#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on April 25, 2024; 16:47 GMT TreeBASE (cc) 1994-2008 Study reference: Park Y., Chen X., & Punja Z. 2006. Molecular and biological characterization of a mitovirus in Chalara elegans (Thielaviopsis basicola). Phytopathology, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1458] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=14; TAXLABELS CeMV_Celery_mosaic_virus CpMV1_NB63_Cowpea_mosaic_virus GaMV_S1_Galinsoga_mosaic_virus L_dsRNA_Sclerotinia_homoeocarpa_mitovirus MS2_Enterobacterio_phage_MS2 OnuMV3a_Ld_Ophiostoma_mitovirus_3a OnuMV4_Ld_Ophiostoma_mitovirus_4 OnuMV5_Ld_Ophiostoma_mitovirus_5 OnuMV6_Ld_Ophiostoma_mitovirus_6 Qbeta_Enterobacteriophage_Qbeta RsM2_1A1_Rhizoctonia_solani_virus ScNV_20S_Saccharomyces_cerevisiae_narnavirus_20S_RNA ScNV_23S_Saccharomyces_cerevisiae_narnavirus_23S_RNA YFV_Yellow_fever_virus ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1007] TITLE RdRp; LINK TAXA = Taxa1; DIMENSIONS NCHAR=717; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] CeMV_Celery_mosaic_virus IKYMKSVRLHITRYICRKPLFIND-SGVSVDKSGFP-TKFIELKKFLNNHESSICYHTRLRIILTLLLLPRGLKPTKIEDAKIKPNFSSITLPFSGT------------------------RMNPIPTWFIKEFVKEYN---------LKLEKP------TYDLSKHYLSPKGGPMGKSTWSSIWSMYALKHE--LHLSLSYFLG----EAYKTLFYLPYLKNMALSY--------GHDVPPKQWPSGKLGIVKDPEGKRRIIAMVDYHSQLVLRSIHDGLLNKLRNLPQDRTYNQD-PNNAW-EENKE--------CFHSLDLSSATDRFPVKLQSRLLTEMYSD----PSFGENWMNLLLNRDYLLPE-----EGLSGERLRYAVGQPMGAYSSWAAFTLSHHLVVAWCTYKSKKVIRSS------QYIILGDDIVIKDNDIARKYIGQMS-KLGVAISMQKTHVS--KDTYEFAKRWMHKGVEISGLPLKGIFYNISHMRRMYTIIFDYLQR--IPSKSNLTSLQLFASCLSGIKFGKRV-YSKALILKLLRNFNISLRYSYGLLTPYELREYILTGFNMGDEVLPSDNRILEWFKGIICD---GVAGKVSTLSREYTKEVNSLEEHRSSQHILNSINIEITYENLQWSPLIIGMFNHINKVSEKCG-EWLYGDVPLMDI----IQQFTLPSADSLSRKDRDINKKIDELDSLI CpMV1_NB63_Cowpea_mosaic_virus FKYLKEVMRLSVRRIANIELEPSKKIFVKLNKFRFPNIIPLPICDQIIRDQNDQVLWASKRLIICLLTILSVHR---VLPTKVVPDYSTIVDPFTG-------------------------VSKTIDQKLLRKAIHLLN------------IKRVKQLKLKITGSMKAGPNGKISLLTSSVDALSFITQPTKIFTYLDFSVRVYKFRGLLLWMWMMCILLITLPYAIV--------SFMLGALIPIMGKLSVVYDQAGKARIVAITNSWIQTAFYSLHLHVFKLLKNIDQDGTFDQERPFKLLIKWLNEP-----TQKFYGFDLTAATDRLPIDLQVDILNIIFK-----NSPGSSWRSLLRIKYKSPQG-----------FLTYAVGQPMGAYSSFAMLALTHHVIVQVAALNSGFTTRFT------DYCILGDDIVIAHDTVASEYLKLME-TLGLSISSGKSVIS--SEFTEFAKKLKGRNNFDIFYRSWFSIIHFEKQILHLCTVFELLRRG-------------------VCELYDLYPQYINKLPKIYLRYNLLIDWVVVAFTNQILIGDRPRADGIRLFDYFVGLEVIPPLLRIMLH---TIKKDWNGLWNSIKYTLNKGFVVSQVR--------------VGLPDWTELFLLPILPSTYIIIRDYCRSFNDLTKL----FGEWWLLR----FESESYQVSILDVIDRLA GaMV_S1_Galinsoga_mosaic_virus VKIFKQIRLHVTRYLCGSPLRINS-MMIGIDKDGWP-KMINFLKPLANGTRSDK------QLLLSILFITRSFVEK--DKSKLVPDWSTITQPRTTQ------------------------KEYIIPSGFIKDWVLNNH---------LGTYKS------EFDDSNHFVSVKSSPTGPSTLTALWGLWNHSYE--SFNWLFKITSLSGVDYLTKIMNWTWLKDLGNKK--------NNKWSKQFLG--SLSLIYDPECKVRIVAMLDYTTQLFLRPIHNDLFKLLKKLPQDRTFTQN-PLNDW-EDNEH--------SFWSIDLTAATDRFPISLQRRLLLYIYSD----PEIANSWQNLLVHREYAR-------NGLN--PIKYSVGQPMGAYSSWPAFTLSHHLVVHWCAHLCN-INKFK------DYIILGDDIVIHNDNIAKKYIEIMG-KLGVGLSNSKTHVS--KDTYEFAKRWIHKGQEISPLPITGIVNNITNPYIVLMNLYDFFKIKRNQYNFSGDILTMLLKLYQGLKIYKGD-KSKKHYYLSLNRFKNLDIFLFALNNTFGYSTYDHKRSFLISKDYSKDLPGPKIMQDLISY---VISTGLSNLTVESVNKSLKFVDTIIDNKNLLNIE---DPNDLSNLPLFKGFQAYISNLRKTVE-GWNNKSISLIEA----SRGLVQMDILPIMKGSNRKILELQTIGKIY L_dsRNA_Sclerotinia_homoeocarpa_mitovirus VQYLKECTRIVQHFVSGHPVFVTDVMPIGLAGGLPT-IIPGTLRTLLRSKDPST-----IRGVLSTLAVYR------IMKMPCKLKLESITDPFKG-------------------------ISDTLPKHEVINGLAALG---------LETPKGKSKHRLTLTNPIIYLLSAGPNHSISMMGIWKDIYAWYISPLFPTLLSFIGRMNRGNVLIDLLRSEVSHWEATGV--------KPSVSPLELKLGKLAIKEEAAGKARVFAMADSITQSVMAPLNSWVFSKLKGLPMDGTFNQQAPLNRLVQLYKEGLLH--DVEFYSYDLSSATDRLPMAFQKQIISVLFG-----SDFADDWATLLVGRDWYL-------KDIP---YRYSVGQPMGALSSWAMLALSHHVIVQIAAMRVG-KLSFT------NYALLGDDIVIADKAVATSYHMIMTQILGVEINLSKSLVS--SNSFELAKRLVTMDGEVSAVGAKNLLVALKSRWGISSVILDLYNKG---------------LALSEQDLRQRF-SSIPTVSKQFG-VDKLLWLVLGPFGFIPSKDGLSAFMKLNRSLSLVDMHILLSCVDEAKF---DLDKKTWEANIQETVHTLLRFGMLSEPAGFEVFS------DFTSSPLYSFIRGQFDNKLSTLVQDKPVRRLIFDGP----PLHFTFYTENWCDGLMEHLTKKIQSDSQET MS2_Enterobacterio_phage_MS2 PTLGSGNDEATRRTLAIAKLREANGDRGQINREGFLHDKSLSWDPDVLQTSIRS---------------------------------------------------------------------------LIGNLLSGYR-----------------------SSLFGQCTFSNGAPMGHKLQDAAPYKKFAEQ-------ATVTPRALRAALLVRDQCAAWIRHAVRY--------NESYEFRLVVGNGVFTVPKNNKIDRAACKEPDMNMYLQKGVGAFIRRRLKSVGIDLNDQSINQRLAQQGSVDG--------SLATIDLSSASDSISDRLVWSFLP---------PELYSYLDRIRSHYGIVDG--------------ETIRWELFSTMGNGFTFELESMIFWAIVKATQIHFGNAG------TIGIYGDDIICPSEIAPRVLEALAY--YGFKPNLRKTFVSG--LFRESCGAHFYRGVDVKPFYIKKPVDNLFALMLILNRLRGWGVVG--------------------GMSDPRLYKVWVRLSSQVPSMFFGGTDLAADYYVVSPPTAVSVYTKTPYGRLLADTRTSGFRLARIAR---ERK-----------------------------------------------FFSEKHDSGRYIAWFHTGGEITDSMK----SAGVRVIRTSEWLTPVPTFPQECGPASSPR OnuMV3a_Ld_Ophiostoma_mitovirus_3a VQYLKECTRIVQHFVSGHPVFVTDVMPIGLAGGLPT-IIPGTLRTLLRSKDSST-----IRGVLSTLAVYR------IMKMPCVLKLESITDPFKG-------------------------ISDTLPKSEIINGLASLG---------FEIPKGRSKHLLTLSNPIIYLLSAGPNHSISMMGIWKDIYAWYVSPLFPTLLSFIGRMNRGNVLIDLLRAEVSYWEATGV--------KPSVSPLDLKLGKLAIKEEAAGKARVFAMADSITQSVMAPLNSWVFSKLKDLPMDGTFNQQAPLNRLVQLYQDGLLH--DVEFYSYDLSSATDRLPMAFQKQIISVLFG-----SKFAKDWATLLVGRDWYL-------KDIP---YRYSVGQPMGALSSWAMLALSHHVIVQIAAMRVG-KLPFT------NYALLGDDIVIADKAVATSYHMIMTQILGVEINLSKSLVS--NNSFEFAKRLVTMDGEVSAVGAKNLLVALKSRWGISSVILDLYNKG---------------LALSEQDLRQRF-SSIPTVSKQFG-VDKLLWLVLGPFGFIPSKDGLSAFMKLNRSLSLVDMHILLSCVDEAKF---DLDKKTWEANIQETVHTLLRFGMLSEPAGFEVFS------DFTSSPLYSFIRGQFGNKLSALVQDKPVRRLIFDGP----LLHFNFYTEGWCDGLMEHLTKKIQSDSQET OnuMV4_Ld_Ophiostoma_mitovirus_4 IKYMKAAKLHITRYMCGKPLYSNN-ENVALDKTGFP-LRFWYLKRLVNDNP---------RALLTLLTYTRRIVPNKSESKARIVKLSTITDPYKG-------------------------KVYTIPKWFILDFISKYN---------LSSTKP------IYTDNDHYLSIKGSPNGKASMSSLYSIISFNSS--NIRYLFNIVG----DYQLVLN--KFYQDLSQFY--------TKYINRDKLGLGKLSIVHDPELKERVIAMVDYTTQFALRPIHNILLNNLSKLPCDRTFTQD-PFHKWNDDHKE--------RYHSLDLSAATDRFPIFLQQKLISLIFND----YEFGKNWRNLLVDRNYDY-------QGIS---YRYSVGQPMGAYTSWAAFTLTHHLVVHWAAELAG-LKNFK------DYIILGDDIVIKNNKVAQIYINLMT-KWGVDISLSKTHVS--YDTYEFAKRWIKNGKEISGISLKGILTNIRHIHVVYMNIFTYLQR--IPS-LNVDILTCVGKLYGYLLIRNRI-KSPNTIKRSLYDFHHSIRYSFGLLNYEEIRNYLHNKFPFDNYYAWPERLVHSKLNEIFKL---EMVESAKSFSKDFMNQSTMLINTVTDNEIM-----------VQW-PLYKGFMNHIEKLKDYIKSKQNQHDIDLLDL----MQNLRFQNLDSIVKKLRNSYTNLIMLDKFW OnuMV5_Ld_Ophiostoma_mitovirus_5 IKYMKAVKLHITKYIANERLLSISGSRVSVDKDGFP-TKFNYIKHIIDSGDIDG-----IRFVMTLLTYTRAINPTKKEYLKIFPDYSTITNEFTGS------------------------NKIAIPNKIIKEFVDYYK---------LANPNNNNNPELQWSRDDHYLSFKSSPNGQSTLHSSYGLFSMIFV--GHTILENILKIVGEKQYHEIIGNHIKKLYHDHR--------LFIPGKIDYLFGKISIVKDPELKMRVIAMVDYHSQFVLKKIHNSLFNKLKLIKSDRTFTQD-PIFTT-PTMGH--------RFWSMDLSAATDRFPIDLQERLLSYLYG-----SEISSAWKQLLIDRTYKTPE-----GDE----LHYKVGQPMGAYSSWAAFTLTHHLVVFYSARMAG-IKDFT------NYILLGDDIVINNDKVAKYYIRTMK-RLGVELSMNKTHVS--KNTYEFAKRWFKNKKEITGLPLRGILNNLNNYGIVFQELFKFHYK--YPHLTNVKLTDIMFIIFKGLKIKGRI-ITNSQLRFNLMKINFLLRYINKLVNFDETRLFYTKFIKSEDISMVNEHNFLDFTRGMLKL---GLTQKIENS----VKELKTFYDDVLKNSFISNIE---NKNDLQYEPLINGLYNKMLIMRNSIDRIVRNKDFDIIDA----MNDMRLDNPEAYLEKIKNSNKPLSNLNDMF OnuMV6_Ld_Ophiostoma_mitovirus_6 VKYLKELRLHITKYISGE-PYRNSLNRVSVDKDGFP-TLCKELKVLVNGTYLEK------RFVLTIITLSKLLIPQ--KSESIPFSTKSITDHWSG--------------------------IDNISNEELDKSCSELN---------ISTREV------QWDVKNFKLLTKAGPHGPQSLTWYHTIKLYDFN--QWLGIIGILPKSVLDLFTETLSYASKLVLPEIK--------SNIKSTKLIR--RLSIVHDPECKERVIAIFDYGSQMVLKPIADVLFDLLRNIPSDRTFTQSPFFTHTDLDNKS--------KFWSIDLSSATDRFPIVFQKRVLQKILG-----KQMTDSWERIMIGSKFLAPD-----GDTVS----YNCGQPMGAQSSWPMFTLAHHVIVRVAANRCG-LSNFD------KYIILGDDIVINNDNVALKYMEIMN-DFKVEISRNKTHVS--NDTYEFAKRWIKNKMEFFPLPIRGIVDNINNKYIIFNILYSFFVEKGNTFLNKDTLLVCVSKFIQLHSLTLKKPIGLNKVKGILYPFNFMLRYRQNLCTNEEIR------IFLGSSTCKRDDYMLPISAKDVSL---ELTRVISAALVGMAYNAEKSLKNIYFDLDKLSPWIGDGFKTGKHPKVMIQSIYNSVKSLSDFGLKMAQNKLTLSAA----MDSLLLVDLDSISSSERIKYIQMKQNICLS Qbeta_Enterobacteriophage_Qbeta PKFGISPDQFRNSYLRAEIMSKYDSFSLGINTEAVAWEKFLAAEAECAKTNLRLYR----------------------------PNYNEDFNFSLG------------------------ETCIHMARRKIVKLLGDSVP---------------------FEAVLRHCRFSGGATTTNSRLYGHPSFKFALA----------------QECTPRAVPYVQALKACTN--------MDLGITKVSPFNKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGVIREKLHLWNIDLNDQTINQVRAYSGSCSN--------ELATVDLSSASDTISLALVELLLP---------PAWFKVLTDLRSRRGMLPDG-------------RIITYEKISSMGNGFTFELESLIFAALARSLCELLNLQPS-----SVTVYGDDIILPSD-ACSSLIEVFS-YVGFRTNEKKTFFDG--PFRESCGKHYFMGVDVTPFYIRHRIVSPSDLILVLNQMYRWATID--------------------GVWDPRVYPVYTKYRRLLPDILRRNVVPDGYGDGALVGSVLTSPFAENRGWVRRVPMIIDKKKDRVRD---ERGSYLYELWSLQQLECDSEFP----------------------------FNGSLVVGTNDGVCTYRHRERVSTAI----SDSVGAYDIVWIPCSSR----VLAPYGDFR RsM2_1A1_Rhizoctonia_solani_virus IKWLKGCSVAIQKCLGKDILKSLRVLTPDLPLNGLS-RGLPRIIPVEDRVKIRRGHVPTIRFWLGLFNLYR------VLKAPSELKLGTITNKFTGDRDGLRALMRFALKFNPFVEFNKLDKKSLAPTKFIMSRSASPSNKVSWFGILTDTRLLREGSPRLWENIQAYLTMVGADQFRFDLDYACSLADRLKSFDDKVDSQGQWIRQVSKSGQVLTQVDSMKSKDSIR--------GHGIGP-GLGLSQFALKEEAAGKIRLFALMDSITQSVMSPLHDYMFAILRNIPNDGTFDQEASIARSQEKAVTAG------KAFSYDLTAATDRLPVILTAFILSTIVGI----RTFGGLWRSILVKRPFGFNSNVAEKLKVSDGPYFYEVGQPMGALSSWPGLALTHHWIVQVAAFRVTNSKSWNT-----EYEILGDDIVIFNELIAQEYLNIMA-VIGCEINLNKSISSRCRPVFEFAKRTCWGFAIVSGISLAQIRAGWRIGGRVANALQFARAG----------LLEPGESLLQAILSRNTFSKGRVLPGYKTESVTSQKALALGVLALLGER---------FRSGIIPLRTVMHAIIDPISK---NLDLKGDAIAIPIKASLHAAYQALVE----------------GDKPQLYPFSKEWNREPKFLENEDKLASRLLHSA----LNKVIILRDQYNWFIAENASEMYFPLSYLN ScNV_20S_Saccharomyces_cerevisiae_narnavirus_20S_RNA GVVVSRGTRSLPPSLRLFRAMTRKWLSVTARGNGVEFAIASAKEFSAACRAGWISG----TVPDHFFMKWLPEPVRRKSGLWAQLSFIGRSLPEGGD-----------------------RHEIEALANHKAALSSSFEVP-------ADVLTSLRNYSEDWARRHLAADPDPSLLCEPCTGNSATFERTRREGGFAQSITDLVSSSPTDNLPPLESMPFGPTQGQALPVHVLEVSLSRYHNGSDPKGRVSVVRERGHKVRVVSAMETHELVLGHAARRRLFKGLRRERRLRDTLKGDFEATTKAFVGCAG------TVISSDMKSASDLIPLSVASAIVDGLEASGRLLPVEIAGLRACTGPQHLVYPD---------GSEITTRRGILMGLPTTWAILNLMHLWCWDSADRQYRLEGHPFRATVRSDCRVCGDDLIGVGPDSLLRSYDRNLGLVGMILSPGKHFRSNRRGVFLERLLEFQTRKTVYEHAVIYRKVGHRRVPVDRSHIPVVTRVT------------------VLNTIPLKGLVRASVLGRDDPPVWWAAAVAESSLLSDYPRKKIFAAARTLRPGLSRQFRRLG-IPPFLPR---ELGGAGLVGPSDRVDAPAFHRKAISSLVWGSDAT-----AAYSFIRMWQGFEGHPWKTAASQETDTWFADYKVTRPGKMYPDRYGFLDGESLRTKSTMLNSAVYETFLGP ScNV_23S_Saccharomyces_cerevisiae_narnavirus_23S_RNA TGRKFPSFSVTDRPARARLAKVYRMGRRLLVGVVCRGESVVSDLKQECADLRRVIFEGSTRIPSSSLWGLVGVLGWTSPERAMQLTFIGRALPYGSP-----------------------DVERRALASHAATLSIPAECHPNYLVAAEQFAKSWADDNLPRKFRIYPIAVQESSCMEYSRAQGGLLQSFRKGFVGYDPAAPSADPDDLELAKERGFSRIRASWYSTFRY-----RGELKSTNQSLEARVAVVPERGFKARIVTTHSASRVTFGHQFRRYLLQGIRRHPALVDVIGGDHRRAVETMDGDFGLLRPDGRLLSADLTSASDRIPHDLVKAILRGIFSD----PDRRPPGTSLADVFDLVLGPYHLHYPDGSE--VTVRQGILMGLPTTWPLLCLIHLFWVELSDWAPARPNHSRGFVLGESFRICGDDLIAWWRPERIALYNQIAVDCGAQFSAGKHLES---KTWGIFTEKVFTVKPVKMKVRVRSEPSLKGYVFSRSSAFSCRMGG--------------------KGITGIRAARLYTIGAMPRWSRRIRDVYPGSLEHRTASQRYGEPVTVYRFGRWSSAIPLRWAVRAPTR---TVGNPVQSLPDWFTVGPAASSVAADSNAFG-----------AVSRVLRRMFPGLPRKLASAGIPPYLPRVFGGGGL----VKSTGLTTKIGAVASRRWMSRIGHDLYRSR YFV_Yellow_fever_virus LAVLRKVKRVVASLMRGLSSRKRRSHDVLTVQFLILGMLLMTGGVTLVRKNRWLLLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPN--------------------------LSPREEPDDIDCWCYGVEN------------VRVAYGKCDSAGRSRRSRRAIDLPTHENHGLKTRQEKWMTGRMGERQLQKIERWFVRNPFFAVTALTIAYLVG-----------SNMTQRVVIALLVLAVGPAYSAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGD----NACKRTYSDRGWGNGCGLFG-----------KGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQEN----WNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGN--SYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPH------------------AATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAIN-------KGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSSIGKLFTQTMKGVERLAVMG ; END; BEGIN TREES; TITLE Tb7597; LINK TAXA = Taxa1; TRANSLATE 1 MS2_Enterobacterio_phage_MS2, 2 YFV_Yellow_fever_virus, 3 OnuMV6_Ld_Ophiostoma_mitovirus_6, 4 OnuMV5_Ld_Ophiostoma_mitovirus_5, 5 OnuMV4_Ld_Ophiostoma_mitovirus_4, 6 ScNV_20S_Saccharomyces_cerevisiae_narnavirus_20S_RNA, 7 ScNV_23S_Saccharomyces_cerevisiae_narnavirus_23S_RNA, 8 OnuMV3a_Ld_Ophiostoma_mitovirus_3a, 9 CpMV1_NB63_Cowpea_mosaic_virus, 10 Qbeta_Enterobacteriophage_Qbeta, 11 CeMV_Celery_mosaic_virus, 12 L_dsRNA_Sclerotinia_homoeocarpa_mitovirus, 13 GaMV_S1_Galinsoga_mosaic_virus, 14 RsM2_1A1_Rhizoctonia_solani_virus; TREE Fig._7 = [&R] ((((14,(12,8)),(((13,((11,5),4)),3),9)),(10,1),(7,6)),2); END;