De novo Sequencing of Novel Mycoviruses From Fusarium sambucinum : An Attempt on Direct RNA Sequencing of Viral dsRNAs.

Autor:	Mizutani Y; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan., Uesaka K; Center for Gene Research, Nagoya University, Nagoya, Japan., Ota A; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan., Calassanzio M; Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy., Ratti C; Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy., Suzuki T; College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan., Fujimori F; Graduate School of Humanities and Life Sciences, Tokyo Kasei University, Itabashi, Japan., Chiba S; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
Jazyk:	angličtina
Zdroj:	Frontiers in microbiology [Front Microbiol] 2021 Apr 13; Vol. 12, pp. 641484. Date of Electronic Publication: 2021 Apr 13 (Print Publication: 2021).
DOI:	10.3389/fmicb.2021.641484
Abstrakt:	An increasing number of viruses are continuously being found in a wide range of organisms, including fungi. Recent studies have revealed a wide viral diversity in microbes and a potential importance of these viruses in the natural environment. Although virus exploration has been accelerated by short-read, high-throughput sequencing (HTS), and viral de novo sequencing is still challenging because of several biological/molecular features such as micro-diversity and secondary structure of RNA genomes. This study conducted de novo sequencing of multiple double-stranded (ds) RNA (dsRNA) elements that were obtained from fungal viruses infecting two Fusarium sambucinum strains, FA1837 and FA2242, using conventional HTS and long-read direct RNA sequencing (DRS). De novo assembly of the read data from both technologies generated near-entire genomic sequence of the viruses, and the sequence homology search and phylogenetic analysis suggested that these represented novel species of the Hypoviridae , Totiviridae , and Mitoviridae families. However, the DRS-based consensus sequences contained numerous indel errors that differed from the HTS consensus sequences, and these errors hampered accurate open reading frame (ORF) prediction. Although with its present performance, the use of DRS is premature to determine viral genome sequences, the DRS-mediated sequencing shows great potential as a user-friendly platform for a one-shot, whole-genome sequencing of RNA viruses due to its long-reading ability and relative structure-tolerant nature. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2021 Mizutani, Uesaka, Ota, Calassanzio, Ratti, Suzuki, Fujimori and Chiba.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu