#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 March 29, 2024; 8:10 GMT TreeBASE (cc) 1994-2008 Study reference: Fory P., Triplett L.R., Ballen C., Abello J., Duitama J., Aricapa M., Prado G., Correa F., Hamilton J., Leach J., Tohme J., & Mosquera G. 2013. Comparative analysis of two emerging rice seed pathogens. Phytopathology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S14408] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=37; TAXLABELS Agrobacterium_tumefaciens_C5A Burkholderai_pseudomallei_T6SS3 Burkholderai_pseudomallei_T6SS5 Burkholderai_thailandensis_T6SS5 Burkholderia_gladioli_BSR3_YP_004348376 Burkholderia_gladioli_BSR3_YP_004359059 Burkholderia_gladioli_BSR3_YP_004362835 Burkholderia_gladioli3848s_contig16 Burkholderia_gladioli3848s_contig265 Burkholderia_glumae_AU6208_1 Burkholderia_glumae_AU6208_2 Burkholderia_glumae_AU6208_3 Burkholderia_glumae_AU6208_4 Burkholderia_glumae_BGR1_YP_002907865 Burkholderia_glumae_BGR1_YP_002907919 Burkholderia_glumae_BGR1_YP_002908402 Burkholderia_glumae_BGR1_YP_002908734 Burkholderia_glumae_BGR1_YP_002910292 Burkholderia_glumae_LMG2196_1_Contig156 Burkholderia_glumae_LMG2196_2_Contig4 Burkholderia_glumae_LMG2196_3_Contig26 Burkholderia_glumae_LMG2196_4_Contig199 Burkholderia_glumae32525_contig300 Burkholderia_glumae32525_contig36 Burkholderia_glumae32525_contig468 Burkholderia_glumae32525_contig64 Burkholderia_pseudomallei_T6SS1 Burkholderia_pseudomallei_T6SS2 Burkholderia_pseudomallei_T6SS4 Burkholderia_pseudomallei_T6SS6 Burkholderia_thailandensis_T6SS1 Burkholderia_thailandensis_T6SS2 Burkholderia_thailandensis_T6SS4 Burkholderia_thailandensis_T6SS6 Ralstonia_eutropha_YP_725168 Ralstonia_eutropha_YP_841946 Vibrio_cholerae_O1 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M17629] TITLE Burkholderia_T6SS; LINK TAXA = Taxa1; DIMENSIONS NCHAR=217; 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 ] [ . . . . . . . . . . . . . . . . . . . . . ] Agrobacterium_tumefaciens_C5A MA-------SVHEKLERVRKPRVHIKYEVETEGAMVVKELPFVVGVLGDFSGN---PTQPLKPFGERKFVQIDRDNFDEVMRRMTPGLNISVANTLQKD---GTDMQVNLK--------FESMDDFEPGAVVQQVPALKALLDARNELRDLLSKADRSEDLERMLEGILQNKTDLAT------------LVSELKEKSGAGE--------------- Burkholderai_pseudomallei_T6SS3 MSAS----SSSQKFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGK---PVAPLPAVADRRFLDIDIDNFDERMKAIKPRVAFAVDNTLSGD---GQLM-VDMT--------FESIEDFSPAAIARMVGPLRQLLEARTQLANLQTYMDGKSGAETLVNQLLQDPALLRS------LAAAPKPQLAGGPDAGNARGAKDAPDTANHDSDA Burkholderai_pseudomallei_T6SS5 ----------MTTNGSVAPKERVNIVYRPATGDAQAEVELPLKVLVLGEFSTA-----ADKPPLEELSPVNVDKDDFNDVMRAQNLQLTLSVPNLLDDQAGEDDRLSVTLG--------FDSVHDFSPDAIVEKVPELKQLIALRDALKALKSPIGNIPGFRRRIQEIVADKGARKQ------------LLDEL----GLDEQ-------------- Burkholderai_thailandensis_T6SS5 ----------MTTNGSVAPKERVNIVYRPATGDAKAEVELPLKVLVLGEFSTA-----DDKPPIEELAPVNVDKDDFNDVMKAQRLTLALSVPNLLDDQAGEDDRLSVALG--------FESIADFSPDAIVETVPELKQLVALRDALKALKGPLGNIPGFRKRIQEIVADKGARKQ------------LLDEL----GLDEQ-------------- Burkholderia_gladioli_BSR3_YP_004348376 MATR----QSSQKFIARNRAPRVQIEYDVELYGAQKKVQIPFVMGVMSDLSGA---NAGELPPIEERKALEIDVDNFDSRMQSMKPRVNFTVPNTLTGE---GNLE-VDIS--------FESMDDFSPAAVARKVDSLARLLEARTQLANLGTYLDGKVGAEKLIAQALKDPALLQS------LSSAPKAADTEPGQE------------------- Burkholderia_gladioli_BSR3_YP_004359059 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSEE---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLQ----------------ALAKQSGGGDKEGE----------- Burkholderia_gladioli_BSR3_YP_004362835 MSAS----SSSQKFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGK--HPSEPLPAVTDRRFLEIDIDNFDERMKAIRPRVAFAVPNTLTGE---GQMM-VDMT--------FESMEDFSPAAIARKVEPLRQLLEARTQLANLQTYMDGKSGAEALVTQLLQDPALLKS------LAAAPKPERH---DAGAAD-----PSEAN----- Burkholderia_gladioli3848s_contig16 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAMEPRAAYQVENKLSEE---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLQ----------------ALAKQSGGGDKEGE----------- Burkholderia_gladioli3848s_contig265 MATR----QSSQKFIARNRAPRVQIEYDVELYGAQKKVQIPFVMGVMSDLSGA---NAGELPPIEERKALEIDVDNFDSRMQSMKPRVNFTVPNTLTGE---GNLE-VDIS--------FESMDDFSPAAVARKVDSLARLLEARTQLANLGTYLDGKVGAEKLIAQALKDPALLQS------LSSAPKAADTEPGQE------------------- Burkholderia_glumae_AU6208_1 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEADG-------------- Burkholderia_glumae_AU6208_2 -S------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVL------------------------------------------- Burkholderia_glumae_AU6208_3 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PLEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDA------------------- Burkholderia_glumae_AU6208_4 ------------------PKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELA---------------------- Burkholderia_glumae_BGR1_YP_002907865 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PIEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDATAGE--------------- Burkholderia_glumae_BGR1_YP_002907919 ----------------------------MHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELAQVATAATQPEGQA--------- Burkholderia_glumae_BGR1_YP_002908402 MS------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVLGQAAVAAQPAVPDQPEVPAVPAVPADGDKPAVEAVPGKPAVKG Burkholderia_glumae_BGR1_YP_002908734 ----------MDSFQREIPKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELAQVATAATQPEGQA--------- Burkholderia_glumae_BGR1_YP_002910292 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEADGKPDDGKNSGE---- Burkholderia_glumae_LMG2196_1_Contig156 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEAD--------------- Burkholderia_glumae_LMG2196_2_Contig4 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PIEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDA------------------- Burkholderia_glumae_LMG2196_3_Contig26 -----------DSFQREIPKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELA---------------------- Burkholderia_glumae_LMG2196_4_Contig199 MS------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVL------------------------------------------- Burkholderia_glumae32525_contig300 MS------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVLGQAAVAAQPAVPDQPEVPAVPAVPADGDKPAVEAVPGKPAVKG Burkholderia_glumae32525_contig36 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PLEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDATAGE--------------- Burkholderia_glumae32525_contig468 ----------MDSFQREIPKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELAQVATAATQPEGQA--------- Burkholderia_glumae32525_contig64 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEADGKPDDGKNSGE---- Burkholderia_pseudomallei_T6SS1 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEIKELPFVVGVVGDLAG--Q-SEIEQPKLRDRKFVNIDRDNFDDVMKAIEPRATFQVENRLSEA---GGKFAVDLK--------FRSINDFNPDEVVGQVEPLRRLLEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLE----------------ALKKSADGGDKQGE----------- Burkholderia_pseudomallei_T6SS2 MAIS----NSSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PLEPLPAVGDRKFFSIDIDNFDERMKAMKPRVAFSVPNTLSGD---GQLM-VDIT--------FESMDDFSPAAIAKKVDALSQLLDARTQLANLQTYMDGKSGAENLVSKVLKDPALLSA------LAKAPKPVAEQAENRESKEKH------------- Burkholderia_pseudomallei_T6SS4 MVRQ----KDGQKFIGESRAPRVQIEYDVEVYGSQKKVELPFVAGVMADLSGD---NVEPLGPVEDRRFQEIDVENFDERMAQIAPSLSYHVKNVLTND---GTLIPIDLT--------FTSMESFEPADVVKRIPELSTLLEARNRLKELLTYMDGKAAAEDVIQELLKSPQWANE------ADAA-EQSGGAGEGGDHQPEEGAK---------- Burkholderia_pseudomallei_T6SS6 MTSKYKASASGQKFIARNRAPRVQIEYDVETYGAERKVQLPFVMGVIADLAGK---RAEPLPDLPERKFLEIDVDNFDERMKSIAPRVAFQVPNTLSGD---GMLS-VDMT--------FESIDDFSPAAIARNVDALRRLLDARTELSNLLSYMDGKHGAEQLIENAINDPALLAS------LVRQPLAADAEGGARQPV-TGTEDDPEIRHE--- Burkholderia_thailandensis_T6SS1 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEIKELPFVVGVVGDLAG--Q-SEVEQPKLRDRKFVNIDRDNFDDVMKAIEPRATFQVENRLSDA---GGKFAVDLK--------FRSINDFNPDEVVGQVEPLRRLLEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLE----------------ALKKGADGGDKQGE----------- Burkholderia_thailandensis_T6SS2 MAIS----NSSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PIEPLPAVGDRKFFSIDIDNFDERMKAMKPRVAFSVPNTLSGD---GQLM-VDIT--------FESMDDFSPAAIAKKVDALSQLLDARTQLANLQTYMDGKSGAENLVSKVLKDPALLSA------LAKAPKPAAQQAENRESKEKH------------- Burkholderia_thailandensis_T6SS4 MVRQ----KDGQKFIGESRAPRVQIEYDVEVYGSQKKVELPFVAGVMADLSGD---NTEPLGPVEDRRFQEVDVENFDERMAQIAPSLSYHVKNVLTND---GTLIPIDLT--------FTSMESFEPAAVVKRIPELSTLLEARNRLKELLTYMDGKAAAEDVIQELLKSPQWANE------ADAAPEQSGGAGEGADHQPEEGAK---------- Burkholderia_thailandensis_T6SS6 MTSKYKASASGQKFIARNRAPRVQIEYDVETYGAERRVQLPFVMGVIADLAGK---RAEPLPDLPERKFLEVDVDNFDERMKSIAPRVAFQVPNTLSGD---GMLS-VDMT--------FESIDDFSPAAIARNVDALRRLLEARTELSNLLSYMDGKHGAEQLIENAINDPELLKT------LVRQPLAASADGGAPAVADTGTADDSEIRHE--- Ralstonia_eutropha_YP_725168 MSVV----NSSQKFIARNRAPRVQIEYDVEVYGSEKRIELPFVMGVLADLSGR---PAEPLPAVADRKFLEIDIDNFDERMKAMKPRVAFAVPNTLSGD---GQLM-VDMT--------FESIEDFSPAAVAGKVDALRQLLEARTQLANLQTYMDGKSGAESLINQLLQDPALLQS------LAKAPKPR------AGDDE-----PQSPQS---- Ralstonia_eutropha_YP_841946 MS------NSLQKWVGRNRPPRVQISYDVEVGDAVEKRELPMVVGLLADLSG--Q-PAVPPPKLKERRFIEIDRDNFDGIMGKIAPRLELSVPDTM-KG---DTNLKVELR--------FDKFSDFHPESLVAQVPRLAKLLEARQQLRDLLGKLDGNDELDVLLERIVNNADELK-------LVRSEADSGAAAAQPETGDATPA----------- Vibrio_cholerae_O1 ----------MSKEGSVAPKERINIKYIPATGDAQAEVELPLKTLVVGDFKGH-----AEQTPLEERATVTVDKNNFEAVMRESELKITATVKNKLTDD--ENAELPVELN--------FKSLADFAPDAVASQVPELKKLIELREALVALKGPLGNIPAFRERLQSLLNSEESREK------------LLAELNLLSGQEEPQA------------ ; END; BEGIN TREES; TITLE Emerging_rice_seed_pathogens; LINK TAXA = Taxa1; TRANSLATE 1 Burkholderia_pseudomallei_T6SS1, 2 Burkholderai_pseudomallei_T6SS3, 3 Burkholderia_pseudomallei_T6SS2, 4 Burkholderia_pseudomallei_T6SS6, 5 Burkholderia_pseudomallei_T6SS4, 6 Burkholderai_pseudomallei_T6SS5, 7 Burkholderia_thailandensis_T6SS1, 8 Burkholderia_thailandensis_T6SS6, 9 Burkholderia_thailandensis_T6SS2, 10 Burkholderia_thailandensis_T6SS4, 11 Burkholderai_thailandensis_T6SS5, 12 Burkholderia_glumae_BGR1_YP_002910292, 13 Burkholderia_glumae_BGR1_YP_002907865, 14 Burkholderia_glumae_BGR1_YP_002908402, 15 Burkholderia_glumae_BGR1_YP_002908734, 16 Burkholderia_glumae_BGR1_YP_002907919, 17 Burkholderia_gladioli_BSR3_YP_004359059, 18 Burkholderia_gladioli_BSR3_YP_004362835, 19 Burkholderia_gladioli_BSR3_YP_004348376, 20 Burkholderia_glumae32525_contig64, 21 Burkholderia_glumae32525_contig36, 22 Burkholderia_glumae32525_contig300, 23 Burkholderia_glumae32525_contig468, 24 Burkholderia_gladioli3848s_contig16, 25 Burkholderia_gladioli3848s_contig265, 26 Ralstonia_eutropha_YP_841946, 27 Ralstonia_eutropha_YP_725168, 28 Agrobacterium_tumefaciens_C5A, 29 Vibrio_cholerae_O1, 30 Burkholderia_glumae_AU6208_1, 31 Burkholderia_glumae_AU6208_2, 32 Burkholderia_glumae_AU6208_3, 33 Burkholderia_glumae_AU6208_4, 34 Burkholderia_glumae_LMG2196_1_Contig156, 35 Burkholderia_glumae_LMG2196_2_Contig4, 36 Burkholderia_glumae_LMG2196_3_Contig26, 37 Burkholderia_glumae_LMG2196_4_Contig199; TREE Tree1 = [&R] ((((((((32:0.0,35:0.0)0.1960:0.0,21:0.0)0.2110:0.0,13:0.0)1.0000:0.07476887,(3:0.0,9:0.0)1.0000:0.05135726)0.8920:0.04887383,(27:0.04595641,(2:0.0579834,18:0.04821129)0.8580:0.0374038)0.8740:0.04687678)0.7770:0.07183099,((4:-0.00664621,8:0.03970406)1.0000:0.22455707,(19:0.0,25:0.0)1.0000:0.26515674)0.4700:0.02322173)0.8790:0.19093476,(5:-3.9824E-4,10:0.0166584)1.0000:0.45854514)0.9930:0.41813477,(((((31:0.0,37:0.0)0.2010:0.0,22:0.0)0.1800:0.0,14:0.0)1.0000:1.04758659,26:0.45241341)0.8430:0.24409516,((1:0.00966818,7:0.00659198)0.8540:0.04814691,(12:-0.00102253,(20:-0.00193743,(30:-0.00368112,(34:-0.00701167,(17:0.00509382,24:0.0029707)0.8230:0.02340457)0.1850:0.00368112)0.1010:0.00193743)0.1570:0.00102253)0.8840:0.06825835)0.9980:0.36187448)0.4740:0.07181233,(28:0.23870194,(((6:0.09852436,11:0.05888305)0.9640:0.32127819,29:0.4119929)0.9960:0.58579135,(16:0.00403226,(15:0.0,(23:0.0,(33:0.0,36:0.0)0.2150:0.0)0.1360:0.0)0.6740:0.00403226)1.0000:0.56006869)0.9920:0.53676815)0.7350:0.1961246); END;