Department of Medical Microbiology, Radboud University Medical Center, and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands.
PLoS One. 2018 Jul 25;13(7):e0200511. doi: 10.1371/journal.pone.0200511. eCollection 2018.
In the last few years, increasing numbers of viruses infecting fungi have been identified. In this study, we used an in silico approach for the analysis of deep RNA sequencing data in order to discover and characterize putative genomic ssRNA or dsRNA mycovirus sequences in Aspergillus fumigatus. RNA sequencing reads of A. fumigatus strains were mapped against the A. fumigatus Af293 reference genome. Unmapped reads were collected for de novo assembly. Contigs were analyzed by Blastx comparison with a mycovirus protein database. Assembled viral genomes were used as template for remapping of RNA sequencing reads. In total, deep RNA sequencing results from 11 A. fumigatus strains were analyzed for the presence of mycoviral genomic RNAs. In 9 out of 11 strains, putative mycoviral RNA genomes were identified. Three strains were infected with two different mycovirus species. Two strains were infected with Aspergillus fumigatus polymycovirus type-1 (AfuPmV-1). Four strains contained fully recovered genomic RNA of unknown narna-like viruses designated as Aspergillus fumigatus narnavirus-1 and Aspergillus fumigatus narnavirus-2 (AfuNV-1 and AfuNV-2). Both viruses showed 38% amino acid sequence identity to Beihai narna-like virus-21. Three strains contained partially recovered genomic RNA of an unknown narna-like virus. Two strains contained fully recovered genomic RNAs of an unknown partitivirus designated as Aspergillus fumigatus partitivirus-2 (AfuPV-2) which showed 50% amino acid sequence identity to Alternaria alternata partitivirus-1. Finally, one strain contained fully recovered genomic RNA of an unknown mitovirus designated as Aspergillus fumigatus mitovirus-1 (AfuMV-1) which showed 34% amino acid sequence identity to Sclerotina sclerotiorum mitovirus. In silico analysis of deep RNA sequencing results showed that a majority of the A. fumigatus strains used here were infected with mycoviruses. Four novel A. fumigatus RNA mycoviruses could be identified: two different Aspergillus fumigatus narna-like viruses, one Aspergillus fumigatus partitivirus, and one Aspergillus fumigatus mitovirus.
在过去的几年中，越来越多的感染真菌的病毒被鉴定出来。在这项研究中，我们使用了一种计算方法来分析 Aspergillus fumigatus 的深度 RNA 测序数据，以发现和描述潜在的基因组 ssRNA 或 dsRNA 真菌病毒序列。将 A. fumigatus 菌株的 RNA 测序reads 映射到 A. fumigatus Af293 参考基因组上。未映射的reads 被收集用于从头组装。通过与真菌病毒蛋白数据库的 Blastx 比较分析 contigs。使用组装的病毒基因组作为模板重新映射 RNA 测序reads。总共分析了 11 株 A. fumigatus 菌株的深度 RNA 测序结果，以确定是否存在真菌病毒基因组 RNA。在 11 株菌株中的 9 株中，鉴定出了潜在的真菌病毒 RNA 基因组。有 3 株被两种不同的真菌病毒感染。有 2 株被 Aspergillus fumigatus polymycovirus type-1（AfuPmV-1）感染。有 4 株含有完全恢复的未知 narnavirus 样病毒的基因组 RNA，被指定为 Aspergillus fumigatus narnavirus-1 和 Aspergillus fumigatus narnavirus-2（AfuNV-1 和 AfuNV-2）。这两种病毒与 Beihai narnavirus-21 的氨基酸序列相似度为 38%。有 3 株含有部分恢复的未知 narnavirus 样病毒的基因组 RNA。有 2 株含有完全恢复的未知部分病毒的基因组 RNA，被指定为 Aspergillus fumigatus partitivirus-2（AfuPV-2），与 Alternaria alternata partitivirus-1 的氨基酸序列相似度为 50%。最后，有 1 株含有完全恢复的未知 mitovirus 的基因组 RNA，被指定为 Aspergillus fumigatus mitovirus-1（AfuMV-1），与 Sclerotina sclerotiorum mitovirus 的氨基酸序列相似度为 34%。对深度 RNA 测序结果的计算分析表明，这里使用的大多数 A. fumigatus 菌株都被真菌病毒感染。可以鉴定出四种新型的 A. fumigatus RNA 真菌病毒：两种不同的 Aspergillus fumigatus narnavirus、一种 Aspergillus fumigatus partitivirus 和一种 Aspergillus fumigatus mitovirus。
