Dolja VV, Krupovic M, Koonin EV. Deep roots and splendid boughs of the global plant Virome. Annu Rev Phytopathol. 2020;58:23–53.
Google Scholar
Lebas B, Adams I, Al Rwahnih M, Baeyen S, Bilodeau GJ, Blouin AG, et al. Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description. EPPO Bull. 2022;52(2):394–418.
Saldarelli P, Boscia D, De Stradis A, Vovlas C. A new member of the family flexiviridae from phlomis fructicosa. J Plant Pathol. 2008;90(2):281–6.
Google Scholar
Adams MJ, Adkins S, Bragard C, Gilmer D, Li D, MacFarlane SA, et al. ICTV Virus Taxonomy Profile: Virgaviridae J Gen Virol. 2017;98(8):1999–2000.
Google Scholar
Harrison BD, Robinson DJ. Tobraviruses. In: Van Regenmortel MHV, Fraenkel-Conrat H, editors. The plant viruses: the Rod-Shaped plant viruses. Boston, MA: Springer US; 1986. pp. 339–69.
Macfarlane SA. Tobraviruses–plant pathogens and tools for biotechnology. Mol Plant Pathol. 2010;11(4):577–83.
Google Scholar
Adams MJ, Antoniw JF. DPVweb: a comprehensive database of plant and fungal virus genes and genomes. Nucleic Acids Res. 2006;34:D382–385.
Google Scholar
van Griethuysen PA, Redeker KR, MacFarlane SA, Neilson R, Hartley SE. Virus-induced changes in root volatiles attract soil nematode vectors to infected plants. New Phytol. 2024;241(5):2275–86.
Google Scholar
Cooper JI, Harrison BD. The role of weed hosts and the distribution and activity of vector nematodes in the ecology of tobacco rattle virus. Ann Appl Biol. 1973;73(1):53–66.
Google Scholar
Nixon HL, Harrison BD. Electron microscopic evidence on the structure of the particles of tobacco rattle Virus582. Microbiology. 1959;21(3):582–90.
Google Scholar
van Belkum A, Cornelissen B, Linthorst H, Bol J, Pley C, Bosch L. tRNA-like properties of tobacco rattle virus RNA. Nucleic Acids Res. 1987;15(7):2837–50.
Google Scholar
Martín-Hernández AM, Baulcombe DC. Tobacco rattle virus 16-Kilodalton protein encodes a suppressor of RNA Silencing that allows transient viral entry in meristems. J Virol. 2008;82(8):4064–71.
Google Scholar
Deng X, Kelloniemi J, Haikonen T, Vuorinen AL, Elomaa P, Teeri TH, et al. Modification of tobacco rattle virus RNA1 to serve as a VIGS vector reveals that the 29K movement protein is an RNA Silencing suppressor of the virus. Mol Plant Microbe Interact. 2013;26(5):503–14.
Google Scholar
Yue N, Jiang Z, Pi Q, Yang M, Gao Z, Wang X, et al. Zn2+-dependent association of cysteine-rich protein with virion orchestrates morphogenesis of rod-shaped viruses. PLoS Pathog. 2024;20(6):e1012311.
Google Scholar
Koenig R, Lesemann DE, Pleij CWA. Tobacco rattle virus genome alterations in the hosta hybrid ‘green fountain’ and other plants: reassortments, recombinations and deletions. Arch Virol. 2012;157(10):2005–8.
Google Scholar
Macfarlane SA. Molecular determinants of the transmission of plant viruses by nematodes. Mol Plant Pathol. 2003;4(3):211–5.
Google Scholar
Heinze C, Von Bargen S, Sadowska-Rybak M, Willingmann P, Adam G. Sequences of tobacco rattle viruses from potato. J Phytopathol. 2000;148(9–10):547–54.
Google Scholar
Kurppa A, Jones AT, Harrison BD, Bailiss KW. Properties of spinach yellow mottle, a distinctive strain of tobacco rattle virus. Ann Appl Biol. 1981;98(2):243–54.
Ashfaq M, McGavin W, Macfarlane SA. RNA2 of TRV SYM breaks the rules for tobravirus genome structure. Virus Res. 2011;160(1–2):435–8.
Google Scholar
Yin Z, Pawełkowicz M, Michalak K, Chrzanowska M, Zimnoch-Guzowska E. The genomic RNA1 and RNA2 sequences of the tobacco rattle virus isolates found in Polish potato fields. Virus Res. 2014;185:110–3.
Google Scholar
Lindner K, Hilbrich I, Koenig R. Molecular characterization of variants of a new ‘rule-breaking’ tobacco rattle virus RNA2 in potatoes. Virus Res. 2018;244:270–5.
Google Scholar
Conti M, Masenga V. Identification and prevalence of pepper viruses in Northwest Italy. J Phytopathol. 1977;90(3):212–22.
Herath V, Romay G, Urrutia CD, Verchot J. Family level phylogenies reveal relationships of plant viruses within the order bunyavirales. Viruses. 2020;12(9):1010.
Google Scholar
Sun MH, Ji YF, Li GH, Shao JW, Chen RX, Gong HY, et al. Highly adaptive phenuiviridae with biomedical importance in multiple fields. J Med Virol. 2022;94(6):2388–401.
Google Scholar
Sasaya T, Palacios G, Briese T, Di Serio F, Groschup MH, Neriya Y, et al. ICTV virus taxonomy profile: phenuiviridae 2023. J Gen Virol. 2023;104(9):001893.
Google Scholar
Kuhn JH, Brown K, Adkins S, de la Torre JC, Digiaro M, Ergünay K, et al. Promotion of order bunyavirales to class bunyaviricetes to accommodate a rapidly increasing number of related Polyploviricotine viruses. J Virol. 2024;98(10):e01069–24.
Google Scholar
Falk BW, Tsai JH. Biology and molecular biology of viruses in the genus tenuivirus. Annu Rev Phytopathol. 1998;36:139–63.
Google Scholar
Navarro B, Zicca S, Minutolo M, Saponari M, Alioto D, Di Serio FA, Negative-Stranded RNA. Virus infecting citrus trees: the second member of a new genus within the order bunyavirales. Front Microbiol. 2018;9.
Lecoq H, Wipf-Scheibel C, Verdin E, Desbiez C. Characterization of the first tenuivirus naturally infecting dicotyledonous plants. Arch Virol. 2019;164(1):297–301.
Google Scholar
Diaz-Lara A, Navarro B, Di Serio F, Stevens K, Hwang MS, Kohl J, et al. Two novel Negative-Sense RNA viruses infecting grapevine are members of a newly proposed genus within the family phenuiviridae. Viruses. 2019;11(8):685.
Google Scholar
Gaafar YZA, Richert-Pöggeler KR, Sieg-Müller A, Lüddecke P, Herz K, Hartrick J, et al. A divergent strain of melon chlorotic spot virus isolated from black medic (Medicago lupulina) in Austria. Virol J. 2019;16(1):89.
Google Scholar
Navarro B, Minutolo M, De Stradis A, Palmisano F, Alioto D, Di Serio F. The first phlebo-like virus infecting plants: a case study on the adaptation of negative-stranded RNA viruses to new hosts. Mol Plant Pathol. 2018;19(5):1075–89.
Google Scholar
Butkovic A, Dolja VV, Koonin EV, Krupovic M. Plant virus movement proteins originated from jelly-roll capsid proteins. PLoS Biol. 2023;21(6):e3002157.
Google Scholar
Chen YM, Sadiq S, Tian JH, Chen X, Lin XD, Shen JJ, et al. RNA Viromes from terrestrial sites across China expand environmental viral diversity. Nat Microbiol. 2022;7(8):1312–23.
Google Scholar
Tokarz R, Sameroff S, Tagliafierro T, Jain K, Williams SH, Cucura DM, et al. Identification of novel viruses in amblyomma americanum, dermacentor variabilis, and Ixodes scapularis ticks. mSphere. 2018;3(2):e00614–17.
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
Bertazzon N, Chitarra W, Angelini E, Nerva L. Two new putative plant viruses from wood metagenomics analysis of an Esca diseased vineyard. Plants. 2020;9(7):835.
Google Scholar
Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, et al. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol. 2020;165(12):3023–72.
Google Scholar
Sadiq S, Harvey E, Mifsud JCO, Minasny B, McBratney AB, Pozza LE, et al. Australian terrestrial environments harbour extensive RNA virus diversity. Virology. 2024;593:110007.
Google Scholar
Dai R, Yang S, Pang T, Tian M, Wang H, Zhang D et al. Identification of a negative-strand RNA virus with natural plant and fungal hosts. Proceedings of the National Academy of Sciences. 2024;121(12):e2319582121.
Gugerli P. Different States of aggregation of tobacco rattle virus coat protein. J Gen Virol. 1976;33(2):297–307.
Google Scholar
Mahillon M, Brodard J, Kellenberger I, Blouin AG, Schumpp O. A novel weevil-transmitted tymovirus found in mixed infection on Hollyhock. Virol J. 2023;20(1):17.
Google Scholar
Mahillon M, Groux R, Bussereau F, Brodard J, Debonneville C, Demal S, et al. Virus yellows and syndrome basses richesses in Western switzerland: A dramatic 2020 season calls for urgent control measures. Pathogens. 2022;11(8):885.
Google Scholar
Dovas CI, Katis NI. A spot nested RT-PCR method for the simultaneous detection of members of the vitivirus and foveavirus genera in grapevine. J Virol Methods. 2003;107(1):99–106.
Google Scholar
Boutsika K, Phillips MS, MacFarlane SA, Brown DJF, Holeva RC, Blok VC. Molecular diagnostics of some trichodorid nematodes and associated tobacco rattle virus. Plant Pathol. 2004;53(1):110–6.
Google Scholar
Mahillon M, Kellenberger I, Dubuis N, Brodard J, Bunter M, Weibel J, et al. First report of tomato brown rugose fruit virus in tomato in Switzerland. New Disease Rep. 2022;45(1):e12065.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Google Scholar
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using spades de Novo assembler. Curr Protocols Bioinf. 2020;70(1):e102.
Google Scholar
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25(9):1189–91.
Google Scholar
Okonechnikov K, Golosova O, Fursov M. UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28(8):1166–7.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.
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(6):587–9.
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(1):268–74.
Google Scholar
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;01(2):518–22.
Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–9.
Google Scholar
Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res. 2008;36:W70–74.
Google Scholar
Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2014;42(Database issue):D699–704.
Google Scholar
Wylie SJ, Tran TT, Nguyen DQ, Koh SH, Chakraborty A, Xu W, et al. A Virome from ornamental flowers in an Australian rural town. Arch Virol. 2019;164(9):2255–63.
Google Scholar
Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540(7634):539–43.
Google Scholar
Velasco L, Arjona-Girona I, Cretazzo E, López-Herrera C. Viromes in xylariaceae fungi infecting avocado in Spain. Virology. 2019;532:11–21.
Google Scholar
Li W, Sun H, Cao S, Zhang A, Zhang H, Shu Y et al. Extreme diversity of mycoviruses present in single strains of rhizoctonia cerealis, the pathogen of wheat Sharp eyespot. Microbiol Spectr 2023;11(4):e00522–23.
Miyauchi S, Kiss E, Kuo A, Drula E, Kohler A, Sánchez-García M, et al. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat Commun. 2020;11(1):5125.
Google Scholar
Holmes EC. The evolution of endogenous viral elements. Cell Host Microbe. 2011;10(4):368–77.
Google Scholar
Hernandez C, Carette JE, Brown DJ, Bol JF. Serial passage of tobacco rattle virus under different selection conditions results in deletion of structural and nonstructural genes in RNA 2. J Virol. 1996;70(8):4933–40.
Google Scholar
Lister RM, Bracker CE. Defectiveness and dependence in three related strains of tobacco rattle virus. Virology. 1969;37(2):262–75.
Google Scholar
Telengech P, Hyodo K, Ichikawa H, Kuwata R, Kondo H, Suzuki N. Replication of single viruses across the kingdoms, fungi, plantae, and animalia. Proc Natl Acad Sci. 2024;121(25):e2318150121.
Google Scholar