Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences, The University of Sydneygrid.1013.3, Sydney, New South Wales, Australia.
Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydneygrid.1013.3, Sydney, New South Wales, Australia.
J Virol. 2022 Dec 21;96(24):e0026022. doi: 10.1128/jvi.00260-22. Epub 2022 May 31.
Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus diversity and abundance in 1,079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analyzing open-source data from the 1000 Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% were single-stranded positive-sense RNA viruses across eight orders, including members of the , , , , and . One-third of the newly described viruses were double-stranded RNA viruses from the orders and . The remaining were negative-sense RNA viruses from the , , , and and the newly proposed . Our analysis considerably expands the known host range of 13 virus families to include lower plants (e.g., and ) and 4 virus families to include alga hosts (e.g., and ). More broadly, however, a cophylogeny analysis revealed that the evolutionary history of these families is largely driven by cross-species transmission events. The discovery of the first 30-kDa movement protein in a nonvascular plant suggests that the acquisition of plant virus movement proteins occurred prior to the emergence of the plant vascular system. Together, these data highlight that numerous RNA virus families are associated with older evolutionary plant lineages than previously thought and that the apparent scarcity of RNA viruses found in lower plants likely reflects a lack of investigation rather than their absence. Our knowledge of plant viruses is mainly limited to those infecting economically important host species. In particular, we know little about those viruses infecting basal plant lineages such as the ferns, lycophytes, bryophytes, and charophytes. To expand this understanding, we conducted a broad-scale viral survey of species across the breadth of the plant kingdom. We found that basal plants harbor a wide diversity of RNA viruses, including some that are sufficiently divergent to likely compose a new virus family. The basal plant virome revealed offers key insights into the evolutionary history of core plant virus gene modules and genome segments. More broadly, this work emphasizes that the scarcity of viruses found in these species to date most likely reflects the limited research in this area.
我们目前对植物病毒的认识主要来自于那些影响经济重要植物的病毒。然而，栽培植物物种仅代表植物界的一小部分和有偏见的子集。在这里，我们通过分析 1KP（1000 种植物转录组计划）的开源数据，描述了来自植物界（古生菌）广泛物种的 1079 个转录组中的病毒多样性和丰度。我们鉴定了 104 种潜在的新病毒，其中 40%是 8 个目中的单链正链 RNA 病毒，包括、、、、和。新描述的病毒中有三分之一是双链 RNA 病毒，来自目和。其余的是负链 RNA 病毒，来自目和以及新提出的目。我们的分析大大扩展了 13 个病毒科的已知宿主范围，包括低等植物（例如和）和 4 个病毒科，包括藻类宿主（例如和）。然而，更广泛地说，共进化分析表明，这些家族的进化历史主要是由跨种传播事件驱动的。在非维管束植物中发现的第一个 30kDa 运动蛋白表明，植物病毒运动蛋白的获得发生在植物维管系统出现之前。这些数据共同表明，许多 RNA 病毒家族与以前认为的更古老的植物进化谱系有关，而在低等植物中发现的 RNA 病毒的明显缺乏很可能反映了缺乏调查而不是不存在。我们对植物病毒的认识主要局限于那些感染经济上重要的宿主物种的病毒。特别是，我们对感染蕨类植物、石松类植物、苔藓植物和轮藻植物等基础植物谱系的病毒知之甚少。为了扩大这方面的认识，我们对植物界广泛物种进行了大规模的病毒调查。我们发现，基础植物蕴藏着广泛的 RNA 病毒多样性，包括一些可能构成新病毒科的高度分化的病毒。基础植物病毒组揭示了核心植物病毒基因模块和基因组片段的进化历史的关键见解。更广泛地说，这项工作强调，迄今为止在这些物种中发现的病毒的稀缺性很可能反映了该领域研究的有限。
