Table_5_Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems.xlsx

Viruses are ubiquitous within all habitats that support cellular life and represent the most important emerging infectious diseases of plants. Despite this, it is only recently that we have begun to describe the ecological roles of plant viruses in unmanaged systems and the influence of ecosystem properties on virus evolution. We now know that wild plants frequently harbor infections by diverse virus species, but much remains to be learned about how viruses influence host traits and how hosts influence virus evolution and vector interactions. To identify knowledge gaps and suggest avenues for alleviating research deficits, we performed a quantitative synthesis of a representative sample of virus ecology literature, developed criteria for expanding the suite of pathosystems serving as models, and applied these criteria through a case study. We found significant gaps in the types of ecological systems studied, which merit more attention. In particular, there is a strong need for a greater diversity of logistically tractable, wild dicot perennial study systems suitable for experimental manipulations of infection status. Based on criteria developed from our quantitative synthesis, we evaluated three California native dicot perennials typically found in Mediterranean-climate plant communities as candidate models: Cucurbita foetidissima (buffalo gourd), Cucurbita palmata (coyote gourd), and Datura wrightii (sacred thorn-apple). We used Illumina sequencing and network analyses to characterize viromes and viral links among species, using samples taken from multiple individuals at two different reserves. We also compared our Illumina workflow with targeted RT-PCR detection assays of varying costs. To make this process accessible to ecologists looking to incorporate virology into existing studies, we describe our approach in detail and discuss advantages and challenges of different protocols. We also provide a bioinformatics workflow based on open-access tools with graphical user interfaces. Our study provides evidence that dicot perennials in xeric habitats support multiple, asymptomatic infections by viruses known to be pathogenic in related crop hosts. Quantifying the impacts of these interactions on plant performance and virus epidemiology in our logistically tractable host systems will provide fundamental information about plant virus ecology outside of crop environments.

病毒广泛分布于所有支持细胞生命的生境中，亦是引发植物重大新发传染病的首要病原类群。尽管如此，直至近年学界才开始逐步阐明植物病毒在非人工管理生境中的生态功能，以及生态系统属性对病毒演化的影响。现已明确野生植物常被多种病毒类群侵染，但关于病毒如何调控宿主性状、宿主如何影响病毒演化与介体互作的诸多问题仍有待解答。为明确研究空白并提出弥补研究短板的可行路径，本研究对具有代表性的植物病毒生态学文献样本开展了定量综合分析，制定了扩充模式病害系统集合的标准，并通过案例研究应用了该标准。本研究发现现有研究在生态系统类型方面存在显著缺口，亟需更多关注。具体而言，亟需更多样化且易开展实验操作的野生双子叶多年生植物研究体系，用于侵染状态的实验操控。基于定量综合分析得到的标准，我们选取了地中海气候植物群落中常见的三种加州本土双子叶多年生植物作为候选模式体系：臭瓜（Cucurbita foetidissima, buffalo gourd）、郊狼瓜（Cucurbita palmata, coyote gourd）以及赖特曼陀罗（Datura wrightii, sacred thorn-apple）。我们通过取自两个不同保护区内多株个体的样本，采用Illumina测序（Illumina sequencing）与网络分析技术对物种间的病毒组（virome）及病毒关联进行了表征。同时，我们还将Illumina测序流程与不同成本的靶向逆转录聚合酶链式反应（RT-PCR）检测方法进行了对比。为便于将病毒学研究融入现有工作的生态学家参考使用，我们详细阐述了研究方法，并讨论了不同实验方案的优势与局限。此外，我们还提供了基于带有图形用户界面的开源工具构建的生物信息学分析流程。本研究证实，干旱生境中的双子叶多年生植物会被多种在相关作物宿主中已被证实具有致病性的病毒侵染，且不表现明显症状。在上述易开展实验操作的宿主体系中，定量解析这些互作对植物生长表现及病毒流行病学的影响，将为阐明作物生境之外的植物病毒生态学提供基础科学依据。