#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; 7:34 GMT TreeBASE (cc) 1994-2008 Study reference: Santos J., Correia V., & Phillips A. 2010. Primers for mating-type diagnosis in Diaporthe and Phomopsis: their use in teleomorph induction in vitro and biological species definition. Fungal Biology, 114(2-3): 255-270. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10264] [ The following blocks are input data for analysis step 5630 ] BEGIN TAXA; TITLE TaxaForAnalysisStep5630; DIMENSIONS NTAX=34; TAXLABELS Diaporthe_G_type_AB119326 Diaporthe_W_type_AB199324 Diaporthe_ambigua_CBS_114015 Diaporthe_ambigua_CBS_123210 Diaporthe_ambigua_CBS_123211 Diaporthe_angelicae_Ph_C094_2 Diaporthe_angelicae_Ph_C121_1 Diaporthe_helianthi_CBS_592_81 Diaporthe_lusitanicae_CBS_123213 Diaporthe_lusitanicae_Di_C001_7 Diaporthe_melonis_CBS_507_78 Diaporthe_neotheicola_CBS_123208 Diaporthe_neotheicola_Di_C004_1 Diaporthe_neotheicola_Ph_C190_1 Diaporthe_neotheicola_Ph_C196_1 Diaporthe_perjuncta_CBS_109745 Diaporthe_sp_Di_C005_3 Diaporthe_strumella_var_longispora_CBS_194_36 Diaporthe_vaccinii_CBS_160_32 Diaporthe_viticola_111 Diaporthe_viticola_Di_C006_2 Phomopsis_cotoneastri_Di_C005_10 Phomopsis_cotoneastri_Di_C005_4 Phomopsis_cotoneastri_Di_C005_7 Phomopsis_cotoneastri_Di_C005_9 Phomopsis_cuppatea_CBS_117499 Phomopsis_sclerotioides_CBS_296_67 Phomopsis_sp_151 Phomopsis_sp_439B4 Phomopsis_sp_Ph_C173_1 Phomopsis_sp_Ph_C180_1 Phomopsis_sp_Ph_C188_1 Phomopsis_viticola_115 Phomopsis_viticola_CBS_114016 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M4872] TITLE 'MAT 1-1-1'; LINK TAXA = TaxaForAnalysisStep5630; DIMENSIONS NCHAR=103; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 ] [ . . . . . . . . . . ] Diaporthe_G_type_AB119326 TTCGCGACTTCAGTGGAGGTTTCACAAACCTGGTGCAGTACGCAGCTGCTGCCATGCGAGAGACTCGTGTGGTCACACCTGATCGCTGGCTCAATACCTATCA Diaporthe_W_type_AB199324 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTACAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Diaporthe_ambigua_CBS_114015 TCCGAGACCACAGTGGGGGATTCAAATCCATCTTGCAATTCGCCGTTGCCGCTATCGAAGAGACTGGTTTGACTCAGCCTGACCTCTGGCTGGACGCCTACAA Diaporthe_ambigua_CBS_123210 TCCGAGACCACAGTGGGGGATTCAAATCCATCTTGCAATTCGCCGTTGCCGCTATCGAAGAGACTGGTTTGACTCAGCCTGACCTCTGGCTGGACGCCTACAA Diaporthe_ambigua_CBS_123211 TCCGAGACCACAGTGGGGGATTCAAATCCATCTTGCAATTCGCCGTTGCCGCTATCGAAGAGACTGGTTTGACTCAGCCTGACCTCTGGCTGGACGCCTACAA Diaporthe_angelicae_Ph_C094_2 TCCGCGATCACAGTGGAGGCTTCGATTCCACCATTCAATTTGCCGTTGCTGCCATCGAGGAGACTGGTTTGACTCAGCCTGACCTCTGGCTGAACACCTACAA Diaporthe_angelicae_Ph_C121_1 TCCGCGATCACAGTGGAGGCTTCGATTCCACCATTCAATTTGCCGTTGCTGCCATCGAGGAGACTGGTTTGACTCAGCCTGACCTCTGGCTGAACACCTACAA Diaporthe_helianthi_CBS_592_81 TCCGAGACCACAGTGGAGGTTTCAGCACCACCATTCAGTTCGCCGTTGCCGCCATTGAGGAGACTGGTTTGACTCAGCCGGACCTCTGGCTCAGCACCTACAA Diaporthe_lusitanicae_CBS_123213 TCCGAGACCACAGTGGAGGATTCGATTCCACCATTCAGTTCGCCGTTGCCGCCATCGAAGAGACTGGATTGACTCAGCCTGACCTCTGGCTCAACACCTACAA Diaporthe_lusitanicae_Di_C001_7 TCCGAGACCACAGTGGAGGATTCGATTCCACCATTCAGTTCGCCGTTGCCGCCATCGAAGAGACTGGATTGACTCAGCCTGACCTCTGGCTCAACACCTACAA Diaporthe_melonis_CBS_507_78 TCCGAGACCACAGTGGAGGATTCGATTCCACCATTCAGTTCGCCGTTGCCGCCATCGAGGAGACTGGTTTGACTTAGCCCGACCTCTGGCTCAGCACCTACAC Diaporthe_neotheicola_CBS_123208 TCCGAGACTTCAGCGACGGCTTCAACAGCACCTTGCAGTACGTCGTCGCTGCCATCGAGGAGACTCATTTGGTTCAGCCTGACCGCTACCTCAACATCCACAA Diaporthe_neotheicola_Di_C004_1 TCCGAGACTTCAGCGACGGCTTCAACAGCACCTTGCAGTACGTCGTCGCTGCCATCGAGGAGACTCATTTGGTTCAGCCTGACCGCTACCTCAACATCCACAA Diaporthe_neotheicola_Ph_C190_1 TCCGAGACTTCAGCGACGGCTTCAACAGCACCTTGCAGTACGTCGTCGCTGCCATCGAGGAGACTCATTTGGTTCAGCCTGACCGCTACCTCAACATCCACAA Diaporthe_neotheicola_Ph_C196_1 TCCGAGACTTCAGCGACGGCTTCAACAGCACCTTGCAGTACGTCGTCGCTGCCATCGAGGAGACTCATTTGGTTCAGCCTGACCGCTACCTCAACATCCACAA Diaporthe_perjuncta_CBS_109745 TCCGTGACTTCAGTGGCGGATTCAAAGGCATATTGCAATACGCCGTCGCTGCCATTGAAGAGACTCGTTTGGTTCCGCCTGACCAGTGGCTCAACGCCTACCA Diaporthe_sp_Di_C005_3 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Diaporthe_strumella_var_longispora_CBS_194_36 TTCGAGACCACAGTGGGGGATTCAAATCCACCTTGCAATTCGCCGTTGCCGCTATCGAAGAGACTGGTTTGACTCAGCCTGACCTCTGGCTGAACGCCTACAA Diaporthe_vaccinii_CBS_160_32 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Diaporthe_viticola_111 TTCGTGACTTCAGTGGAGGATTCCTCAACATGCTACAGTACGCCGACATTGCTGTTGCGGAGACTGGTGTGGTCCATCCTTTTCGCTGGCTCAAGACCTACCA Diaporthe_viticola_Di_C006_2 TTCGTGACTTCAGTGGAGGATTCCTCAACATGCTACAGTACGCCGACATTGCTGTTGCGGAGACTGGTGTGGTCCATCCTTTTCGCTGGCTCAAGACCTACCA Phomopsis_cotoneastri_Di_C005_10 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Phomopsis_cotoneastri_Di_C005_4 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Phomopsis_cotoneastri_Di_C005_7 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Phomopsis_cotoneastri_Di_C005_9 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Phomopsis_cuppatea_CBS_117499 TCCGAGATCACAGTGGAGGATTCGATTCCACCATTCAGTTCGCCGCTGCCGCCATCGAAGAGACTGGTTTGACTCAGCCTGACCTCTGGCTCAACACCTACAA Phomopsis_sclerotioides_CBS_296_67 TCCGAGACCACAGTGGGGGATTCAAATCCACCTTGCAATTCGCCGTTGCCGCTATCGAAGAGACTGGCTTGACTCAGCCTGACCTCTGGCTGAACGCCTACAA Phomopsis_sp_151 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Phomopsis_sp_439B4 TCCGAGATTTCAGTGGCGGCTTCAAGAGCACCCTGCAATACGCCGTTGCCGCCATCGAAGAGACTCGTTTGACTCAGCCTGACCGCTGGCTCAACACCTACAA Phomopsis_sp_Ph_C173_1 TCCGAGACTTCAGCGACGGCTTCAACAGCACCTTGCAGTTCGTCGTCGCTGCCATCGAGGAGACTCATCTGGTTCAGCCTGACCGCTACCTCAACGTCTACAA Phomopsis_sp_Ph_C180_1 TTCGAGACCACAGCGGGGGTTTCAGCTCCACCATCCAATTCGCCGTTGCTGCAATCGAGGAGACTGGTTTGACTCAGCCTGACCTCTGGCTCAACACCTACAA Phomopsis_sp_Ph_C188_1 TCCGAGATCACAGTGGAGGATTTGATTCCACCATTCAGTTCGCCGTTGCCGCCATCGAAGAGACTGGTTTGACTCAGCCTGACCTCTGGCTCAACACCTACAA Phomopsis_viticola_115 TCCGAGACTACAGTGGCGGCTTCAACAGCACCTTGCAATACGCCGTTGCCGCCATTGAAGAGGCTCGTTTGACTCAGCCTGACCGCTGGCTCAGTACCTACAA Phomopsis_viticola_CBS_114016 TCCGAGACTACAGTGGCGGCTTCAACAGCACCTTGCAATACGCCGTTGCCGCCATTGAAGAGGCTCGTTTGACTCAGCCTGACCGCTGGCTCAGTACCTACAA ; END; BEGIN CODONS; CODONPOSSET CodonPositions (CHARACTERS = 'MAT 1-1-1') = N: 1-103; CODONPOSSET * CodonPositions (CHARACTERS = 'MAT 1-1-1') = N: 1-103; END; [ The following blocks are output data for analysis step 5630 ] BEGIN TREES; TITLE Tb11289; LINK TAXA = TaxaForAnalysisStep5630; TREE Fig._3 = [&R] (((((((((Diaporthe_lusitanicae_CBS_123213,Diaporthe_lusitanicae_Di_C001_7),(Phomopsis_sp_Ph_C188_1,Phomopsis_cuppatea_CBS_117499)),Diaporthe_melonis_CBS_507_78),(Diaporthe_angelicae_Ph_C094_2,Diaporthe_angelicae_Ph_C121_1)),(Phomopsis_sp_Ph_C180_1,Diaporthe_helianthi_CBS_592_81)),(Phomopsis_sclerotioides_CBS_296_67,Diaporthe_strumella_var_longispora_CBS_194_36,(Diaporthe_ambigua_CBS_123211,Diaporthe_ambigua_CBS_123210,Diaporthe_ambigua_CBS_114015))),(Phomopsis_viticola_115,Phomopsis_viticola_CBS_114016)),(Diaporthe_W_type_AB199324,(Phomopsis_cotoneastri_Di_C005_10,Phomopsis_cotoneastri_Di_C005_9,Diaporthe_vaccinii_CBS_160_32,Phomopsis_cotoneastri_Di_C005_7,Phomopsis_sp_439B4,Diaporthe_sp_Di_C005_3,Phomopsis_cotoneastri_Di_C005_4,Phomopsis_sp_151))),(Phomopsis_sp_Ph_C173_1,(Diaporthe_neotheicola_Di_C004_1,Diaporthe_neotheicola_Ph_C196_1,Diaporthe_neotheicola_Ph_C190_1,Diaporthe_neotheicola_CBS_123208)),(Diaporthe_perjuncta_CBS_109745,(Diaporthe_G_type_AB119326,(Diaporthe_viticola_111,Diaporthe_viticola_Di_C006_2)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6897] END;