#NEXUS BEGIN TAXA; DIMENSIONS NTAX=42; TAXLABELS Arabidopsis_thaliana_AtSPL1 Arabidopsis_thaliana_AtSPL2 Arabidopsis_thaliana_AtSPL3 Arabidopsis_thaliana_AtSPL4 Arabidopsis_thaliana_AtSPL5 Arabidopsis_thaliana_AtSPL6 Arabidopsis_thaliana_AtSPL7 Arabidopsis_thaliana_AtSPL8 Arabidopsis_thaliana_AtSPL9 Arabidopsis_thaliana_AtSPL10 Arabidopsis_thaliana_AtSPL11 Arabidopsis_thaliana_AtSPL12 Arabidopsis_thaliana_AtSPL13 Arabidopsis_thaliana_AtSPL14 Arabidopsis_thaliana_AtSPL15 Arabidopsis_thaliana_AtSPL16 Glycine_max_GmSPL1a Glycine_max_GmSPL1b Glycine_max_GmSPL2 Glycine_max_GmSPL6 Glycine_max_GmSPL8 Glycine_max_GmSPL9 Glycine_max_GmSPL9b Glycine_max_GmSPL12b Glycine_max_GmSPL13 Glycine_max_GmSPL14 Glycine_max_GmSPL16 Glycine_max_GmSPL17 Medicago_sativa_MsSPL2 Medicago_sativa_MsSPL3 Medicago_sativa_MsSPL4 Medicago_sativa_MsSPL6 Medicago_sativa_MsSPL9 Medicago_sativa_MsSPL12 Medicago_sativa_MsSPL13 Medicago_truncatula_MtSPL1a Medicago_truncatula_MtSPL1b Medicago_truncatula_MtSPL2 Medicago_truncatula_MtSPL6 Medicago_truncatula_MtSPL8 Medicago_truncatula_MtSPL9 Medicago_truncatula_MtSPL14 ; END; BEGIN CHARACTERS; Title Differentially_expressed_SPL_genes_in_miR156OE_M._sativa_plants; DIMENSIONS NCHAR=229; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Arabidopsis_thaliana_AtSPL1 tgtcaggtcgaaaactgtgaagctgatcttagtaaagttaaggattatcatagacgccataaggtctgtgagatgcattccaaggctactagtgccactgtcggaggtatcttgcagcgcttttgtcagcaatgtagtaggttccatcttcttcaggagtttgatgaaggaaagagaagttgtcgtagacgtttggctggccataataaacgtcggaggaaaacaaat- Arabidopsis_thaliana_AtSPL2 tgtcaagttgaaggctgtaatcttgatctttcatcagctaaagactatcatcggaaacataggatttgtgaaaatcattcaaagtttcctaaagtcgttgtgagtggcgtagagcgtcggttctgccaacaatgtagcaggttccactgtctctctgagtttgatgagaagaaacgtagctgtcgccgacgtctctcagatcacaatgcaagacgtcgcaagccaaat- Arabidopsis_thaliana_AtSPL3 tgtcaggtcgagagttgtaccgcggatatgagcaaagccaaacagtaccacaaacgacacaaagtctgccagtttcatgccaaagctcctcatgttcggatctctggtcttcaccaacgtttctgccaacaatgcagcaggtttcacgcgctcagtgagtttgatgaagccaagcggagttgcaggagacgcttagctggacacaacgagagaaggcggaaaagcaca- Arabidopsis_thaliana_AtSPL4 tgccaagtagatagatgcacagctgatatgaaagaggcaaaactgtatcaccggagacacaaagtgtgtgaagttcatgcaaaggcatcttctgtctttctctcaggacttaaccaacgcttttgtcaacaatgcagtaggtttcatgacctccaagagtttgatgaagctaagagaagttgcaggaggcgcttagctggacacaatgagcgaagaaggaagagctct- Arabidopsis_thaliana_AtSPL5 tgccaggtcgataggtgcactgttaatttgactgaggccaagcagtattaccgcagacacagagtatgtgaagtacatgcaaaggcatctgctgcgactgttgcaggggtcaggcaacgcttttgtcaacaatgcagcaggtttcatgagctaccagagtttgatgaagctaaaagaagctgcaggaggcgcttagctggacacaatgagaggaggaggaagatctct- Arabidopsis_thaliana_AtSPL6 tgtcaagtttatgggtgtagtaaggatctgagctcttcgaaagattaccacaaaaggcatagagtttgcgaggctcattcgaaaacttctgtggtcatagttaatggtcttgaacagaggttttgtcaacagtgcagcaggtttcatttcctctcagagtttgatgatggcaaaagaagttgcagaaggcgattagccggtcacaatgaacgaagaaggaaacctgca- Arabidopsis_thaliana_AtSPL7 tgtcaggttccggattgtgaagcggatattagcgagctcaaagggtaccataagaggcatagggtttgtctccgttgcgctaccgccagctttgttgtgcttgatggagagaataagagatactgtcaacagtgtggaaagtttcatttgctcccggactttgatgaaggaaaacgcagctgtcggagaaagctagagcgtcacaacaacagacggaaaaggaaacct- Arabidopsis_thaliana_AtSPL8 tgccaagcagagggatgcaacgcggatctgagccacgcgaaacactaccacagaaggcacaaagtgtgcgaattccactcaaaagcatcgacggttgtagccgccggactaagccaaaggttttgccagcaatgcagcaggttccatttgctgtcggaattcgacaacgggaaacggagctgccgtaagcgacttgctgaccataaccgccgccgccgtaaatgtcac- Arabidopsis_thaliana_AtSPL9 tgccaagtggaaggttgtgggatggatctaaccaatgcaaaaggttattactcgagacaccgagtttgtggagtgcactctaaaacacctaaagtcactgtggctggtatcgaacagaggttttgtcaacagtgcagcaggtttcatcagcttccggaatttgacctagagaaaaggagttgccgcaggagactcgctggtcataatgagcgacgaaggaagccacag- Arabidopsis_thaliana_AtSPL10 tgccaaattgatggctgtgagctggatctctcatcttctaaggattatcatcgcaagcatagagtctgcgaaacgcattcaaagtgcccaaaagttgttgtgagtggcctggaacgtcgtttctgccaacagtgtagcaggttccatgctgtctcagaatttgatgaaaagaaacgaagctgccgcaaacgtctttctcatcataatgcaaggcgtcgcaagccacaa- Arabidopsis_thaliana_AtSPL11 tgccaaattgatggctgtgaactggatctctcatctgctaagggttatcatcgtaagcacaaagtctgcgaaaagcattcaaagtgcccaaaagttagcgtgagtggcctggaacgtcggttctgccaacagtgtagcaggttccatgctgtctctgaatttgatgagaagaaacgaagctgccgaaaacgtctttctcatcataatgcgaggcgtcgtaagccacaa- Arabidopsis_thaliana_AtSPL12 tgtcaggtagacaactgtggagctgatttaagcaaagttaaggattatcatagacgtcataaggtctgtgagattcattctaaagctactactgcacttgttggaggaattatgcagcggttttgtcagcaatgtagtaggtttcatgtgcttgaagagtttgatgagggaaagagaagttgccgtagacgtttggctgggcataataagcgtagaagaaaagcaaat- Arabidopsis_thaliana_AtSPL13 tgtcttgttgatggatgtgattctgattttagtaattgtagagagtatcataagagacataaagtttgtgatgttcattcaaaaactcctgtggttactattaatggtcataaacagaggttttgtcaacaatgcagcaggtttcatgctttggaggagtttgatgaagggaagagaagttgtaggaaacgtcttgatggacataatcgaagacgacggaagccgcag- Arabidopsis_thaliana_AtSPL14 tgtcaggttgataattgtactgaagatttgtctcatgctaaggattatcatagaaggcataaagtttgtgaagttcatagtaaagctactaaagctcttgttggtaaacagatgcagaggttttgccaacagtgtagcaggtttcatctgctttctgagtttgatgaggggaagagaagttgtaggcgtagattggctggccataatcgacggaggaggaaaactacg- Arabidopsis_thaliana_AtSPL15 tgccaagtggaaggttgtagaatggatctaagcaatgttaaagcttattactcgagacacaaagtttgttgcattcactctaaatcatctaaagtcattgtctctggtcttcatcaaaggttttgtcaacaatgtagcaggtttcaccagctttctgagtttgacttggagaaaagaagttgtcgcagaagactcgcttgtcataacgaacgacgaagaaaaccacaa- Arabidopsis_thaliana_AtSPL16 tgtcaggttgataattgtaaggaagatttatcaattgctaaggattatcatagaagacataaagtttgtgaggttcatagcaaagctactaaagctcttgttgggaaacagatgcagaggttttgccaacagtgtagcaggtttcatctgctttctgagtttgatgaggggaagagaagttgtaggcgtagattggatggtcataacaggcggaggagaaaaacacag- Glycine_max_GmSPL1a tgtcaagttgatggttgtagcgctgatctaagtgaagctaagccctaccataggcgtcacaaggtttgtgagtaccatgccaaggctcctgccgtactcattggagaccagcaccaacggttttgccaacaatgtagtaggtttcatgagctatcagaattcgatgactcaaaaaggagttgcagaagacgtttggctggacataatgagaggcgtcgcaaaaatgca- Glycine_max_GmSPL1b tgccaagtggacaattgtgatgctgatctgagtgaagctaagcagtaccacagaagacacaaggtttgtgagtaccatgccaaggctccttccgtacacatggcagggctgcaacaaaggttttgccaacaatgtagcagattccatgtgctatcagaatttgatgactcaaagaggagttgtagaacgcggttggctgggcataatgagaggcgtcgcaaatatgca- Glycine_max_GmSPL2 tgtcaggcagagatatgtggtgctgatttgactgttgcaaagaggtaccatcgccgtcataaggtgtgtgagcttcattccaaggctccttctgtgatggttgcaggactgaggcagaggttttgccagcaatgtagcaggttccatgagctggcagagtttgatgaagctaaaagaagctgccggagacgcttggccagacacaacgagcggcgccggaaaagcaac- Glycine_max_GmSPL6 tgtcaagtttatggttgtaacatggatcttagctcctcaaaagattaccacaaaaggcataaagtttgtgatgctcactccaaaacagctaaagttattgtaaatggaattgaacagaggttttgtcagcagtgcagcaggtttcatttgctagctgagttcgatgatggtaagcgcagttgtcgcaggcgtctagcaggacacaatgaacgccgaaggaaaccccaa- Glycine_max_GmSPL8 tgccaggccgagggttgcaatgctgatctgtcgcaagccaagcactatcaccgccgccacaaggtgtgcgagtttcactccaaagccgccaccgtcatcgccgccggcttgactcagcgattctgccagcaatgcagcaggttccatcttctttctgagtttgataacggaaaacgtagctgcaggaagagattggcagatcataatcgccgcagaagaaaaactcaa- Glycine_max_GmSPL9 tgtcaggttgagggctgcaaagtagatctgagtggtgctaaggcttactattctaggcacaaagtttgtaccatgcactccaagttccctactgttattgttgctggtttggagcaaaggttttgccaacagtgtagcaggtttcatctgctttctgaatttgatgaaggaaaacgaagctgccgcaggcgacttgctggtcataatgagcgccgacgaaagcccccg- Glycine_max_GmSPL9b tgtcaagttgaagggtgcaaagtagatctgagtgatgcaaaagcttactattctagacacaaggtctgtggcatgcactctaaatccccttcagtcattgttgctggtcttcaacaaaggttttgtcaacagtgtagcaggtttcatcagcttcctgagtttgatcaaggaaaaagaagttgccgtaggcgactagctggccataatgaacgtcggagaaagccccca- Glycine_max_GmSPL12b tgtcaggcagagatgtgtggtgctgatttgactgttgcaaagaggtaccatcgccgccataaggtgtgtgagcttcattccaaggctccttctgtgatggttgcaggactgaggcagaggttttgccagcaatgtagcaggttccaagagctggcagagtttgatgaagctaaaagaagctgccggagacgcttggccagacataacgagcggcgccggaaaagcaat- Glycine_max_GmSPL13 tgccttgtggatgggtgcaattcagatcttagcaattgtagagattatcataggcgccataaggtgtgtgagctccattccaagaccccagaggtcacaattggtggcttcaagcaaaggttctgccaacaatgtagcaggttccattcgctggagcaatttgatgaaagaaaaagaagctgcagaaaacgtttagatggacacaatagaaggagaagaaagccccag- Glycine_max_GmSPL14 tgccaggtggacaactgcagagaggatctgtcgaaggcgaaggactatcaccggagacacaaggtgtgtgaggctcatagcaaggcctccaaagcgcttctcgcgaatcaaatgcaaagattctgccagcagtgtagcaggtttcatcctctctcggagtttgatgaggggaagcggagctgccgccggagactcgccggacacaaccggcgccggcggaagacgcag- Glycine_max_GmSPL16 tgttctgttgatggatgcaattctgacctcagtgattgcagagattatcacaggcgccatagggtctgcgaaaagcactccaaaaccccggttgtgttggtgggggggaaacaacagaggttctgccaacaatgcagcaggtttcattcacttggggagtttgatgaggttaagaggagttgtaggaaacggcttgacgggcataacaggcgccggaggaaacctcag- Glycine_max_GmSPL17 tgtcaggttgcgggctgcaaagtagatctgagtggtgctaaggcttactattctaggcacaaagtttgtgccatgcactccaagtcccctactgtcactgttgctggtttggagcaaaggttttgccaacagtgtagcaggtttcatctgctttctgaatttgatcaaggaaaacgtagctgccgcaagcgacttgctggccataatgagcgccgacgaaagccccca- Medicago_sativa_MsSPL2 tgccaagcagagaggtgtggagctgatttgacggatgcaaagagataccatcgccgccataaagtgtgtgagtttcattccaaggcacctgttgtggtggttgcagggatgaggcagaggttttgtcaacaatgtagcaggttccatgacttggtagagtttgatgagtctaaaagaagctgccgcaggcggttggctggacacaatgaacggcgccggaaaaccaac- Medicago_sativa_MsSPL3 TGTCAAGTTGATAACTGTAATGCTGATCTAAGTGTTGCTAAGCAGTACCATAAGCGCCATAAGGTTTGTGAATACCATTCTAAGGCTCATTCCGTACTCATTTCAGAGCTTCAACAAAGGTTTTGCCAGCAATGTAGCAGGTTTCATGAGGTATCAGAATTTGATGACTTGAAAAGGAGTTGTAGGAGGCGTTTGGCTGGACATAACGAGAGGCGCCGCAAAAGCACG- Medicago_sativa_MsSPL4 TGTCAAGTGGAGAATTGTGATGCTGATCTTAGTGAAGCTAAGCAATATCACCGGAGACATAAGGTCTGTGAGTATCATGCCAAAGCACCTACCGTACACATTGCAGGATTGCAGCAAAGGTTTTGTCAGCAATGTAGCAGATTCCATGGACTATCTGAATTTGATGACTCAAAAAGAAGTTGCAGAAGGCGTTTGGCTGGGCATAATGAGAGGCGCCGCAAAAGTGCA- Medicago_sativa_MsSPL6 TGCCAAGTTTATGGTTGTAACATGGATCTTAGCTCCTCGAAAGATTACCACAAAAGGCATAAAGTTTGTGACGTTCACTCCAAGACAGCTAAAGTTATCGTCAATGGTGTTGAACAGAGGTTTTGTCAGCAGTGCAGCAGGTTCCATCTGGTAACTGAGTTCGACGATGGTAAGCGCAGTTGTCGCAGGCGTCTAGCTGGACACAATGAGCGCCGAAGGAAACCTCAG- Medicago_sativa_MsSPL9 TGTCAAGTTGAAGGATGTAAACTAGATCTGACTGATGCTAAAGCTTACTATTCTAGACACAAAGTTTGTAGCATGCACTCTAAGTGCCCAACTGTTACTGTTTCTGGTCTACAACAAAGGTTTTGTCAACAATGTAGCAGATTTCATCAGCTTGCTGAGTTTGATCAAGGAAAAAGAAGTTGCCGGAGACGACTAGCTGGTCATAACGAGCGTCGCAGAAAGCCCCCA- Medicago_sativa_MsSPL12 TGCCAGGTGGAAGGTTGTGGCCTCGACCTCTCTTTGGCTAAAGATTACCATCGGAAACATAGAATTTGTGACAGTCATTCCAAATCGCCTGTGGTGGTAGTAGCTGGTTTGGAGCGTCGATTTTGCCAGCAGTGTAGCAGGTTCCATGATCTCTCAGAGTTTGATGATAAAAAAAGAAGCTGCAGACGCCGTCTTTCAGATCACAATGCAAGGCGTCGCAAACCTCAG- Medicago_sativa_MsSPL13 TGTCTTGTGGATGGGTGCAATTCTGATCTTAGTAATTGTAGAGATTATCATAGGCGTCATAAGGTTTGTGAACTTCATTCTAAGACTCCAGAGGTTACAATTTGTGGCCTTAAACAAAGGTTCTGCCAACAGTGTAGCAGGTTTCATTCGCTGGAGCAATTTGATGAAAGAAAAAGAAGCTGTAGGAAACGTTTAGATGGACACAACCGAAGAAGAAGAAAACCACAG- Medicago_truncatula_MtSPL1a tgtcaggtggaggattgtcgcgcagatcttaacaacgcgaaagattatcaccgacgtcataaagtttgtgagatacattcaaaggctagtaaagcccttgtcggaaatgcgatgcagcggttctgccaacaatgtagtaggtttcacttgcttcaagagtttgatgaaggaaagagaagctgtcgaagacgtttggcaggccataataaaaggaggagaaaaacaaat- Medicago_truncatula_MtSPL1b tgtcaggttgaagactgtggtgcagatctgagtagaggcaaggattatcacagacgtcataaagtttgtgagatgcattctaaggctagtagggctcttgtgggaaatgcaatgcagaggttttgtcaacagtgtagtaggtttcacatacttgaagagttcgatgaaggaaagagaagctgtcgaagacgcttggctggccataacaaacgtagaaggaaaacaaat- Medicago_truncatula_MtSPL2 tgccaggtggaaggttgtggcctcgacctctcttttgctaaagattaccatcggaaacatagaatttgtgacagtcattccaaatcgcctgtggtggtagtagctggtttggagcgtcgattttgccagcaatgtagcaggttccatgatctctcagagtttgatgataaaaaaagaagctgcagacgccgtctttcagatcacaatgcaaggcgtcgcaaacctcag- Medicago_truncatula_MtSPL6 tgccaagtttatggttgtaatatggatcttagctcctcgaaagattaccacaaaaggcataaagtttgtgatgttcactccaagacagctaaagttatcgtcaatggtgttgaacagaggttttgtcagcagtgcagcaggttccatctagtagctgagttcgacgatggtaagcgcagttgtcgcaggcgtctagctggacacaatgagcgccgaaggaaacctcag- Medicago_truncatula_MtSPL8 tgtcaagccgaaggttgcaatgctgatctatctcaggctaagcattaccaccgccgccacaaagtttgtgagtttcactcgaaggcagccaccgtcgttgcagctgggttgactcagcggttctgccagcaatgcagcaggttccatcttctatctgagtttgataatggaaaacgtagctgcaggaagagattggctgatcataatcgtcgtaggagaaaaactcag- Medicago_truncatula_MtSPL9 tgtcaagttgaaggatgtaaactagatctgactgatgctaaagcttactattctagacacaaagtttgtagcatgcactctaaatcccctactgttactgtttctggtcttcaacaaaggttttgtcaacaatgtagcagatttcatcagcttgctgagtttgatcaaggaaaaagaagttgtcggagacgactagctggtcataatgagcgtcgcagaaagccccca- Medicago_truncatula_MtSPL14 tgtcttgtggatgggtgcaattctgatcttagtaattgtagagattatcataggcgtcataaggtttgtgaacttcattccaagactccagaggttacaatttgtggccttaaacaaaggttctgccaacagtgtagcaggtttcattcactggagcaatttgatgaaagaaaaagaagttgtaggaaacgtttagatggacacaaccgaaggagaagaaaacctcaa- ; END; BEGIN TREES; Title Differentially_expressed_SPL_genes_in_miR156OE_M._sativa_plants; LINK Taxa = Taxa; TRANSLATE [0] 1 Arabidopsis_thaliana_AtSPL1, [1] 2 Arabidopsis_thaliana_AtSPL2, [2] 3 Arabidopsis_thaliana_AtSPL3, [3] 4 Arabidopsis_thaliana_AtSPL4, [4] 5 Arabidopsis_thaliana_AtSPL5, [5] 6 Arabidopsis_thaliana_AtSPL6, [6] 7 Arabidopsis_thaliana_AtSPL7, [7] 8 Arabidopsis_thaliana_AtSPL8, [8] 9 Arabidopsis_thaliana_AtSPL9, [9] 10 Arabidopsis_thaliana_AtSPL10, [10] 11 Arabidopsis_thaliana_AtSPL11, [11] 12 Arabidopsis_thaliana_AtSPL12, [12] 13 Arabidopsis_thaliana_AtSPL13, [13] 14 Arabidopsis_thaliana_AtSPL14, [14] 15 Arabidopsis_thaliana_AtSPL15, [15] 16 Arabidopsis_thaliana_AtSPL16, [16] 17 Glycine_max_GmSPL1a, [17] 18 Glycine_max_GmSPL1b, [18] 19 Glycine_max_GmSPL2, [19] 20 Glycine_max_GmSPL6, [20] 21 Glycine_max_GmSPL8, [21] 22 Glycine_max_GmSPL9, [22] 23 Glycine_max_GmSPL9b, [23] 24 Glycine_max_GmSPL12b, [24] 25 Glycine_max_GmSPL13, [25] 26 Glycine_max_GmSPL14, [26] 27 Glycine_max_GmSPL16, [27] 28 Glycine_max_GmSPL17, [28] 29 Medicago_sativa_MsSPL2, [29] 30 Medicago_sativa_MsSPL3, [30] 31 Medicago_sativa_MsSPL4, [31] 32 Medicago_sativa_MsSPL6, [32] 33 Medicago_sativa_MsSPL9, [33] 34 Medicago_sativa_MsSPL12, [34] 35 Medicago_sativa_MsSPL13, [35] 36 Medicago_truncatula_MtSPL1a, [36] 37 Medicago_truncatula_MtSPL1b, [37] 38 Medicago_truncatula_MtSPL2, [38] 39 Medicago_truncatula_MtSPL6, [39] 40 Medicago_truncatula_MtSPL8, [40] 41 Medicago_truncatula_MtSPL9, [41] 42 Medicago_truncatula_MtSPL14; TREE Fig._6 = ((26:0.16457,(8:0.14308,(21:0.06861,40:0.05419):0.06964):0.03427):0.010225,((((14:0.03471,16:0.04018):0.08067,((1:0.07248,12:0.06787):0.02375,(36:0.07781,37:0.08009):0.02888):0.02878):0.04165,((3:0.14208,(4:0.08493,5:0.0905):0.0531):0.01876,((29:0.07333,(19:0.01017,24:0.01176):0.05824):0.0741,((17:0.08485,30:0.0862):0.00692,(18:0.06939,31:0.06219):0.02597):0.05748):0.00728):0.02175):0.00175,((7:0.25387,(27:0.15436,(13:0.10673,(25:0.05368,(35:0.01368,42:0.01263):0.03623):0.06213):0.01888):0.04382):0.00554,(((34:0.00559,38:0.00318):0.11981,(2:0.09972,(10:0.03649,11:0.03368):0.07572):0.02602):0.07391,((6:0.09529,(20:0.0375,(32:0.00853,39:0.00901):0.03268):0.06017):0.05307,((9:0.08758,15:0.08347):0.04884,((22:0.01866,28:0.0252):0.05852,(23:0.04761,(33:0.01718,41:0.00914):0.04449):0.02536):0.0345):0.03303):0.00652):0.0101):0.00949):0.010225); END;