A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations

Abstract

Trichoderma genus includes soil-inhabiting fungi that provide important ecosystem services in their interaction with plants and other fungi, as well as biocontrol of fungal plant diseases. A collection of Trichoderma isolates from Sardinia has been previously characterized, but here we selected 113 isolates, representatives of the collection, and characterized their viral components. We carried out high-throughput sequencing of ribosome-depleted total RNA following a bioinformatics pipeline that detects virus-derived RNA-directed RNA polymerases (RdRps) and other conserved viral protein sequences. This pipeline detected seventeen viral RdRps with two of them corresponding to viruses already detected in other regions of the world and the remaining fifteen representing isolates of new putative virus species. Surprisingly, eight of them are from new negative-sense RNA viruses, a first in the genus Trichoderma. Among them is a cogu-like virus, closely related to plant-infecting viruses. Regarding the positive-sense viruses, we report the presence of an ‘ormycovirus’ belonging to a recently characterized group of bisegmented single-stranded RNA viruses with uncertain phylogenetic assignment. Finally, for the first time, we report a bisegmented member of Mononegavirales which infects fungi. The proteins encoded by the second genomic RNA of this virus were used to re-evaluate several viruses in the Penicillimonavirus and Plasmopamonavirus genera, here shown to be bisegmented and encoding a conserved polypeptide that has structural conservation with the nucleocapsid domain of rhabdoviruses.

Complete Genome Characterization of Penicillimonavirus gammaplasmoparae, a Bipartite Member of the Family Mymonaviridae

“…Overall, this study represents the complete genome characterization of Penicillimonavirus gammaplasmoparae, and conclusively demonstrates its bipartite genome nature, a novel feature in the Mymonaviridae family. As suggested by Pagnoni et al [27], we predict this bipartite feature as a rule rather than the exception for the genus Penicillimonavirus.…”

“…During the final redactional stage of this study, a publication also hypothesized the existence of divided genomes for some Mymonaviridae on the basis of sequence homologies between Trichoderma harzianum mycovirus 1 RNA and a molecule they tentatively associate with Trichoderma harzianum mycovirus 2 RNA [ 27 ]. They also performed data mining efforts parallel to those reported here, indicating that molecules with homologies with the second RNA they associate with ThMV2 are also systematically identified in metagenomic datasets from which viral segments belonging to Penicillimonavirus or Plasmopamonavirus genus members were identified, suggesting that a bipartite genome might be a feature of these two genera (although ThMV1, which also appears to be a member of the Plasmopamonavirus genus has an undivided genome).…”

Monitoring the directed evolution to a tripartite genome from a bipartite torradovirus genome

“…CC-BY-ND 4.0 International license made available under a Evolution of multipartitism is an interesting aspect of virus evolution that has received some theoretical and experimental attention (Leeks et al, 2023): furthermore, the more detailed evolutionary history of viruses inferred from recent description of the virosphere shows more and more examples of closely related monopartite viruses that have close relative bipartite viruses (Edgar et al, 2022;Neri et al, 2022). Some examples are the case of the genera closterovirus and crinivirus in the Closteroviridae family (Fuchs et al, 2020) or a mix of monopartite and bipartite genomes in the genus Penicillimonavirus in the Mymonaviridae family (Pagnoni et al, 2023). Often, modelling mathematically the natural transition from monopartitism to multipartitism takes in consideration the fact that shorter RNA are easier to replicate, but that any non-cell autonomous element of the virus life cycle is complicated by mutli-segmentation, for example, requiring all the segments to be coordinately transported to a neighboring cells.…”