Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses. Issue 1 (16th December 2020)

• Record Type: Journal Article
• Authors: Chiba, Yuto; Oiki, Sayoko; Yaguchi, Takashi; Urayama, Syun-ichi; Hagiwara, Daisuke
• Is Part Of: Virus evolution. Volume 7:Issue 1(2021)
• Publication Date: 2020-12-16
• Subjects: RNA virus -- viral genome -- FLDS -- RdRp -- Aspergillus fumigatus; Viruses -- Evolution -- Periodicals; 579.2138
• DOI: 10.1093/ve/veaa101
• Languages: English
• ISSNs: 2057-1577

Abstract

Abstract: By identifying variations in viral RNA genomes, cutting-edge metagenome technology has potential to reshape current concepts about the evolution of RNA viruses. This technology, however, cannot process low-homology genomic regions properly, leaving the true diversity of RNA viruses unappreciated. To overcome this technological limitation, we applied an advanced method, Fragmented and Primer-Ligated Double-stranded (ds) RNA Sequencing (FLDS), to screen RNA viruses from 155 fungal isolates, which allowed us to obtain complete viral genomes in a homology-independent manner. We created a high-quality catalog of 19 RNA viruses (12 viral species) that infect Aspergillus isolates. Among them, nine viruses were not detectable by the conventional methodology involving agarose gel electrophoresis of dsRNA, a hallmark of RNA virus infections. Segmented genome structures were determined in 42 per cent of the viruses. Some RNA viruses had novel genome architectures; one contained a dual methyltransferase domain and another had a separated RNA-dependent RNA polymerase (RdRp) gene. A virus from a different fungal taxon ( Pyricularia ) had an RdRp sequence that was separated on different segments, suggesting that a divided RdRp is widely present among fungal viruses, despite the belief that all RNA viruses encode RdRp as a single gene. These findings illustrate the previously hidden diversity and evolution of RNA viruses, and prompt reconsideration of the structural plasticity of RdRp.