Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer.
Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer.
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DOI：
10.1016/j.virusres.2017.10.020
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发表时间：
2018-01-15
期刊：
影响因子：
5
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Dolja VV;Koonin EV
病毒宏基因组学扩展了已知的RNA病毒多样性，强调了病毒进化与宿主之间的联系。基因组比较显示，RNA病毒之间基因模块改组的程度比以前认为的要大。扩展的系统发育分析暗示了RNA病毒在不同宿主之间广泛的水平病毒运输。植物和脊椎动物RNA病毒组的进化似乎是由无脊椎动物大量RNA病毒组的HVT驱动的。病毒宏基因组学是一个年轻的研究领域，但它已经改变了我们对病毒多样性和进化的理解，并在一个新的水平上阐明了病毒进化与宿主进化和生态之间的联系。在这篇综述文章中，我们研究了RNA病毒进化的新图景，RNA病毒是真核病毒组的主要组成部分，它是从宏基因组数据分析中出现的。通过宏基因组学，许多RNA病毒群的主要扩展允许为保守的病毒基因（主要是RNA依赖性RNA聚合酶（RdRp））构建大幅改进的系统发育树。特别是，一个新的超家族的广泛，小的正链RNA病毒被描绘，团结tombus样和noda样病毒。通过宏基因组学和传统方法发现的RNA病毒的基因组结构的比较揭示了不同病毒基因组之间基因模块改组的程度，远远超过了以前对这种进化现象的认识。最引人注目的是，在RdRp的系统发育分析中包含宏基因组数据导致鉴定了许多强有力的支持组，这些组包括来自不同宿主的RNA病毒，包括不同的原生生物、动物和植物。尽管潜在的警告，特别是，不完整和不均匀的真核生物类群的采样，这些非常意外的发现揭示了不同宿主之间的水平病毒转移（HVT）的RNA病毒进化的中心方面。无脊椎动物，特别是线虫和节肢动物的大量和多样的病毒组似乎是水库，植物和脊椎动物的病毒组通过多次HVT事件进化而来。
Virus metagenomics has expanded known RNA virus diversity and emphasized connections between evolution of viruses and hosts. Genome comparisons revealed that the extent of gene module shuffling among RNA viruses is greater than previously thought. Expanded phylogenetic analysis implied pervasive horizontal virus transport between diverse hosts of RNA viruses. Evolution of plant and vertebrate RNA viromes appears to be driven by HVT from vast RNA viromeof invertebrates. Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp). In particular, a new superfamily of widespread, small positive-strand RNA viruses was delineated that unites tombus-like and noda-like viruses. Comparison of the genome architectures of RNA viruses discovered by metagenomics and by traditional methods reveals an extent of gene module shuffling among diverse virus genomes that far exceeds the previous appreciation of this evolutionary phenomenon. Most dramatically, inclusion of the metagenomic data in phylogenetic analyses of the RdRp resulted in the identification of numerous, strongly supported groups that encompass RNA viruses from diverse hosts including different groups of protists, animals and plants. Notwithstanding potential caveats, in particular, incomplete and uneven sampling of eukaryotic taxa, these highly unexpected findings reveal horizontal virus transfer (HVT) between diverse hosts as the central aspect of RNA virus evolution. The vast and diverse virome of invertebrates, particularly nematodes and arthropods, appears to be the reservoir, from which the viromes of plants and vertebrates evolved via multiple HVT events.
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影响因子：
3.8
作者：
Bekal, Sadia;Domier, Leslie L.;Bhalerao, Kaustubh
通讯作者：
Bhalerao, Kaustubh
影响因子：
6.4
作者：
Culley AI;Mueller JA;Belcaid M;Wood-Charlson EM;Poisson G;Steward GF
通讯作者：
Steward GF
DOI：
10.1146/annurev-virology-031413-085540
发表时间：
2015-01-01
期刊：
ANNUAL REVIEW OF VIROLOGY, VOL 2
影响因子：
--
作者：
Chow, Cheryl-Emiliane T.;Suttle, Curtis A.
通讯作者：
Suttle, Curtis A.
影响因子：
3.7
作者：
Brussaard, CPD;Noordeloos, AAM;Bratbak, G
通讯作者：
Bratbak, G
影响因子：
3.8
作者：
Bekal, Sadia;Domier, Leslie L.;Lambert, Kris N.
通讯作者：
Lambert, Kris N.