Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res. 2018;46(D1):D708–17.
Google Scholar
Kotta-Loizou I. Mycoviruses and their role in fungal pathogenesis. Curr Opin Microbiol. 2021;63:10–8.
Google Scholar
Hillman BI, Annisa A, Suzuki N. Viruses of plant-interacting fungi. Adv Virus Res. 2018;100:99–116.
Google Scholar
Keçeli SA. Mycoviruses and importance in mycology. Mikrobiyol Bul. 2017;51:404–12.
Google Scholar
Xie J, Jiang D. Understanding the diversity, evolution, ecology, and applications of mycoviruses. Annu Rev Microbiol. 2024;78(1):595–620.
Google Scholar
Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR., et al. Consensus statement: virus taxonomy in the age of metagenomics. Nat Rev Microbiol. 2017;15:161–8.
Google Scholar
Zhang H, Xie J, Fu Y, Cheng J, Qu Z, Zhao Z, et al. A 2-kb mycovirus converts a pathogenic fungus into a beneficial endophyte for Brassica protection and yield enhancement. Mol Plant. 2020;13(10):1420–33.
Google Scholar
Nuss DL. Biological control of chestnut blight: an example of virus-mediated attenuation of fungal pathogenesis. Microbiol Rev. 1992;56:561–76.
Google Scholar
Feau N, Dutech C, Brusini J, Rigling D, Robin C. Multiple introductions and recombination in Cryphonectria hypovirus 1: perspective for a sustainable biological control of chestnut blight. Evol Appl. 2014;7(5):580–96.
Google Scholar
Yu X, Li B, Fu Y, Xie J, Cheng J, Ghabrial SA, et al. Extracellular transmission of a DNA mycovirus and its use as a natural fungicide. Proc Natl Acad Sci U S A. 2013;110:1452–7.
Google Scholar
Jia J, Fu Y, Jiang D, Mu F, Cheng J, Lin Y, et al. Interannual dynamics, diversity and evolution of the virome in Sclerotinia sclerotiorum from a single crop field. Virus Evol. 2021;7:veab032.
Google Scholar
Li P, Bhattacharjee P, Wang S, Zhang L, Ahmed I, Guo L. Mycoviruses in Fusarium species: an update. Front Cell Infect Microbiol. 2019;9:257.
Google Scholar
Ruiz-Padilla A, Rodríguez-Romero J, Gómez-Cid I, Pacifico D, Ayllón MA. Novel mycoviruses discovered in the mycovirome of a necrotrophic fungus. MBio. 2021;12:e03705–03720.
Google Scholar
Deng Y, Zhou K, Wu M, Zhang J, Yang L, Chen W, et al. Viral cross-class transmission results in disease of a phytopathogenic fungus. ISME J. 2022;16:2763–74.
Google Scholar
Zhou K, Zhang F, Deng Y. Comparative analysis of viromes identified in multiple macrofungi. Viruses. 2024;16(4):597.
Google Scholar
Shin TY, Lee MR, Park SE, Lee SJ, Kim WJ, Kim JS. Pathogenesis-related genes of entomopathogenic fungi. Arch Insect Biochem Physiol. 2020;105(4):e21747.
Google Scholar
Hussain M, Hamid MI, Wang N, Bin L, Xiang M, Liu X. The transcription factor SKN7 regulates conidiation, thermotolerance, apoptotic-like cell death and parasitism in the nematode endoparasitic fungus Hirsutella minnesotensis. Sci Rep. 2016;6:30047.
Google Scholar
Zhang W, Li X, Ma L, Urrehman U, Bao X, Zhang Y, et al. Identification of microrna-like rnas in Ophiocordyceps sinensis. Sci China Life Sci. 2019;62(3):349–56.
Google Scholar
Liu Y, Yang Y, Wang B. Entomopathogenic fungi Beauveria bassiana and Metarhizium anisopliae play roles of maize (Zea mays) growth promoter. Sci Rep. 2022;12(1):15706.
Google Scholar
Yang L, Li X, Bai N, Yang X, Zhang KQ, Yang J. Transcriptomic analysis reveals that rho GTPases regulate trap development and lifestyle transition of the nematode-trapping fungus Arthrobotrys oligospora. Microbiol Spectr. 2022;10(1):e0175921.
Google Scholar
Liu Q, Li D, Jiang K, Zhang KQ, Yang J. AoPEX1 and AoPEX6 are required for mycelial growth, conidiation, stress response, fatty acid utilization, and trap formation in Arthrobotrys oligospora. Microbiol Spectr. 2022;10(2):e0027522.
Google Scholar
Duan S, Liu Q, Shen Y, Zhu L, Yuan H, Yang J. AoRan1 is involved in regulating conidiation, stress resistance, secondary metabolism, and pathogenicity in Arthrobotrys oligospora. Microorganisms. 2024;12(9):1853.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics (Oxford, England). 2014;30:2114–20.
Google Scholar
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. Meta-SPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Google Scholar
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. Iq-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74.
Google Scholar
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9.
Google Scholar
Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, et al. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 2015;43:W580–4.
Google Scholar
Mu F, Li B, Cheng S, Jia J, Jiang D, Fu Y, et al. Nine viruses from eight lineages exhibiting new evolutionary modes that co-infect a hypovirulent phytopathogenic fungus. PLoS Pathog. 2021;17:e1009823.
Google Scholar
Liu C, Guo M, Wang J, Sun Y, Bian Y, Xu Z. Prevalence and diversity of mycoviruses occurring in Chinese Lentinula edodes germplasm resource. Virology. 2023;582:71–82.
Google Scholar
Shi N, Hu F, Wang P, Zhang Y, Zhu Q, Yang G, et al. Molecular characterization of two dsRNAs that could correspond to the genome of a new mycovirus that infects the entomopathogenic fungus Beauveria bassiana. Arch Virol. 2021;166(11):3233–7.
Google Scholar
Osaki H, Sasaki A, Nomiyama K, Tomioka K. Multiple virus infection in a single strain of Fusarium poae shown by deep sequencing. Virus Genes. 2016;52(6):835–47.
Google Scholar
Sadiq S, Chen YM, Zhang YZ, Holmes EC. Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota. Virus Evol. 2022;8(1):veac055.
Google Scholar
Ohkit S, Lee Y, Nguyen Q, Ikeda K, Suzukib N, Nakayashiki H. Three ourmia-like viruses and their associated RNAs in Pyricularia oryzae. Virology. 2019;534:25–35.
Google Scholar
Xu ZY, Wu SS, Liu LJ, Cheng JS, Fu YP, Jiang DH, et al. A mitovirus related to plant mitochondrial gene confers hypovirulence on the phytopathogenic fungus Sclerotinia sclerotiorum. Virus Res. 2015;197:127–36.
Google Scholar
Vainio EJ. Mitoviruses in the conifer root rot pathogens Heterobasidion annosum and H. parviporum. Virus Res. 2019;271:197681.
Google Scholar
Hong Y, Cole TE, Brasier CM, Buck KW. Evolutionary relationships among putative RNA-dependent RNA polymerases encoded by a mitochondrial virus-like RNA in the Dutch elm disease fungus, Ophiostoma novoulmi, by other viruses and virus-like RNAs and by the Arabidopsis mitochondrial genome. Virology. 1998;246:158–69.
Google Scholar
Polashock JJ, Hillman BI. A small mitochondrial double-stranded (ds) RNA element associated with a hypovirulent strain of the chestnut blight fungus and ancestrally related to yeast cytoplasmic T and W dsRNAs. Proc Natl Acad Sci U S A. 1994;91:8680–4.
Google Scholar
Ayllón MA, Turina M, Xie J, Nerva L, Marzano SL, Donaire L, Jiang D, Consortium IR. ICTV Virus Taxonomy Profile: Botourmiaviridae. J Gen Virol. 2020;101(5):454–5.
Google Scholar
Lian Z, Das S, Luo J, Andika IB, Sun L. Complete genome sequence of a novel ourmia-like mycovirus infecting the phytopathogenic fungus Botryosphaeria dothidea. Arch Virol. 2021;166(12):3461–5.
Google Scholar
Brown D. The encyclopedia of virology plus. Trends Biochem Sci. 1997;22(1):34–5.
Google Scholar
Rastgou M, Habibi M, Izadpanah K, Masenga V, Milne R, Wolf Y, et al. Molecular characterization of the plant virus genus ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin. J Gen Virol. 2009;90(10):2525.
Google Scholar
Guo J, Zhou X, Xie F, Cao J, Liu S, Zhong J, et al. Hypovirulence caused by mycovirus in Colletotrichum fructicola. Front Plant Sci. 2022;13:1038781.
Google Scholar
Liu L, Xie JT, Cheng JS, Fu YP, Li GQ, Yi X, et al. Fungal negative-stranded RNA virus that is related to bornaviruses and nyaviruses. Proc Natl Acad Sci U S A. 2014;111:12205–10.
Google Scholar
Kuhn JH, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, et al. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol. 2022;167(12):2857–906.
Google Scholar
Hao F, Wu M, Li G. Molecular characterization and geographic distribution of a Mymonavirus in the population of Botrytis cinerea. Viruses. 2018;10(8):432.
Google Scholar
Marzano LSY, Nelson BD, Ajayi-Oyetunde O, Bradley CA, Hughes TJ, Hartman GL, et al. Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens. J Virol. 2016;90:6846–63.
Google Scholar
Lin YH, Fujita M, Chiba S, Hyodo K, Andika IB, Suzuki N, et al. Two novel fungal negative-strand RNA viruses related to mymonaviruses and phenuiviruses in the shiitake mushroom (Lentinula edodes). Virology. 2019;533:125–36.
Google Scholar
Niu Y, Zhang T, Zhu Y, Yuan Y, Wang S, Liu J, et al. Isolation and characterization of a novel mycovirus from Penicillium digitatum. Virology. 2016;494:15–22.
Google Scholar
Nerva L, Turina M, Zanzotto A, Gardiman M, Gaiotti F, Gambino G, et al. Isolation, molecular characterization and virome analysis of culturable wood fungal endophytes in esca symptomatic and asymptomatic grapevine plants. Environ Microbiol. 2019;21:2886–904.
Google Scholar
Robles Luna G, Peña EJ, Borniego MB, Heinlein M, García ML. Citrus psorosis virus movement protein contains an aspartic protease required for autocleavage and the formation of tubule-like structures at plasmodesmata. J Virol. 2018;92(21):e00355-e418.
Google Scholar
García ML, Bó ED, da Graça JV, Gago-Zachert S, Hammond J, Moreno P, et al. ICTV virus taxonomy profile: Ophioviridae. J Gen Virol. 2017;98(6):1161–2.
Google Scholar
Debat H, Garcia ML, Bejerman N. Expanding the repertoire of the plant-infecting Ophioviruses through metatranscriptomics data. Viruses. 2023;15(4):840.
Google Scholar
Kotta-Loizou I, Coutts RH. Studies on the virome of the entomopathogenic fungus Beauveria bassiana reveal novel dsRNA elements and mild hypervirulence. PLoS Pathog. 2017;13(1):e1006183.
Google Scholar
Melzer MJ, Bidochka MJ. Diversity of double-stranded RNA viruses within populations of entomopathogenic fungi and potential implications for fungal growth and virulence. Mycologia. 1998;90:586–94.
Google Scholar
Wang P, Yang G, Shi N, Zhao C, Hu F, Coutts RHA, et al. A novel partitivirus orchestrates conidiation, stress response, pathogenicity, and secondary metabolism of the entomopathogenic fungus Metarhizium majus. PLoS Pathog. 2023;19:e1011397.
Google Scholar