The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster.
The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster.
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DOI：
10.1371/journal.pbio.1002210
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发表时间：
2015-07
期刊：
影响因子：
9.8
通讯作者：
Obbard DJ
中科院分区：
文献类型：
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作者：
Webster CL;Waldron FM;Robertson S;Crowson D;Ferrari G;Quintana JF;Brouqui JM;Bayne EH;Longdon B;Buck AH;Lazzaro BP;Akorli J;Haddrill PR;Obbard DJ
黑腹果蝇是研究病毒感染和抗病毒免疫的重要无脊椎动物模型，也是昆虫-病毒协同进化研究的热点。在这里，我们使用宏基因组学的方法，以确定超过20个以前未检测到的RNA病毒和DNA病毒与野生D。黑腹菌这些病毒不仅包括已知昆虫病原体的远亲，而且还包括新的昆虫感染病毒群。通过对病毒衍生的小RNA进行测序，我们表明这些病毒代表了果蝇的活跃感染。我们发现，RNA病毒的小RNA的数量和性质不同，我们检测到siRNA和一种新的miRNA的DNA病毒。对小RNA的分析还使我们能够鉴定与已知病毒缺乏可检测序列相似性的推定病毒序列。通过对2,000多只野生成年果蝇的调查，我们发现超过30%的果蝇是由果蝇基因组引起的。黑腹果蝇携带可检测到的病毒，超过6%携带多种病毒。然而，尽管沃尔巴克氏体内共生体的流行率很高，但我们无法检测到沃尔巴克氏体的存在与任何病毒的存在之间的任何关系。使用公开的RNA-seq数据集，我们表明果蝇实验室中的病毒群落与野生环境中的病毒群落非常不同，但一些新发现的病毒仍然广泛存在于实验室品系中，并且在细胞培养中无处不在。通过对从野外采集的果蝇个体中分离到的病毒进行测序，我们发现有些病毒在D。黑腹果蝇D. simulans。我们的研究结果为果蝇中宿主-病毒相互作用提供了一个必要的进化和生态背景，新报道的病毒序列将有助于发展D。黑腹果蝇进一步作为分子和进化病毒研究的模型。宏基因组RNA和小RNA的测序鉴定了20多种与果蝇（Drosophila melanogaster）相关的新病毒，大规模调查显示，许多病毒在实验室和野外很常见。果蝇（Drosophila melanogaster）被广泛用作分子生物学和遗传学的模式物种。它的进化历史也被广泛研究，帮助我们了解自然选择如何塑造基因组。果蝇的研究在确定昆虫免疫系统如何与病毒相互作用以及宿主和病毒之间的共同进化如何塑造宿主免疫系统方面特别有价值。了解昆虫病毒的共同进化是很重要的，因为一些病毒，如那些引起人类登革热和黄热病的病毒，也会感染它们的昆虫媒介，而且因为蜜蜂和其他传粉媒介的病毒与传粉媒介的减少有关。虽然我们对苍蝇如何识别和对抗病毒病原体有了越来越好的了解，但我们仍然需要了解它们在野外遇到并相互作用的病毒。在这篇论文中，我们对大量野生果蝇的所有遗传物质进行了测序，并用它来识别20多种新病毒。然后，我们调查个别野生苍蝇和实验室股票，以找出哪些病毒是常见的，哪些是罕见的，以及它们感染的果蝇物种。我们的研究结果提供了有价值的工具和进化和生态的角度来看，这将有助于改善果蝇作为宿主病毒生物学的模型在未来。
Drosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs, we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2,000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont—which is known to be protective against virus infections in Drosophila—we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets, we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host–virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research. Sequencing of metagenomic RNA and small RNA identifies more than 20 new viruses associated with the fruit fly Drosophila melanogaster, and large-scale surveys show that many are common in the lab and in the field. The fruit fly Drosophila melanogaster is extensively used as a model species for molecular biology and genetics. It is also widely studied for its evolutionary history, helping us understand how natural selection has shaped the genome. Drosophila research has been particularly valuable in determining how the insect immune system interacts with viruses and how co-evolution between hosts and viruses can shape the host immune system. Understanding insect–virus coevolution is important because some viruses—such as those which cause dengue and yellow fever in humans—also infect their insect vectors, and because the viruses of bees and other pollinators are implicated in pollinator decline. Although we have an increasingly good idea of how flies recognise and combat viral pathogens, we still have much to learn about the viruses they encounter and interact with in the wild. In this paper, we sequence all of the genetic material from a large collection of wild fruit flies and use it to identify more than 20 new viruses. We then survey individual wild flies and laboratory stocks to find out which viruses are common, which are rare, and which species of fruit fly they infect. Our results provide valuable tools and an evolutionary and ecological perspective that will help to improve Drosophila as a model for host–virus biology in the future.