Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America.
PLoS One. 2019 Jul 24;14(7):e0219207. doi: 10.1371/journal.pone.0219207. eCollection 2019.
The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
由于真菌中病毒感染的隐蔽性和对主要致病性和/或具有经济重要性的真菌的集中研究，真菌中 RNA 病毒的分布和多样性还不完全了解。由于已知大多数感染真菌的病毒都具有单链或双链 RNA 基因组，因此转录组数据为在没有任何病毒感染先验知识的情况下查询各种真菌样本中的病毒提供了机会。在这里，我们描述了对子囊菌亚门 Pezizomycotina 真菌所有转录组数据集的系统调查。使用一种简单但有效的计算管道，该管道使用在正常 RNA-seq 分析过程中丢弃的读取，然后在从头组装的连续体中识别病毒 RNA 依赖性 RNA 聚合酶 (RdRP) 基序，从 44 种不同真菌中鉴定出 59 种病毒。在所鉴定的病毒中，88%被确定为新种，68%据我们所知，是从真菌种中首次描述的病毒。对核苷酸和推断的蛋白质序列的综合分析描述了这些病毒与已知的真菌病毒序列之间的系统发育关系，并支持多达四个新科和两个新属的分类。因此，这些结果更深入地了解了真菌病毒多样性的范围，同时也增加了真菌宿主的分布。此外，这项研究表明，分析 RNA-seq 数据有助于快速发现新病毒。
