Biology subjects

Migheli, Q.

Publications and source records attributed to Migheli, Q..

2 recordsLinked to original sources

bioRxiv2026

A viroid-like RNA can be transmitted among different Trichoderma species affecting their antagonistic capacity

Viroids are small, circular non-coding RNAs that autonomously replicate in plants, exploiting host cellular machinery for replication and spread. Recent studies reveal that viroid-like agents can infect filamentous fungi, suggesting cross-kingdom interactions. In this study, we report the discovery and the characterization of TsvlRNA1 in Trichoderma spirale, a transmissible viroid-like RNA containing a hammerhead ribozyme in one polarity strand. Bioinformatic data, molecular validation, and reverse genetics experiments demonstrate that TsvlRNA1 is circular with an active ribozyme essential for replication. TsvlRNA1 replicates autonomously and transmits horizontally between Trichoderma species, eliciting 21-23 nt viroid-derived small RNAs consistent with RNA silencing targeting. The biocontrol capacity of Trichoderma against Rhizoctonia solani is variably modulated by TsvlRNA1, with effects ranging from positive to negative depending on host strain. In T. spirale, data suggests genotype-by-agent interactions influence antagonistic potential negatively. TsvlRNA1 transmission via horizontal routes is prevalent, and the viroid-like RNA fails to infect plant hosts experimentally. These results highlight so-far the underappreciated ecological and functional diversity of viroid-like agents in fungi, with implications for fungal biology, biocontrol, and genotype-phenotype relationships in eukaryotes. ImportanceSpecies of the fungal genus Trichoderma play a central role in sustainable agriculture by controlling fungal plant pathogens and supporting plant growth. For this reason, Trichoderma-based products represent a substantial share of the global market for microbial biofungicides. Viroids are the smallest known infectious agents, and their presence in filamentous fungi has only recently been discovered. Consequently, little is known about their biology, transmission, or interactions with fungal hosts. In this study, we describe TsvlRNA1, a viroid-like RNA associated with T. spirale, representing only the second viroid-like RNA to be biologically characterized in fungi. We show that TsvlRNA1 can influence the ability of Trichoderma to inhibit Rhizoctonia solani, a major plant pathogen, demonstrating its biological relevance. Unexpectedly, TsvlRNA1 can be transmitted between different Trichoderma species. This finding raises concerns about the possible transfer of genetic traits between fungi, including those related to fungicide resistance, with important implications for agricultural biocontrol. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/702247v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1b6de6eorg.highwire.dtl.DTLVardef@c52141org.highwire.dtl.DTLVardef@a61fcorg.highwire.dtl.DTLVardef@1a6f0a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

A collection of Trichoderma isolates from natural environments in Sardinia, a biodiversity hotspot, reveals a complex virome that includes negative-stranded mycoviruses with unprecedented genome organizations

The Trichoderma genus includes soil-inhabiting fungi that provide important ecological services in their interaction with plants and other fungi. They are exploited for biocontrol. A collection of Trichoderma isolates from the Sardinia island (a biodiversity hotspot) had been previously characterized. Here we started a characterization of the viral components associated to 113 selected Trichoderma isolates, representatives of the collection. We carried out NGS sequencing of ribosome depleted total RNA following a bioinformatic pipeline that detects virus RNA-dependent RNA polymerases (RdRP) and other conserved virus protein sequences. This pipeline detected 17 viral RdRPs. Two of them correspond to viruses already detected in other regions of the world. The remaining 15 represent isolates of new virus species: surprisingly, eight of them are from new negative stranded RNA viruses, which for the first time are reported in the genus Trichoderma. Among them is a cogu-like virus, very closely related to plant-infecting viruses. Regarding the positive strand viruses, it is noticeable the presence of an ormycovirus belonging to a recently characterized group of bi-segmented ssRNA genome viruses with still uncertain phylogenetic assignment. Finally, for the first time we report a bipartite mononegavirales-infecting fungi: the proteins encoded by the second genomic RNA were used to re-evaluate a number of viruses in the Penicillimonavirus and Plasmopamonavirus genera, here shown to be bipartite and to encode a conserved polypeptide having structural conservation with the nucleocapsid (NC) domain of members of the Rabhdoviridae. IMPORTANCE Trichoderma is a genus of fungi of great biotechnological impact in multiple industrial fields. The possibility to investigate a diverse collection of Trichoderma isolates allowed us to characterize both double-stranded and single-stranded virus genomes belonging to three of the major phyla that constitute the RNA viral kingdom, thus further increasing the taxa of viruses infecting this genus. To our knowledge here we report for the first time negative-stranded RNA viruses infecting Trichoderma spp. and through in silico structural analysis a new conserved domain of nucleocapsids common among some mymonavirids. Obtaining such a library of mycoviruses could be the basis for further development of targeted virus-induced gene silencing or gene editing (VIGS/VIGE) tools; in addition, the many biotechnological applications of this fungus, will require to assess the qualitative (commercial) stability of strains, linked to positive or negative effects caused by mycovirus infections.

microbiology↗