The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization

Abstract

Mutualistic plant-associated fungi are recognized as important drivers in plant evolution, diversity and health. The discovery that mycoviruses can take part and play important roles in symbiotic tripartite interactions has prompted us to study the viromes associated with a collection of ericoid and orchid mycorrhizal (ERM and ORM, respectively) fungi. Our study, based on high-throughput sequencing of transcriptomes (RNAseq) from fungal isolates grown in axenic cultures, revealed in both ERM and ORM fungi the presence of new mycoviruses closely related to already classified virus taxa, but also new viruses that expand the boundaries of characterized RNA virus diversity to previously undescribed evolutionary trajectories. In ERM fungi, we provide first evidence of a bipartite virus, distantly related to narnaviruses, that splits the RNA-dependent RNA polymerase (RdRP) palm domain into two distinct proteins, encoded by each of the two segments. Furthermore, in one isolate of the ORM fungus Tulasnella spp. we detected a 12 kb genomic fragment coding for an RdRP with features of bunyavirus-like RdRPs. However, this 12 kb genomic RNA has the unique features, for Bunyavirales members, of being tri-cistronic and carrying ORFs for the putative RdRP and putative nucleocapsid in ambisense orientation on the same genomic RNA. Finally, a number of ORM fungal isolates harbored a group of ambisense bicistronic viruses with a genomic size of around 5 kb, where we could identify a putative RdRP palm domain that has some features of plus strand RNA viruses; these new viruses may represent a new lineage in the Riboviria, as they could not be reliably assigned to any of the branches in the recently derived monophyletic tree that includes most viruses with an RNA genome.

Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses

“…This consistency in the viral sequences from different countries suggests that viruses with irregular genome structures are widely distributed, meaning that the event leading to the atypical structures did not occur locally. During revision of this manuscript, Dr. Turina and his colleagues reported a virus with a split RdRp that infects the ericoid mycorrhizal fungi Oidiodendron maius ( Sutela et al. 2020 ), which further supports our finding that AfuNV2 from three A. fumigatus strains and MoNV1 from a P. oryzae strain possess divided RdRp sequences on different genome segments.…”

“…A most intriguing finding was the presence of a divided RdRp gene. No examples like this irregular form have been reported in any other RNA viruses known to infect living creatures ( on the way of reviewing process, another example was reported ( Sutela et al. 2020 ), see below).…”

Armillaria root rot fungi host single-stranded RNA viruses

“… 2663f. Tulasnella ambivirus 4 28 30% 95% 5e-73 Armillaria borealis ambi-like virus 2 g AbAlV2 MW423806 A . borealis N40 4,529 49.1% 411,654f.…”

“…Our understanding of the virosphere has recently been revolutionized by high-throughput sequencing (HTS) studies, which have revealed many novel viruses representing yet unassigned virus groups related to but phylogenetically distinct from classified members of the orders Bunyavirales, Serpentovirales, Hepelivirales, Martellivirales, Tolivirales and Tymovirales , many of which have traditionally known to include only viruses that infect animals or plants ( https://talk.ictvonline.org/ictv-reports/ictv_online_report/ ). Furthermore, metagenomic studies have revealed the common occurrence of newly discovered evolutionary lineages of mycoviruses, such as the viral family Mymonaviridae in order Mononegavirales 26 , the viral family Botourmiaviridae in order Ourlivirales 27 , and the unclassified virus group tentatively named “ambiviruses” 28 , 29 .…”

Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

“…Finally, PcoNSRV2 clusters with two unclassified fungal orthobunyaviruses, Botrytis cinerea orthobunya-like virus 1 (QKW91261) and Tulasnella bunyavirales-like 1 (QPB44676). The latter has an unprecedented 12 kb genome organization containing three ORFs, the largest one encoding the RdRp, the second largest ORF encoding an unknown protein with Tom22 motifs (mitochondrial translocase family) and the smallest ORF encoding a nucleocapsid protein [ 70 ]. This unique genome feature remains to be confirmed in PcoNSRV2 because no 5′ and 3′ RACE has been carried out yet.…”