UMR 1332 BFP, INRA, University of Bordeaux, Villenave d'Ornon, France.
UMR 1332 BFP, INRA, University of Bordeaux, Villenave d'Ornon, France
J Virol. 2019 Dec 12;94(1). doi: 10.1128/JVI.01462-19.
Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components of ecosystems, there is a need to explore the diversity and richness of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and virion-associated nucleic acids (VANA), have been used and compared here for the description of the virome of complex plant pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. A novel bioinformatics strategy was used to assess viral richness not only at the family level but also by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. A large viral diversity dominated by novel dsRNA viruses was detected in all sites, while a large between-site variability limited the ability to draw a clear conclusion on the impact of cultivation. A trend for a higher diversity of dsRNA viruses was nevertheless detected in unmanaged sites (118 versus 77 unique OTUs). The dsRNA-based approach consistently revealed a broader and more comprehensive diversity for RNA viruses than the VANA approach, whatever the assessment criterion. In addition, dissimilarity analyses indicated both approaches to be largely reproducible but not necessarily convergent. These findings illustrate features of phytoviromes in various ecosystems and a novel strategy for precise virus richness estimation. These results allow us to reason methodological choices in phytovirome studies and likely in other virome studies where RNA viruses are the focal taxa. There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them but also on the comparative performance-methodological approaches for their study. We used and compared two viral sequence enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA), for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing us to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is recommended because it consistently provided a more comprehensive description of the analyzed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.
宏基因组研究表明，植物病毒的多样性直到最近才被严重低估。作为生态系统的重要组成部分，需要探索与植物种群相关的病毒的多样性和丰富度，并了解影响其在空间和时间上多样性的驱动因素。本研究比较了两种病毒序列富集方法，双链 RNA（dsRNA）和病毒相关核酸（VANA），用于描述代表未管理和栽培生态系统中最常见植物物种的复杂植物池的病毒组。本研究使用了一种新的生物信息学策略，不仅在科水平上评估病毒丰富度，还通过确定保守病毒结构域聚类后的分类操作单元（OTU）来评估病毒丰富度。在所有采样点均检测到以新型 dsRNA 病毒为主的大量病毒多样性，而站点间的巨大差异限制了确定栽培影响的能力。尽管如此，在未管理的采样点中仍检测到 dsRNA 病毒更高的多样性（118 个而非 77 个独特 OTU）。基于 dsRNA 的方法始终比 VANA 方法揭示更广泛和更全面的 RNA 病毒多样性，无论评估标准如何。此外，相似性分析表明，无论采用何种评估标准，两种方法的重现性均较高，但不一定具有一致性。这些发现说明了不同生态系统中植物病毒组的特征以及一种用于精确病毒丰富度估计的新策略。这些结果使我们能够推理植物病毒组研究中的方法选择，也可能推理其他以 RNA 病毒为重点类群的病毒组研究中的方法选择。目前，有关植物病毒种群及其影响因素的知识存在很大差距，也有关于比较研究它们的方法的性能方法的知识差距。我们使用并比较了两种病毒序列富集方法，双链 RNA（dsRNA）和病毒相关核酸（VANA），用于描述代表未管理和栽培生态系统中最常见植物物种的复杂池中的植物病毒组。通过确定保守病毒结构域聚类后的分类操作单元（OTU）来评估病毒丰富度。有一些有限的证据表明栽培对病毒种群有影响。这些结果提供了允许我们推理病毒组研究中方法选择的数据。对于主要对 RNA 病毒感兴趣的研究人员，推荐使用 dsRNA 方法，因为它始终能更全面地描述分析的植物病毒组，但它明显低估了 DNA 病毒和噬菌体。
