Maclot François, Candresse Thierry, Filloux Denis, Rott Philippe, Malmstrom Carolyn, van der Vlugt René, Massart Sébastien, Roumagnac Philippe
Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium.
UMR Biologie du fruit et pathologie, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Bordeaux University, Bordeaux, France.
Virologie (Montrouge). 2021 Feb 1;25(1):29-42. doi: 10.1684/vir.2021.0879.
Plant virus ecology began to be explored at the end of the 19 century. Since then, major advances have revealed complex virus-host-vector interactions in a variety of environments. These advances have been accelerated by development of new technologies for virus detection and characterization, the latest of which being high-throughput sequencing (HTS). HTS technologies have proved to be effective for non-targeted characterization of all or nearly all viruses present in a sample without requiring prior information about virus identity, as would be needed for virus-targeted tests. Phytoviromic studies have thus made important advances, including characterization of the complex interactions between phytovirus dynamics and the structure of multi-species host communities, and documentation of the effects of anthropogenic ecosystem simplification on plant virus emergence and diversity. However, such studies must overcome challenges at every stage, from plant sampling to bioinformatics analysis. This review summarizes major advances in plant virus ecology, in association with technological developments, and presents key considerations for use of HTS in the study of the ecology of phytovirus communities.
植物病毒生态学研究始于19世纪末。自那时起，重大进展揭示了在各种环境中复杂的病毒-宿主-载体相互作用。病毒检测和鉴定新技术的发展加速了这些进展，其中最新的技术是高通量测序（HTS）。事实证明，高通量测序技术对于无针对性地表征样品中存在的所有或几乎所有病毒非常有效，无需像针对病毒的检测那样事先了解病毒的特性。因此，植物病毒组学研究取得了重要进展，包括表征植物病毒动态与多物种宿主群落结构之间的复杂相互作用，以及记录人为导致的生态系统简化对植物病毒出现和多样性的影响。然而，此类研究在从植物采样到生物信息学分析的每个阶段都必须克服挑战。本综述总结了植物病毒生态学与技术发展相关的主要进展，并提出了在植物病毒群落生态学研究中使用高通量测序的关键注意事项。
