我们的研究结果揭示了显着的多样性的花椰菜花叶病毒科，并有重要的意义，了解植物副aretroviruses.IMPORTANCE的起源和宏观进化很少有病毒已被记录在植物以外的被子植物。病毒偶尔可以整合到宿主基因组中，形成内源性病毒元件（EVEs）。内源性植物副逆转录病毒（EPRV）广泛存在于被子植物中。在这项研究中，我们进行了全面的比较和系统发育分析，发现EPRV存在于裸子植物和蕨类植物的基因组中。我们在裸子植物和蕨类植物基因组中鉴定了许多EPRV，揭示了植物副逆转录病毒多样性的前所未有的深度。植物副黄病毒主要进行跨种传播，被子植物副黄病毒至少出现过三次。我们的研究为植物副逆转录病毒的多样性和宏观进化提供了新的见解。
Endogenous viral elements (paleoviruses) provide "molecular fossils" for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms, but little is known about EPRVs in earlier-branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known as Caulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs within the genomes of gymnosperms and ferns. The known angiosperm viruses constitute only a minor part of the Caulimoviridae diversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity of Caulimoviridae, raising the possibility that many exogenous Caulimoviridae remain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs might define a unique group of repetitive elements and represent important components of euphyllophyte genomes. Evolutionary analyses suggest an ancient origin of Caulimoviridae and at least three independent origins of Caulimoviridae in angiosperms. Our findings reveal the remarkable diversity of Caulimoviridae and have important implications for understanding the origin and macroevolution of plant pararetroviruses.IMPORTANCE Few viruses have been documented in plants outside angiosperms. Viruses can occasionally integrate into host genomes, forming endogenous viral elements (EVEs). Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms. In this study, we performed comprehensive comparative and phylogenetic analyses of EPRVs and found that EPRVs are present in the genomes of gymnosperms and ferns. We identified numerous EPRVs in gymnosperm and fern genomes, revealing an unprecedented depth in the diversity of plant pararetroviruses. Plant pararetroviruses mainly underwent cross-species transmission, and angiosperm pararetroviruses arose at least three times. Our study provides novel insights into the diversity and macroevolution of plant pararetroviruses.