Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses
Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses
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DOI：
10.1128/mbio.02027-20
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发表时间：
2020-09-01
期刊：
影响因子：
6.4
通讯作者：
James, T. Y.
中科院分区：
文献类型：
--
作者：
Myers, J. M.;Bonds, A. E.;James, T. Y.
真菌病毒在真菌界中广泛分布，据称是常见的，尽管大多数已知来自最近分化的两个门（子囊菌门和担子菌门，统称为Dikarya）的宿主。为了增加我们对真菌病毒流行率和多样性的了解，我们对早期分歧谱系中的真菌进行了大规模调查，使用基于培养和转录组挖掘的方法来寻找RNA病毒。总的来说，333株分离株中有21.6%为RNA真菌病毒阳性。这是一个更大的比例比预期的基础上，以前的分类广泛的真菌病毒调查，是一个强大的系统发育组成部分，真菌病毒感染的暗示。我们新发现的病毒序列是多样的，由双链RNA，正义单链RNA（ssRNA）和负义ssRNA基因组组成，包括在公共数据库中缺乏代表性的新谱系。这些鉴定的病毒可分为2目、5科和5属;然而，一半的病毒在分类学上仍未归属。此外，我们确定了一个谱系的病毒样序列的成员的藻菌科和被孢霉目，似乎是新的基因来源于整合的病毒RNA依赖的RNA聚合酶基因的基因组。这两种筛选方法在检测病毒方面基本一致;因此，我们认为基于培养的检测是快速评估实验室培养物是否被病毒感染的一种具有成本效益的方法。本研究使用培养物收集和公开可用的转录组来证明真菌病毒在早期分歧真菌谱系的实验室培养物中是丰富的。本研究发现的真菌病毒的功能和多样性将有助于指导未来对真菌病毒起源和生态功能的研究。重要信息病毒是进化和生态系统功能的关键驱动力，越来越多地被认为是真菌的共生体。早期分支的真菌分布广泛，在生态学上很重要，并构成了该王国的大部分系统发育多样性。感染真菌早期分化谱系的病毒几乎完全没有研究过。在这项研究中，我们通过两种替代方法筛选真菌中的病毒：经典的基于培养的方法和转录组挖掘。我们的大规模调查的结果表明，早期分歧谱系有较高的感染率比以前报道的其他真菌类群和实验室菌株在世界各地的主机感染，其影响是未知的。在这些基础真菌谱系中发现的真菌病毒的功能和多样性将有助于指导未来对真菌病毒起源及其进化后果和生态影响的研究。
Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions.IMPORTANCE Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts.