#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 January 23, 2020; 5:36 GMT TreeBASE (cc) 1994-2008 Study reference: Chen H. 2016. The interaction between an invertebrate-specific miRNA and the ancient cholinergic neuroendocrine system augments the early-stage immune response of adult oyster against bacterial challenge. Open Biology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S19473] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=11; TAXLABELS Bos_mutus Crassostrea_gigas Homo_sapiens Hydra_vulgaris Lingula_anatina Manacus_vitellinus Mus_musculus Pteropus_alecto Rattus_norvegicus Strongylocentrotus_purpuratus Xenopus_laevis ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M37012] TITLE 'Metazoan Choline Transporter-like Proteins'; LINK TAXA = Taxa1; DIMENSIONS NCHAR=912; 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 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Bos_mutus -------------------------------SSKREWKP-LEDRSCTDIPWLLLFILFCIGMGFICGFSVATGAAARLVSGYDSYGNICGQKN--AELEAIPNSGMDHTHRKYVFFLDPCNLDLINRKIKSVALCVAACPRQELKTISDVQKFAEINGSALCSYDLKPSEYAS-SKA--KGLCPKLPVPASAPIPFFHRCAPVNISCYA--------------KFAEALITFVSDNSVLHRLISGVMTSKEIILGLCLLSLVLSMILMVIIRYISRILVWILTFLLILGSLAGTGVLWWLYAKQRK--SPKETVIPDQPQVA----EAN--------LRALLIYAISATVFTVILFLVMLVMRKRVALTIALFHVAGKVFIHLPLLVFQPFWTFFALVLFWVYWIMTLLFLGTAGSAVQNEQ----------------------------GFVEFKMSGPLQYMWWYHVVGLIWISEFILACQQMTVAGAVVTYYFTRDKR-NLPFTPILASVNRLIRYHLGTVAKGSFIITLVKIPRMILMYIHSQLKGK---ENACARCVLKSCICCLWCLEKCLNYLNQNAYTATAINSTNFCTSAKDAFVILVENALRVAAINTVGDFMLFLGKVLIVCSTGLAGVMLLNYQQDYTVWVLPLIIVCLFAFLVAHCFLSIYEMVVDVLFLCFAVDTKYNDG-SPGREFYMDKVLMEFVENSRKAMKEAGK---GGVAD-------ARELKPMVGGD------------------------EGA---------------------------------------------------------------------------------------------------------------------------------------- Crassostrea_gigas -------------------MPCFNFLQDSAEDKADLTNP-IKNRGCTDIIILILFVLFWAGMIFIAAFSITHGDAWRLVYGYDSFGNTCDEDNTGKAVENVSFSGMNMEGKGFVFILD------ILDPVNSMKLCVNKCPGQDLNTTVDIARFAVTEGSYLCRYDIKDTDYSADLVK--KGICPGR-VFASEPL--LNRCVPKQIFSTAG-------------DIFAKFFDFVNSSDLFQKVLHDLMTGWREMLILCFVALGFGALMVLLIRFLASVIVWFIITIAIIGSIAGTAGLWWTYMDKKRFIDDKEDDNIPLLNVD----IDS--------EQAFMIYSIIATVLTVILLLVILVMRKRIGLTVTLFHEAGKCLADVPILLLQPLWTFIILVFFFVYWIIILAFLATAEKATVDKTT---------------------------GFVRYTEHENVSYLWWYHLIGLIWTSEFIIACQQLVVSGAVATWYFTRDKK-NLSCT-ICKSTKLLIFHHLGSVAFGAFIITLVKLPRWILMYMQKKTKGS---QNTCVQYAMKCCICCLWCLEKCLKYLNQNAYTVVAIQGTNFCSSAKKAFMTLVSNALRVAAINSVGDFVLFLGKIGVCAATGAVGIFWFKSKEELNYYAIPVLLVCIFAYFIAHCFLSTYEMVIDALLLCFCHDTDINDG-SPERRYYASVSLQKYIEEGSNQITAISK----GDE-----------------EPASP------------EAARL----------------------------------------------------------------------------------------------------------------------------------------------- Homo_sapiens -------------------MGCCSSASSAAQSSKREWKP-LEDRSCTDIPWLLLFILFCIGMGFICGFSIATGAAARLVSGYDSYGNICGQKN--TKLEAVPNSGMDHTQRKYVFFLDPCNLDLINRKIKSVALCVAACPRQELKTLSDVQKFAEINGSALCSYNLKPSEYTTSPKS--SVLCPKLPVPASAPIPFFHRCAPVNISCYA--------------KFAEALITFVSDNSVLHRLISGVMTSKEIILGLCLLSLVLSMILMVIIRYISRVLVWILTILVILGSLGGTGVLWWLYAKQRR--SPKETVTPEQLQIA----EDN--------LRALLIYAISATVFTVILFLIMLVMRKRVALTIALFHVAGKVFIHLPLLVFQPFWTFFALVLFWVYWIMTLLFLGTTGSPVQNEQ----------------------------GFVEFKISGPLQYMWWYHVVGLIWISEFILACQQMTVAGAVVTYYFTRDKR-NLPFTPILASVNRLIRYHLGTVAKGSFIITLVKIPRMILMYIHSQLKGK---ENACARCVLKSCICCLWCLEKCLNYLNQNAYTATAINSTNFCTSAKDAFVILVENALRVATINTVGDFMLFLGKVLIVCSTGLAGIMLLNYQQDYTVWVLPLIIVCLFAFLVAHCFLSIYEMVVDVLFLCFAIDTKYNDG-SPGREFYMDKVLMEFVENSRKAMKEAGK---GGVAD-------ARELKPMIK--------------------------------------------------------------------------------------------------------------------------------------------------------------------- Hydra_vulgaris MGCCGKNEQEPIELIAENGTANQPGKYGKTKTHDPSFNGPIKNRSCTDIICCLIFVLYIVGMLIVGFLAFSWGSPTKLLYPTDSRGNLCGVGTFADRKNLFYFDLLECIPSSLSDIYSITSCKTTQICVKDCPSQNTFYLTADKSNLYCQYEVNLNTTSKSISQLVNEGSCAKYTLQSEALAYRCIPTVVGNTLTEFLSSQSTKTNQNITSSNGKPLNEENLKWGTIAQSILLNLQNIGHRVISDIQISWYWILAAFGITMAVSLIYIFIMRWFAGLIVWLTIYLVLTITGYATYYSFTEYKRLAAN-DTSSITFVFTTNLS---SYKN-------MKSTWLVIGCICAFVLLVLILLLLALRKRISIAVQLIKEGSRSLTAMTSTLFFPIIPWFLQLILFAWFVVVLIYLSTSTSAKYEQVKNSSFTGIACDAMGAAKQFIDINNTTSCSFVIYNTNDNILRLQVFHLLGWFWLMNFIIAFGQCSLAGAFASWYWAWDKNKDIPSLPLLMSVGRTLRYHTGSLAFGSLIIAIVQLIRAALEYIEYKLTGQGAQPSPVTKFLLKCLKCCFWCLEKFLKFLNKNAYIEIAVYGKNFCVSAKNAFMLLMRNILRVAVLDKVTDFLLFIGKLSITAGMGIASFYFFHKEKNMNYYFTPIVIITVGAWVVSTAFFGVYEMAINTIFLCFLEDCERHDG-SPDKPYYMSKKLMKILNKKNKKTIDEK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Lingula_anatina ---------------MCGCCGCGDDGKDTEDGGQRGSNPMVKKRGCTDIIVLVVFILFWVGMIYIAVYSIVNGDAFRLLYGYDSYGNTCGEKNEMTVMSN--FSGKDFHDRKYVFFMD------IIRPKSSLEVCVEKCPDRELKNAQELIAFYNETGVSLTRYDITPYECTDKDLQNTKGPCPVFPVHHSADI--LSRCIPASFSNFTS-------------NLKETVLGYLNEFDIFRYVIADLYASWKLMLLLAGIAFVLAIAVVVLIRFIASVVVWVILALAIIGSLAGTGFLWWTYVEKKNSMDMKTANEIPFLQIE----IDS--------ENAFLAYSIIATILTVILLLVILVLRKRIALAVALFNEAGKCIVAVPMILVQPVWTFICLILFYVYWVVVLAYISTAGTAVLDKDT---------------------------GFVNYEESQPVRYMWWYHLVGLIWTSEFIIACQQLVVAGAVAKWYFTRDKK-TLKNP-LGDAVCMLILHHMGSVAFGAFIITLVKLPRWILMYLHEKLNGS---QNKCAQYCLKCCICCLWCLEKCLKFLNQNAYTIVAIRGTNFCSSARKAFTTIVSNVLRVAAINSVGDFILFLGKVAVMTGTGAIGILMFKGDPNLHYFFIPVLLVFVFSYFIAHGFLSIYEMVIDALLLCFCEDCQINDGVTPGREYYMDPSLMKFVKNSSEAIAALNKRRDGGGEDVTDGGVPARESTPLRGEQPSPGGKADVTDDQQQETARI----------------------------------------------------------------------------------------------------------------------------------------------- Manacus_vitellinus ------------------------------KSSKREWKP-LEDHSCTDVPWLLLFILFCIGMGFICGYSIATGAAARLLSGYDSYGNICGQKN--VKVEGIVNSGLDLTHKKYVFFLDPCNIDIVHQKIKSLALCVSACPRKELKTLADIQKFAETNGSTLCSYELQSSEYTTDPRA--AKLCPKYPVPESAPIPFFHRCAPVNISCYA--------------KFAEALITFVSDSSVLHRLISGVMTSKEIIMGLCLLSLVLSMILMVIIRYISRVLVWIVTILVILGSLGGTGVLWWLYAKKRM--SAS----ALETQIA----KDN--------LQALLIYAIAATVFTVILFLIMLIMRKRVALTIALFHVAGKVFIHLPLLVFQPFWTFFVLILFWAYWITVLLFLGTTGSPVPNEE----------------------------GFVEFRMVGPLKYMWWYHAVGLIWISEFILACQQMTVAGAVVTYYFTREKR-NLPFTPILASVNRLVCYHLGTVAKGSFIITLVKIPRMILMYIQTQLKGK---ENACARCMLKACICCLWCLEKCLTYLNQNAYTATAINSTNFCTSAKDAFVILVENALRVAAINTVGDFMLFLGKVLIVCSTGLAGVMLLNYQRDYTIWVLPLIIVCLFAFLVAHCFLSIYEMVVDVLFLCFAIDTKYNDG-SPGREFYMDKVLMEFVENSRKSMKEAGR---GGGAE-------SRELKPM----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Mus_musculus -------------------------------SSKREWKP-LEDRSCTDIPWLLLFVLFCIGMGFICGFSVATGAAARLVSGYDSYGNICGQRN--AKLEAIPNSGLDHTHRKYVFFLDPCNLDLINRKIKSIALCVAACPRQELKTLSDVQKFAEINGSALCSYNIKPSEYTLTSKS--SGFCPKLPVPASAPIPFFHRCAPVNISCYA--------------KFAEALITFVSDNSVLHRLISGVMTSKEIILGLCLLSLVLSMILMVIIRYISRVLVWILTVLVILGSLGGTGVLWWLYAKQRR--SPKEAVIPEQLQIA----EDN--------LRALLIYAISATVFTVILFLIMLVMRKRVALTIALFHVAGKVFIHLPLLVFQPFWTFFALVLFWAYWIMTLLFLGTTGSAVQNEQ----------------------------GFVEYKISGPLQYMWWYHVVGLIWISEFILACQQMTVAGAVVTYYFTRDKR-NLPFTPILASVNRLIRYHLGTVAKGSFIITLVKIPRMVLMYIHSQLKGK---ENACARCMLKSCICCLWCLEKCLSYLNQNAYTATAINSTNFCTSAKDAFVILVENALRVAAINTVGDFMLFLGKVLIVCSTGLAGIMLLNYQQDYTVWVLPLIIVCLFAFLVAHCFLSIYEMVVDVLFLCFAIDTKYNDG-SPGREFYMDKVLMEFVENSRKAMKEAGK---GGAAD-------ARELKPMLRKR------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pteropus_alecto ----MLKNLETTPGQSTYLLKAVFPQKDKLKSSKREWKP-LEDRSCTDIPWLLLFILFCIGMGFICGFSVATGAAARLVSGYDSFGNICGQKN--AKLEGIPNSGMDHTHRKYVFFLDPCNLDLINRKIKSVALCVAACPRQELKTLSDVQKFADINGSALCSYTLKPSEYTIPSKA--SGVCPKLPVPASAPIPFFHRCAPVNISCYA--------------KFAEALITFVSDNSVLHRLISGVMTSKEIILGLCLLSLVLSMILMVIIRYISRVLVWIVTVLVILGSLGGTGVLWWLYAKQRK--SPKETVIPEQLQVA----EDN--------LRALLIYAISATVFTVILFLIMLVMRKRVALTIALFHVAGKVFIHLPLLVFQPFWTFFALVLFWAYWIMTLLFLGTAGSAVQNEQ----------------------------GFVEFRVSGPLQYMWWYHVVGLIWISEFILACQQMTVAGAVVTYYFTRDKR-NLPFTPILASVSRLIRYHLGTVAKGSFIITLVKIPRMILMYLHSQLKGK---ENACARCVLKSCICCLWCLEKCLNYLNQNAYTATAINSTNFCTSAKDAFVILVENALRVAAINTVGDFMLFLGKVLIVCSTGLAGIMLLNYQQDYTVWVLPLIIVCLFAFLVAHCFLSIYEMVVDVLFLCFAIDTKYNDG-SPGREFYMDKVLMEFVENSRKAMKEAGK---GGVAD-------ARELKPMEALQRIISTLANKNDEIQNFIDTLNQTLKGVQENSSNILTELDEEFDSLYSILDEVKESMINSIKQEQARKLQELQSQLSQCNNALENSEELLEFATRSLDIKEAEEFSKVQKKDKLWVDSKYMQKDHQQMRSGSLALFLDGQVAKTPPNVVRLEPFRMGMKMTDTK Rattus_norvegicus -------------------MGCCSSAS-AAQSSKREWKP-LEDRSCTDIPWLLLFVLFCIGMGFICGFSVATGAAARLVSGYDSYGNICGQRN--AKLEAIANSGLDHTHRKYVFFLDPCNLDLINRKIKSMALCVAACPRQELKTLSDVQKFAEINGSALCSYNIKPSEYTLTAKS--SAFCPKLPVPASAPIPFFHRCAPVNISCYA--------------KFAEALITFVSDNSVLHRLISGVMTSKEIILGLCLLSLVLSMILMVIIRYISRVLVWILTILVILGSLGGTGVLWWLYAKQRS--SPKETVIPEQLQIA----EDN--------LRALLIYAISATVFTVILFLIMLVMRKRVALTIALFHVAGKVFIHLPLLVFQPFWTFFALVLFWAYWIMTLLFLGTTGSAVQNEQ----------------------------GFVEYKISGPLQYMWWYHVVGLIWISEFILACQQMTVAGAVVTYYFTRDKR-NLPFTPILASVNRLIRYHLGTVAKGSFIITLVKIPRMILMYIHSQLKGK---ENACARCMLKSCICCLWCLEKCLSYLNQNAYTATAINSTNFCTSAKDAFVILVENALRVAAINTVGDFMLFLGKVLIVCSTGLAGIMLLNYQQDYTVWVLPLIIVCLFAFLVAHCFLSIYEMVVDVLFLCFAIDTKYNDG-SPGREFYMDKVLMEFVENSRKAMKEAGK---GGAAD-------ARELKPMLRKR------------------------------------------------------------------------------------------------------------------------------------------------------------------- Strongylocentrotus_purpuratus -----------------------------------------------------------MDLGYVTYLALRDGNPDRLIYGDDSYGNICGKKN--NPIENVSLSGRDMTDK---------------------------------------------------------------------------------------------------------------------------------PALADIEKSWREIVYLCLIAFGLSITVVIALRFLAAYIIWSMVFGFILGSMGGSGFLWYMWYIARAALRETPAEYNDWLNLSPGSNVDSGLSPDFRTLSPLHTPLRNTENITAILLLILLVMFKRIALVVTLFKEAGKAIGAMPFLLTQPLWTSLFLLSFCAAWVYIYLYIATAGHPKATPD----------------------------GLVEYVKDSFSKYMGWYYIFGLLWVTQFILACQECTIAGAIAEWFFARDK--SLLSTPILKSIYRIIRYHLGSLAFGSLLIAIIMFIRIVLGYIQSKLKGA---KSAPAQYCLKCMQCILWLFEKVLRYINRNAYIEIAIYGYNFCKAAQKAFSVLVSNALRVAAINSVGDFLLLLGKFAVTACVVVIGLQLLQDREDLNCYAIPIALAGVCAFFISHVFLLVYEMAIDTLFLCFCEDSERNDG--VQKPYFMSKQLMTFVENAKKAQAISKD-----AKD------AAKEARV------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Xenopus_laevis -----------------------MGCCGSTQNSKRDWRP-LEEHSCTDIPWLLLFILFCVGMGFICGFSIATGAASRLVFGYDSYGNICGQKN--TKIEGFINSGLDHSNNKYVFFLDPCKLDLVNRKIKSIALCVSECPREELQTLNDVKKFAETNGSALCDYSLTPSQYTTDSRA--PSLCPKLPVPKSAPIPFFHRCAPVNISCYA--------------KFAEALITFVSDNSVLHRLISGVMTSKEIIMGLCLLSLVLSMILMVIIRYISRVLVWIITILVVLGSLGGTGVLWWLYADNKK--SLNENLPPDQLQVS----KDN--------LQALLVYAIAATVFTVILLLMMLIMRKRVALTIALFNVAGKVFIHLPLLVFQPFWTFFALLLFWVYWVMVLLFLGTAGDPFTNEQ----------------------------GFVEFRINGPLQYMWWYHLVGLIWISEFILACQQMTIAGAVVTYYFTRNKN-DLPFTPILASVNRLIRYHLGTVAKGAFIITLVKIPRMILMYIHSQLKGK---ENACARCMLKSCICCLWCLEKCLAYLNQNAYTATAINSTNFCTSAKDALVILVENALRVAAINTVGDFMLFLGKILIVSCTGLAGIMLLNYQRDYTVWVLPLIIVCLFAFLVAHCFLSIYEMVVDVLFLCFAIDTKYNDG-SPGKEFYMDKVLMEFVEDSRRALKEP-----GSTAE-------GRELKPMASGTSTA---------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN TREES; TITLE 'Metazoan Choline Transporter-like Proteins'; LINK TAXA = Taxa1; TRANSLATE 1 Crassostrea_gigas, 2 Lingula_anatina, 3 Xenopus_laevis, 4 Mus_musculus, 5 Homo_sapiens, 6 Rattus_norvegicus, 7 Strongylocentrotus_purpuratus, 8 Hydra_vulgaris, 9 Bos_mutus, 10 Pteropus_alecto, 11 Manacus_vitellinus; TREE Imported_tree_1 = [&R] ((((((((4:0.00414922,6:0.0021866):0.01274693,(9:0.02546154,10:0.01536046):0.00402752):0.01484204,5:0.012993):0.01484204,11:0.06236946):0.01855265,3:0.06698759):0.30030624,(1:0.23531656,2:0.19789846):0.09428673):0.15181532,7:0.37083368):0.07372483,8:0.6067685); END;