#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 May 22, 2024; 1:10 GMT TreeBASE (cc) 1994-2008 Study reference: Guo L., Hyde K.D., & Liew E. 2001. Detection and taxonomic placement of endophytic fungi within frond tissues of Livistona chinensis based on rDNA sequences. Molecular Phylogenetics and Evolution, 20(1): 1-13. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S683] BEGIN TAXA; TITLE 'P2-6a'; DIMENSIONS NTAX=14; TAXLABELS Amphisphaeria_umbrina Candida_glabrata Claviceps_purpurea Dothidea_hippophaeos Elsinoë_australis Gelasinospora_nigeriensis Glomerella_graminicola Hypocrea_rufa Ophiostoma_ulmi 'P2-6' Phaeocryptopus_gaeumannii Saccharomyces_cerevisiae Torulaspora_delbrueckii Xylaria_hypoxylon ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2263] TITLE 'ITS1 5.8S ITS2 with P2-6'; LINK TAXA = 'P2-6a'; DIMENSIONS NCHAR=580; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Amphisphaeria_umbrina AAGAGTTT---ACA-AAACTCCCA-AACCCATGTGAAT---TTACCC----CTG-TTGCCTCGGCGGA-A---GT-TACCCTGTAG-CAC-CTACCCTACAG-------CGGTTCGAGCCTACCCTGTAA----CCCGCCGGTGGATTTTGAAACTCT-TGT-TATTACAG---TGTCATCTGAGCG--TCTTATTCTAAATAA-GTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGA-TTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCATTAGTATTCTATTGG-GCATGCCTGTTCGAGCGTCATTTCGACCATT--AAGCC--------TAGCTTAGCGTTGGGAATCTACTGTCCGGGCGGAGCTACCTGTAGCTTACCCTGTAGTTCCTGAAAATGAACGGCGGATTCG--TGGTGTCCTCTGA-GCGTAGTAAT---------ATTTCTCGCT---TCTGTTAGGTGCTACGATCT--GGCAGTTAA---------CCC-AATCT-T------ Candida_glabrata AGGTGTTTTATCACACGACTCGAC--A-CTTTCTAATTACTACACACAGTGGAGTTTACTTTACTACTATCTTTTGTTCGTTGGGGGAACGCTCTCTTTCGGGG----GGGAGTTCTCCCAGTGGATGCAAACACAAACAAATATTTTTTT--AAACTAATTCAGTCAACA-CAAGA--TTTCTTTT-----AGTAGAAAACAACTTCAAAACTTTCAACAATGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCTCTGGTATTCCGGGGG-GCATGCCTGTTTGAGCGTCATTTC-CTTCTCA-AACACATTGT--G---TTTGGTAGTGAGTGATACTCGTTTT--------TGAGTTAACTTGAAATTGTAGGCCATATCAGTATGTGGGACACGAGCGCAAGCTTCTCTATTAATCTGCTGCTC-------GTTTGCGCGA-G--CGGCGGGGGTTAATACTGTATTAGGTTTTACCAACTCGGTGTTGATCTAGGGAGGG Claviceps_purpurea CCGAGTT-----TA-CAACTCCCA-AACCCATTGTGAACTTATACCC-AAAACG-TTGCCTCGGCGGACACA-GCGGTACCCGA-GCCCC-CGCAAGGGAGCAAA--GGCGCCC-----CGTCCGCCAGGGGACCAAAACTCTT-CTGTAT-ACCCATAGCGGCATGTCTG---AGTGGATTTA--A--AAAC-----AAATGA-ATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGACTTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGTATTCTGGCGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTC--AAGCCCTGCTTGG--TGTTGGGGACCGGCTCAGCGGGTGCGGG-----CTTC--GGCCCGCCCCGTGCCGCCCCCGAAATGGATCGGCGGT--CTCGTCGCAGCCTTCTTTGCGTAGTAAC---------ATAC-CACCTCGCAACAGGAGCGCGGCGCGGCCACTGCCGTAAA------ACGCCC-AACTTTTTAGA-G Dothidea_hippophaeos CGACCTAA---AAAATCGCGACCACTTCCAACCCTCTGTTGTTATAACTACCTTGTTGCTTTGGCGGGACC--GTTCGGTCCTCC-------GAGCGCACCAG-------TCCT-----CGGACAGGTGA----GCGCCCGCCAGAGT-CCAACCAAACTCTTGTTTTTAA-CCAGTCGTCTGAGTA--TAAAATTTTAATTAA-ATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTACACCACTC--AAGCACT-----G---CTTGGTATTGGGC-----ATCGTCCGTC----GAAAGGCG----------GGCGTGCCTCGAAGACCTCGGCGGGGTTT---CTCCAACTTCGG-GCGTAGTAGAGTTAAA---TCGAACGTCT-TATAAG--CTTGGTGGGACTCCATTGCCGTTAAACCTTT-------TATTTTTATA-GG Elsinoë_australis AAGGGTTTCCGAAAGGAGCCCGAACTCCCCACCCTTTGCTGTTGCGAAT--CT-GTTGCTTCGGCGGGCCC--GCCCCCCCATCCCTGGG-GGGGCGGCCGGG-------CCTCA----CCGCCCGGACA----GCGCCCGCCGGAGGACCGAATCAACTCTGTTTTT-AACCATAATGTCGGAGTA--CTTTTGTACAATCAA-ATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTTCACCAATC--AAGCCCC-----G---CTTGGTATTAGGCGCCTGGCCGCCCCCC----CCGTGGCC----------GGCCCGCCCGAAATGCATCGGCGAGG------CACCGACCCCCG-GCGTGTTAGAATTTC-----GAAACGTC---AGGAGCACCGGTGTTAAC--CTCTGCCGTGAAACCTTT-CAAAC-TATTTTTCTAA-G Gelasinospora_nigeriensis CAGAGTTG---CAA--AACTCCCACAAACCATCGCGAATC-TTACCC-GTAC-GGTTGCCTC-GGCGCTGGCGGTCCGGAAGGCCCTCGG-GCCCCCGGATCCTCGGGTCTCCC-GCTCG--CGGGAGGCTGGCCCGCCGGAGTGCCGAA--ACCAAACTCTTGATATTTTATGTCTC-TCTGAGTA--AACTT-TT-AAATAA-GTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCTCGCCAGTATTCTGGCGA-GCATGCCTGTTCGAGCGTCATTTCAACCATC--AAGCTCT---------GCTTGCGTTGGGGATCCGCGG--CTGC-----CCGC----------------GGTCCCTCAAAAACAGTGGCGGGCTCG-CTAGTCA-CACCGA-GCGTAGTAAC----------TCTACATC--GTTCTGGTCGTGCGGCGGGT-TCTTGCCGTAAA------ACCCCCCAATTTCT-AA-GG Glomerella_graminicola TCGAGTT-----AC-CG-CTCTAC-AACCCTTTGTGAAC--ATACCT--AACTG-TTGCTTCGGCGGGCAGGGGGTCCCCCCGGGGACGC-CCTCCCGGCCCC-----GCCCCC-----CTACCAGGGGACGTGGCGCCCGCCGGAGGATA--CCCAACTCTATTTTAACGACGTTTCTTCTGAGTG--GCACAAGC-AAAT-A-ATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGCATTCTGGCGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTC--AAGCTCTGCTTGG--TGTTGG-----GGCCCTACGGTTGACG-------TA------------------GGCCCTCAAAGGTAGTGGCGGACCCTCCCGG-AGCCTCCTTTGCGTAGTAAC---------TA--ACGTCTCGCA-TCGGGATCCGGAGGGACTCTTGCCGTAAA------ACCCCCCAATTTTTCAATGG Hypocrea_rufa CCGAGTT-----TA-CAACTCCCA-AACCCAATGTGAACC-ATACC--AAACTG-TTGCCTCGGCGGGGTCACGCCCCGGGTGC-GTCGC-AGCCCCGGAACCA---GGCGCCC------GCCGGAGGGACCAACCAAACTCTTTCTGTAG-TCCCCTCGCGGACGTTATTTTTACAGCTCTGAGCA--AAAATTCA-AAATGA-ATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGTATTCTGGCGG-GCATGCCTGTCCGAGCGTCATTTCAACCCTCG-AACCCCTCCGGGG--GGTCGGCGTTGGGGACTTCGGGAACCC------CTAA--GACGGGATCC----CGGCCCCGAAATACAGTGGCGGT--CTCGCCGCAGCCTCTCATGCGCAGTAGT---------TTGCACAACTCGCACCGGGAGCGCGGCGCGTCCACGTCCGTAAA------ACACCC-AACTTCTGAAATG Ophiostoma_ulmi CAGAGTTT---TTT-CAACTCCCA-ACCCTTGCGAA--CC-GTACCCCGTTCTGTTTGCTTCTGGCGGGAGGGGAGGGGCGCGTCTTCGG-GGCGCTGCCTC-TC---TCTCCCAGGTCCTTCGGGCGCCCGCCACGGCCGCGAGCCGCCTGAACCTTTTCTAAACCAGTAACGAAACGTCTGAGAA--ACAAA-CA-AAAACA-GCCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCAAAATGCGATACGTAATGCGAATTGCAGAATTCAG-GAGTCATCGAA-TCTTTGAA-CGCACATTGGGCCCGCCAGTATTCTGGCGG-GCATGCCTGTCCGAGCGTCATTTCCCCCCTCAGATGCCCTTTTGGGAGGGCTGGTGTTGGGCTCCTGCCCT-CTGC-----GTGC--G-A-----------GGGCCCTCAAAACCAGTGGCGGGCCCGTCTGGTTGGCTCCGA-GCGCAGTACCGAACGCAAGTTCTCTCTCTCGCTCTGCAGCCCCGGTCGGTGCCCAGCCGTCAACGGCGCTCGGCCCTGCTTGC--A-GG 'P2-6' CTGAGTT-----TA-CG-CTCTAC-AACCCTTTGTGAAC--ATACCTATAACTG-TTGCTTCGGCGGGTAGGGTCTCCGC-----GAC---CCTCCCGGCCTC-------CCGC-----CT-CCGGGCGGGTCGGCGCCCGCCGGAGGATA-ACCAAACTCTGATTTAACGACGTTTCTTCTGAGTG--GTACAAGC-AAAT-A-ATCAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC-AAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGCATTCTGGCGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTC--AAGCTCTGCTTGG--TGTTGG-----GGCCCTACAGCTGATG-------TA------------------GGCCCTCAAAGGTAGTCGCGAACCCTCTCGGGAGCCTCCTTTGCGTAGTAAC---------TT-TACGTCTCGCACTGGGGATCCGGAGGGACTCTTGCCGTAAA------ACCCCC-AACTTTCCAAAGG Phaeocryptopus_gaeumannii AAGGGTTA---TTCGTAGCC-CGACCTCCAA{AC}CCTTTGTTGTTATAACTACCTCGTTGCTTTGGCGGGACC--GCTCGGTC-TC--------GAGCTG-CTGG-------TCTT-----CGGCCCGGCAA----GTGCCCGCCAGAGT-CTACTCAAACTCTTGTTTT-AA-CCGGTCGTCTGAGT---TAAACTTTTAATTAA-ATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAAATCTTTGAAACGCACATTGCGCTCCCTGGTATTCCGGGGGAGCATGCCTGTTCGAGCGTCATTACACCACTC--AAGCACT-----G---CTTGGTATTAGGCC----ATCGTCCCCC----GAAAGGTG----------GGCGTGCCTCAAACACCTCGGCGGAACCT---CACCGGCTTTGG-GCGTAATAAAATTTC----TC-AACGTCT-TATAAGTACCGGTTCTGACTCCTTTGCCGTTAAACCCCA-------AACTTTTAAA-GG Saccharomyces_cerevisiae TGTGCTTTTGTTATAGGACTTAAA--ACCG-TTTCAATACAACACACTGTGGAGTTTTCATATCTTTG-CAACTTTTTCTTTGGG----------CATTCG-A-----GCAATCGGGGCCAGAGGTAACAAACACAAACAATTTTATTTATTCATTAAATTTTTGTCAAAAACAAGAATTTTCGTAACTGGAAATTTTAAAATA-TTAAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTG-?CCCCTTGGTATTCCAGGGG-GCATGC-TGTTTGAGCGTCATTTC-CTTCTCA-AACA--TTCT--G---TTTGGTAGTGAGTGATACTCTTTG----------GAGTTAACTTGAAATTGCTGGCCTTTTCA-----TTG--GATGTTTTTTT--TT-TCCAAAGAGAGGTTTCTCT------GCGTGCTTGA-GGTATAATGCAAGTACGGTCGTTTTAGGTTTTACCAACTGCGGCTAATCTTTTTTATAC Torulaspora_delbrueckii ACTGTTTCTCTGTCTGCGGTTCAC---TGCCTAAAAATTATACACACACTGGAGTTTTCTTTTAAAACACTTCTTCTTCTTTGGG----------C-TT---------GCAA--GAGCCCGGAGTTGACAAACACAAACAATTTTGTT-AT--ATTATAATCAAGTCAAAACCAA----TTTCGTTA-T-GAAATAC-AAATAA-TTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCAGGGG-GCATGCCTGTTTGAGCGTCATTTC-CTTCTCA-AAGAACTCTT--C---TTTGGTAGTGAGTGACACTCTTTCT--------AGAGTTAACTTGAAATTGCTAGCCATATAA-----TAGCTGTTGATTGCTGACTT-TGGACGGAGCGATTTGTCCA-----GTCTGCT-G-----ATACCG--ATT---GTCGTATTAGGTTTTACCAACTTCGACGG-ACGTAGTGTTAG Xylaria_hypoxylon AAGAGTTT---TGATAAACTCCCA-AACCCATGTGAA-C--TTACCT--T-CTG-TTGCCTCGGCAGGTCGC-GTCTACCCTGTGGGCAC-CTACCCTGTAGGAC----CCGACCTGGTGGTCGCGGTCATG--CCTGCCGGTGGCCCTTTAAACTTTCTGTGTATTCTAT---GTTATTCTGAGTT--GGCAACTA-AAATAA-GTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCATTAGTATTCTAGTGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTT--AAGCCCCT----GTCGCTTAGTGTTGGGAGCCTACAGTC--------------------TT---CTGTAGCTCCCTAAAGTTAGTGGCGGAGTCG--GTTTGTACTCTAG-ACGTAGTAGA---------TTCTATCTCG---TCTAT-AGTTAAGCCGGTCTCTTGCCGTAAAA------CCCCCTAATTTCTCAA-GG ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS1 5.8S ITS2 with P2-6') = N: 1-580; CODONPOSSET CodonPositions (CHARACTERS = 'ITS1 5.8S ITS2 with P2-6') = N: 1-580; END;