Fig. 3: Phylogenetic analysis of Tombusviridae family viruses based on RdRp domains.

Phylogenetic tree of different strains of viruses belonging to the Tombusviridae family. The maximum likelihood (ML) method was used based on the amino acid sequences of the functional domains of the viral RNA-dependent RNA polymerase (RdRp) (PF00998), with the LG + F + R5 matrix identified as the best model for amino acid substitution. Known genera are shown in different colors. The sample identified in this study is indicated by a yellow arrow. The numbers at each main node represent bootstrap values as percentages (1000 replicates). The scale bar indicates the amino acid divergence per site between sequences. JUAV was clustered into a clade of ungrouped viruses outside this family, supported by a bootstrap value of 94%. The genome organization of the identified genus and ungrouped viruses, such as Mute swan virus and Serdyukov virus, shows a similar genome organization to JUAV, clustering in the same clade in the ML phylogenetic tree. Phylogenetic tree: TCV/NC_003821: Turnip crinkle virus; CCFV/NC_001600/Australia: Cardamine chlorotic fleck virus; HCRSV/NC_003608/ ElSalvado: Hibiscus chlorotic ringspot virus; JINRV/NC_002187: Japanese iris necrotic ring virus; MNSP/NC_001504: Melon necrotic spot virus; PSNV/NC_004995/Japao/2002: Pea stem necrosis virus; SoYMMV/NC_011643/Coreiado: Soybean yellow mottle mosaic virus; CPMoV/NC_003535/Nigeria: Cowpea mottle virus; NLVCV/NC_009017/Alaska/20: Nootka lupine vein-clearing virus; SCV/NC_001780: Saguaro cactus virus; CbMV/NC_021926/USA/2002: Calibrachoa mottle virus; AnFBV/NC_007733/USA/2006: Angelonia flower break virus; CarMV/NC_001265: Carnation mottle virus; PFBV/NC_005286 /Espanha/20: Pelargonium flower break virus; HnRSV/NC_014967/USA/2011: Honeysuckle ringspot virus; PelRSV/NC_026240: Pelargonium ringspot virus; ELV/NC_026239: Elderberry latent virus; PCRPV/NC_005985: Pelargonium chlorotic ring pattern virus; RrLDV/NC_020415/USA/2009: Rosa rugosa leaf distortion virus; MCMV/NC_003627: Maize chlorotic mottle virus; PLPV/NC_007017/Alemanha/2: Pelargonium line pattern virus; CMMV/NC_0111108/ReinoUnid: Cocksfoot mild mosaic virus; TPAV/NC_021705/USA/2005: Thin paspalum asymptomatic virus; PMV/NC_002598/USA/1957: Panicum mosaic virus; GaMV/NC_001818: Galinsoga mosaic virus; FNSV/NC_020469/Colombia/2: Furcraea necrotic streak virus; TNVA/NC_001777: Tobacco necrosis virus A; OMMV/NC_006939/Portugal/2: Olive mild mosaic virus; OLV1/NC_001721/Italia: Olive latent virus 1; TLeV1/NC_015227/USA/2006: Trailing lespedeza virus 1; CLSV/NC_007816/Canada/200: Cucumber leaf spot virus; YSV/NC_022895/Nigeria/199: Yam spherical virus; PoLV/NC_000939: Pothos latent virus genes; MWLMV/NC_009533/USA/2007: Maize white line mosaic virus; JCSMV/NC_005287/Ira/2006: Johnsongrass chlorotic stripe mosaic virus: BBSV/NC_004452/China/1980: Beet black scorch virus; TNVD/NC_003487/Hungria/19: Tobacco necrosis virus D; LWSV/NC_001822/Franca/199: Leek white stripe virus; MNeSV/NC_007729: Maize necrotic streak virus; CBLV/NC_004725/Bulgaria/2: Cucumber Bulgarian latent virus; EMCV/NC_023339/Israel/200: Eggplant mottled crinkle virus; PLV/AY100482: Pear latent virus; LNV/DQ011234/Taiwan: Lisianthus necrosis virus; LNSV/JN700748/USA/1998: Lettuce necrotic stunt virus; MPV/NC_020073/Marrocos/19: Moroccan pepper virus; CNV/NC_001469: Cucumber necrosis virus; CyRSV/NC_003532: Cymbidium ringspot virus; PeNSV/NC_005285: Pelargonium necrotic spot virus; PNSV/AJ607402: Pelargonium necrotic spot virus; AMCV/NC_001339: Artichoke mottled crinkle virus; CIRV/GQ259480/Italia/2009: Carnation Italian ringspot virus; CIRV/NC_003500: Carnation Italian ringspot virus; GALV/NC_011535/Japao: Grapevine Algerian latent virus; TBSV/NC_001554: Tomato bushy stunt virus; PEMV2/NC_003853: Pea enation mosaic virus-2; CMoV/KF533713/ReinoUnido: Carrot mottle virus; CMoV/NC_011515/Alemanha/2: Carrot mottle virus; CMoMV/NC_001726 /Australia: Carrot mottle mimic virus; GRV/NC_003603/AfricadoSul: Groundnut rosette virus; ETBTP/NC_024808/Ethiopian: Ethiopian tobacco bushy top virus; TBTV/NC_004366/China/2001: Tobacco bushy top virus; OPMV/NC_027710/NovaZeland: Opium poppy mosaic virus; OCST/NC_003633: Oat chlorotic stunt virus; BYDVGAV/NC_004666: Barley yellow dwarf virus-GAV; DRVX1/AB033715: Dianthovirus RVX1; CRV/NC_003530: Carnation ringspot virus; RCNMV/NC_003756: Red clover necrotic mosaic virus; SCNMV/NC_003806: Sweet clover necrotic mosaic virus; Juruaca_BEAN401933: Virus Juruaçá; OBDV/NC_001793: Oat blue dwarf virus; GFkV/NC_003347/Italia/199: Grapevine fleck virus; APLV/NC_020470/Colombia/1: Andean potato latent virus; NCBV/NC_001990/AfricadoSu: Nudaurelia capensis beta virus; DpTV/NC_005898/China/2005: Dendrolimus punctatus tetravirus; HEV/KR872417: Hepatitis E virus; CuTV/NC_015521/USA/1988: Cutthroat trout virus; PLRV/NC_001747: Potato leafroll virus; PEMV1/NC_003629: Pea enation mosaic virus-1; SCPMV/NC_001625: Southern cowpea mosaic virus; HcRNAV/NC_007518: Heterocapsa circularisquama RNA virus; NV/NC_002690: Nodamura virus; SJNNV/NC_003448: Striped Jack nervous necrosis virus; EPMS2/NC_001417: Enterobacterio phage MS2; EPQB/NC_001890: Enterobacteria phage Qbeta; TAstV1/NC_005790/USA/2000: Turkey astrovirus 2; RA/NC_025346/USA/2010: Rabbit astrovirus; TaV/AF282930: Thosea asigna virus; WAC/NC_004541: Walrus calicivirus; SaV/NC_010624/Tailandia/2: Sapovirus Mc10; NAV1/NC_007916/ReinoUnido: Newbury agent 1 virus; RHDV/NC_001543/China/1991: Rabbit hemorrhagic disease virus; PRRSV/NC_001961/Americado: Porcine respiratory and reproductive syndrome virus; ToTV/NC_009013/Espanha/20: Rice tungro spherical virus; CRLVpot/NC_006271/USA/200: Broad bean wilt virus 2; RTSV/NC_001632: Bean pod mottle virus; PYFV/NC_003628: Parsnip yellow fleck virus; SDV/NC_003785/Japao/1979: Satsuma dwarf virus; TomRSV/NC_003840: Tomato ringspot virus; BPMV/NC_003496: Cherry rasp leaf virus; BBWV2/NC_002690: Tomato torrado virus; IAPV/NC_009025/Israel/200: Cricket paralysis virus; CrPV/NC_003924/Australia: Israel acute paralysis virus of bees; ssRNAV/NC_007522/Japao/20: Schizochytrium single-stranded RNA virus; RsRNAV1/NC_018613/Japao: Rhizosolenia setigera RNA virus 01; PnPV/NC_003113/Taiwan/199: Perina nuda virus; ChPV2/NC_024766/HongKong: Chicken picornavirus 2; DHV1/NC_008250/USA/1949: Duck hepatitis A virus 1; HPeV/NC_001897: Human parechovirus; SPaV1/NC_018226/Franca/20: Swine pasivirus 1; SePV1/NC_009891/Canada/20: Seal picornavirus type 1; KuV/KC935379/Hungria/2011: Kunsagivirus 1; HAV/NC_001489: Hepatitis A virus; AEV/NC_003990: Avian encephalomyelitis virus; PSV1/NC/003987: Porcine sapelovirus 1; EVC96/KF495604/China/2011: Human enterovirus C96; SVV001/NC_011349/USA/2002: Seneca valley virus; EMCV/NC_001479: Encephalomyocarditis virus; MSP1/JQ814851/China/2010: Miniopterus schreibersii picornavirus 1; ERAV/NC_003982: Equine rhinitis A virus; HCoV/NC_023984/Holanda/19: Human cosavirus; ERBV1/NC_003983: Equine rhinitis B virus 1; PTV1/NC_003985: Porcine teschovirus 1; BHuV1/NC_018668/Hungria/2: Bovine hungarovirus 1; >MoVA2/NC_023987/Hungria/2: Mosavirus A2; RoV2/NC_024070/Gambia/200: Rosavirus 2; CPDV/NC_021178/HongKong/2: Canine picodicistrovirus; TVH/NC_021201/USA/2008-20: Turkey hepatitis virus 2993D; SaliV-FHB/NC_025114/China: Salivirus FHB; TV3/NC_014413/China/2006: Turdivirus 3; SakoVA/NC_022802/Portugal: Feline sakobuvirus A; AV/NC_001918/Paquistao/19: Aichi virus; TuGV/NC_018400/Hungra/201: Turkey gallivirus; TV1/NC_014411/China/2007: Turdivirus 1; JSY/NC_028380/China/2015: Chicken sicinivirus JSY. Phylogenetic analysis was repeated independently three times with consistent results.