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

Trichoderma genus includes soil-inhabiting fungi that provide important ecosystem services in their interaction with plants and otherfungi, 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 carriedout high-throughput sequencing of ribosome-depleted total RNA following a bioinformatics pipeline that detects virus-derived RNAdirectedRNApolymerases(RdRps)andotherconservedviralproteinsequences.ThispipelinedetectedseventeenviralRdRpswithtwoofthemcorrespondingtovirusesalreadydetectedinotherregionsoftheworldandtheremainingifteenrepresentingisolatesofnewputativevirusspecies.Surprisingly,eightofthemarefromnewnegative-senseRNAviruses,airstinthegenusTrichoderma.Amongthemisacogu-likevirus,closelyrelatedtoplant-infectingviruses.Regardingthepositive-senseviruses,wereportthepresenceofan'ormycovirus'belongingtoarecentlycharacterizedgroupofbisegmentedsingle-strandedRNAviruseswithuncertainphylogeneticassignment.Finally,fortheirsttime,wereportabisegmentedmemberofMononegaviraleswhichinfectsfungi.TheproteinsencodedbythesecondgenomicRNAofthisviruswereusedtore-evaluateseveralvirusesinthePenicillimonavirusandPlasmopamonavirusgenera,hereshowntobebisegmentedandencodingaconservedpolypeptidethathasstructuralconservationwiththenucleocapsiddomainofrhabdoviruses.