#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 September 18, 2025; 21:24 GMT

TreeBASE (cc) 1994-2008

Study reference:
Ah-fong A., Shrivastava J., & Judelson H.S. 2017. Lifestyle, gene gain and loss,
and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora
infestans and Pythium ultimum during potato tuber colonization. BMC Genomics,
.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S21575]

BEGIN TAXA;
        TITLE  Taxa;
        DIMENSIONS NTAX=19;
        TAXLABELS
            Arabidopsis_thaliana
            Babesia_bigemina
            Capsaspora_owczarzaki
            Crassostrea_gigas
            Deinococcus_misasensis
            Eimeria_tenella
            Gallus_gallus
            Gekko_japonicus
            Homo_sapiens
            Myxococcus_virescens
            Plasmodium_vivax
            Populus_trichocarpa
            Pythium_arrhenomanes
            Pythium_irregulare
            Pythium_ultimum
            Solanum_lycopersicum
            Tetrahymena_thermophila
            Theileria_parva
            Toxoplasma_gondii
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M42645]

	TITLE Phytophthora_infestans_and_Pythium_ultimum;
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=231;
	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 ]
[                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Arabidopsis_thaliana        -------AIQ------ALGRGFDVTSDVRLL-GAPGSR--LVRIEEGQFLLPNVPADIDCSRGNSGTQRISVCSFHEMAEEFNVRSGVKCFNAMFNYTGSYFIPLYDVKLLHNEIRRAV---PSSWASLASFIENYGTHIVTSVTIGGR--DVVYIRQHQSSPLP-GGDQSHARWAETVPAAPDIINMTFTPIVSLLELTRAIELYLEYKPP-------------------
Babesia_bigemina            ------AAIR------YLGSGYDIVFGNPLGDVDPGYRDPVLKLDWTELKEPRGGWIRPELSCRQAETVDHVNTIEDYKKELSVDAKISGFSASGGYKTFTYCLRYVAGIPMPSFKNDVEELPEKFHPWIKFFKKYGTHYTTVIHLGGKVTNQIQMKKTDVAAIQIGGDVSMQEWTRSLYRKPMPIKVNLDSIKTLIEFDVALKYYSELYGI-------------------
Capsaspora_owczarzaki       ------PNIA------YLGRGYDVVRGNPQSTVDPGIRASIMVLEHAEFYVPDNVDVIMEPVNRFESSSKLVRSEQSYKTMLESDLKIRSFSASESYQQVAETVSYRARLLTAEFRHAVQRLPALFSAYDDLLETFGTHYMHEVTMGGRGMQRFSIDMSEAATLDIGGETSLKDWARTVGSNPVPIRMQVAPIIELLPLASYLASYCESVSGDKVKFTRENNNTTLPFYGN
Crassostrea_gigas           -------NLG------YIGRGYDLFKGNPLTDVDQGFRLPIMELPYTHYRIPDNVDVISESSAKFGSSLHTVQSESDYKKMLSVDASVNSFSASASYQKNSRAVVYRARMVNDYFEKAVMLLPMEDEMYINLVREFGTHYTTEVVMGAKAVQQLTFSKSDLSKLEIGGNESLREWARSADEKPVPIQYKMSSIESLL----------------------------------
Deinococcus_misasensis      ------PNIE------FLGRGYDLLLTDPLD-ASSGVKATVIALQYQKFRFPDGTQNAPDPGGTTSLTFQQMFRQTDYQSQFGETATISKFSLSESYSQS-YTVNFTPALMDTDFANAVGNLSSAS-TYQQFIQQFGTHYSTSVGFGGRAYQYTVVEATTFSSMVSGGRDDWDHWVSSVVDQPVPIALTLAPLSDLLALETAISNYLQANGA-------------------
Eimeria_tenella             VHLAGAPASEPSDDEDFLGSGYNLVFGNPLGDGDPGFRAPVIAFDWGHTLQPKGGYIRPYVSCQSAETIEEIESLKDYVTDLTADAQVDPFSGSLNFRKIAYCIRYEAGFTTEAFNKAVAKLPSSFVQWMEFFSDFGTHVTTNIKLGGKITKQIRVLKEHAQDL-VGGRQELSQWEKSVAALPMPVQYQLQPLTRLL-YRSASSFYSQAFGY-------------------
Gallus_gallus               ------PGTD------IVGSGLDVTTMS-LTETKPTSRCVVCRLHEGRWRAGSKCRKRSSLATGRKSMKTLVSQTQNWKVGLRVALHPGSHSRVAEFGMQ--CVHYWISAPSSHFLHAVRSLPPHYPDYADLLAAYGTHYIHSAQLGGLLRSITAIRSCRAAMMGEGGEENYAKWLSSLQRLPGLVASIVRPLHTLLPLKAAVSHYIAWRAL-------------------
Gekko_japonicus             ------PGHN------LAGEGFDVTTLERKGAMTQWESDGTCNLC--QLPLAAADWEV-DVSCRRKLHSSLQESGNDWRMGLEVEVKPESHSKMADFSID--CVFYKFRILTQHFRRALKVLPAKYLEYHQLIETYGTHFITKLHLGGRVRDVTAIRECETVLDGVGGNEAFQEWAEGLKTMPGLVSYSLAPIHTLVALRQAVSEYVTRRAL-------------------
Homo_sapiens                ------PGAW------LAGEGVDVTSLRRSGSTQRFLRDGTCTLCENALPLALTNWRAQGSGCQRHVTRAKVSSTNDWKVGLDVTPKPTSHSQAANFAAQ--CRFYSFHVLHPDFKRALGDLPHHFPAYLRLISNYGTHFIRAVELGGRISALTALRTCELALEGVGGTEQYSAWVNSLPGSPGLVDYTLEPLHVLLDLRRALSQYLTDRAR-------------------
Myxococcus_virescens        -------NID------FLGRCYDVIRINPLDLGGGATTESIVQIPPESLYIPEGTRYLSESRGERTSRTQTWFSSFDFSHSFEHTVSAGSFSASLTYRQFSFFEDCSIELLSSRFTQEVAKL----NACAAFIKTFGTHYAREVTFGGRMYQRVHISSKEYSRFVVGGTTDFNEWVKSIRQDPKPLKLDLKPLYELFSMMQAVDTHIRTEGF-------------------
Plasmodium_vivax            ------QGTE------YLGVGYDFIFGNPIGDVDPGYRDSIIKLTYPKNINPNGSYVRNEISCNRSENESEISTMSEYTKELSVDASIGSFSASTGYTSVSYCFKYMASLLSDQFVRAISLLPSYFESWMYFFKNFGTHVSTLIHLGGKITQQVKISKNEYKAMNIGGTKNFEKWAKSIKDNPMPIKGEYEPLSRIL-YEEALQFYISVNVP-------------------
Populus_trichocarpa         -------SIQ------ALGRGFDVTSDIRLL-GATGSR--LVHIDDEHVVLPNVSFDIDCSKENRSIERIPVCSFHEMAGQFNEKSGISSFNGMFNFTGSHFIPLYKVQILLEEVKRAV---PSSWASLASFIESYGTHIVTSATIGGR--DVVYIRQHQASPLS-GGDQSHAKWAETVQLAPDVINMTFTPIVSLLELARAVDLYLEYKPP-------------------
Pythium_arrhenomanes        ------GTIA------WMSDWEQL--------AESG------------WTCPAEAAILPMASCLQQSSSDAISSTKSFQRVLQKDCSVASFSGSKAMASMAVCVDYVASLVLPDFAAAVNELPLSYVRFFRFIQLYGTHYTTRVEMGGKIIRRVEIKESDVQTLQIGGSEDWRLWAATTTADPMPIRYRLSPLVELVNFEQAVADYIAAYGK-------------------
Pythium_irregulare          ------PGID------YVGAGYDLVFGNPDGSTDPGFRIHLIKFTWNDWTCPKELTIMPQTSCMQQSSSSMISSTKSFQQVLQKDAKVTSFSGSNAMSTMAVCVEYSASLTLVHFNSAVSELPLVYIKYFRFIQMFGTHFTTKVEMGGKIIHRVEIKQSDVSLLQVGGSEDWREWAKSTMDTPMPIRYTLTSLVDLIAFEQAVTDYISAYGR-------------------
Pythium_ultimum             ------PGID------YLGAGYDLVFGNPDGSTDPGFRVHIIKFTWSNWTCPNELTILPQTSCMQQSSSSKIESTKSFQQVLQKDAKVTAFSGSRTMATMAVCVEYSATLPLAQFSSAVAELPLMYIKYFRFIQLFGTHYTTKVEMGGKIIHRVEIKQSDVSVMEVGGSDDWREWAKSTMDTPMPIRYTLTSLVDLVAFEQAVADYIAAYGR-------------------
Solanum_lycopersicum        -------SIQ------ALGRGFDVTSDIRLL-GAPGSR--LVHLDEENILLPNVTVDIECSQELRTIEATPVFTFHEMAKYFNAISNIFSFNSMFNFTGSHVIPLFTVRLLRDEIKRAV---PYSWASLASFIENYGTHIVTSATIGGR--DVVYIKQHQSSPLL-GGDQSHDKWASTVETSPDVINMTFTPIVSFLELSRAIELYLEYKPP-------------------
Tetrahymena_thermophila     ------PNVQ------YLGSGYNIYFANPHSTLDPGFTSGILELDYNNYYVPDNVSLTVEKSCIVSFQSQEVNSLSQYRDSLSSSVQFQKFSASSDYQEVARCSIFQLDVLTPQLQQALFTL--AFNDYYDFIDTWGTHVVTSVNLGSRFGYKYQMDKYQSNQLTIGATQDPLSWAQQTLDTPMPINISILSFDDFLGVISNLSQYLQTYCA-------------------
Theileria_parva             NSIGDDPDVE------YLGSGYDIIFGNPLGDMDQGYRNPVIRLNWEDLKEPRGSWIRPEYSCRQSETIDHVNTVDDFKKELSVDAQASSFSASTGYKNFTYCLRYVGGITTDEFKKAVEALPDKFLPWMQFIKMFGTHFTTIVHLGGKITHQVQIDKSDVLHMQIGGDNSLNNWAKELYKRPMPIKIKLESIKSLL-FDEALKFYSETYGV-------------------
Toxoplasma_gondii           ------PAIN------YLGAGYDHVRGNPVGDGDPGIRPPVLRFTYAQVLQPLGGYVRQYVACRQSETISELSNLSDYQNELSVDASLQSFSASTGYRDFNYCMRYEAGVVTLAFAAGVSQLPDVFPIWISFIEQFGTHFLVRLFAGGKMTYQVTAKRSEVEKMRIGGRAALAAWADTVEELPMPVKFEVQPLYHLL-FKQAVTFYSKAVGL-------------------
;
END;