#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 April 26, 2024; 19:03 GMT TreeBASE (cc) 1994-2008 Study reference: Boyden G.S., Donoghue M.J., & Howarth D.G. 2012. Duplications and expression of RADIALIS-like genes in Dipsacales. International Journal of Plant Sciences, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S12770] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=84; TAXLABELS Acanthocalyx_alba_1A Acanthocalyx_alba_1B Acanthocalyx_alba_2A Acanthocalyx_alba_2B Acanthocalyx_alba_3 Antirrhinum_majus_AmRL1 Antirrhinum_majus_RADIALIS Antirrhinum_majus_RL2 Antirrhinum_majus_RL3 Antirrhinum_majus_RL4 Arabidopsis_thaliana_AtRL1 Arabidopsis_thaliana_AtRL2 Arabidopsis_thaliana_AtRL3 Arabidopsis_thaliana_AtRL4 Arabidopsis_thaliana_AtRL5 Arabidopsis_thaliana_AtRL6 Bournea_leiophylla_RAD Centranthus_ruber_2Ba Centranthus_ruber_2Bb Cryptothladia_chinensis_1A Cryptothladia_chinensis_1Ba Cryptothladia_chinensis_1Bb Cryptothladia_chinensis_2A Cryptothladia_chinensis_2Ba Cryptothladia_chinensis_2Bb Cryptothladia_chinensis_3 Diervilla_sessilifolia_1B Diervilla_sessilifolia_2A Diervilla_sessilifolia_2B Dipelta_floribunda_1A Dipelta_floribunda_1B Dipelta_floribunda_2B Dipsacus_pilosus_2Ba Dipsacus_pilosus_2Bb Dipsacus_pilosus_2Bc Fedia_cornucopiae_2Ba Fedia_cornucopiae_2Bb Fedia_cornucopiae_2Bc Gratiola_officinalis_RAD Heptacodium_miconioides_1A Heptacodium_miconioides_1B Heptacodium_miconioides_2A Heptacodium_miconioides_2B Kolkwitzia_amabilis_2A Kolkwitzia_amabilis_2B Lonicera_maackii_1A Lonicera_morrowii_2A Lonicera_x_bella_1A Lonicera_x_bella_1B Lonicera_x_bella_2A Lonicera_x_bella_2B Lonicera_x_bella_3 Morina_longifolia_1B Morina_longifolia_2A Morina_longifolia_2Ba Morina_longifolia_2Bb Morina_longifolia_3 Populus_trichocarpa_eugene3.00020323 Populus_trichocarpa_fgenesh4_pm.C_LG_IV000458 Populus_trichocarpa_gw1.57.329.1 Populus_trichocarpa_gw1.V.1367.1 Sambucus_canadensis_1A Sambucus_canadensis_2A Sixalix_atropurpurea_1A Sixalix_atropurpurea_2Ba Sixalix_atropurpurea_2Bb Symphoricarpos_occidentalis_1A Symphoricarpos_orbiculatus_1B Symphoricarpos_orbiculatus_2A Symphoricarpos_orbiculatus_2B Symphoricarpos_orbiculatus_3 Valerianella_eriocarpa_1A Valerianella_eriocarpa_2B Valerianella_locusta_2B Veronica_montana_RAD Viburnum_acerifolium_1B Viburnum_acerifolium_2A Viburnum_acerifolium_2B Vitis_vinifera_GSVIVT01031975001 Vitis_vinifera_GSVIVT01031982001 Vitis.vinifera_GSVIVT01018944001 Weigela_hortensis_1B Weigela_hortensis_2A Weigela_hortensis_2B ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M13174] TITLE 'RADIALIS-like genes'; LINK TAXA = Taxa1; DIMENSIONS NCHAR=291; 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] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .] Acanthocalyx_alba_1A ATGGCTTCGACT---------------CGTGGTTCTGGCCGCCCTTGGTCCGCCAAGGAGAACAAAGCCTTCGAAAGAGCATTGGCGGTTTACGACAAAGACACCCCAGACCGTTGGGCTAACGTGGCTAGGGCCGTG---GAGGGACGAACACCGGAAGAAGTGAAGAAGCACTATGAAATTCTAGTGGAGGATATCAAGTATATTGAGAGTGGGAAAGTGCCCTTCCCCAACTACAGGACC---ACCGGTGGT---AACATGAAA---------------ACTGACGAG Acanthocalyx_alba_1B ---------------------------------------------------------------------------AGGGCGTTGGCGGTGTTCGACAAGGACACCCCCGACCGTTGGGACAACGTGGCAAGGGCCGTG---GGGGGCCGGACCCCAGAAGAAGTGAAGAGGCATTATGAAATCCTCGTGGAAGACATCAAGTTTATAGAGAGCGGTAGAGTTCCCTTCCCAAACTACAGG--------------------------------------------------- Acanthocalyx_alba_2A ----------------------------------------------------------------------------------------------------------------------ACAACATTGCGAGAGCGGTG---GGTGGAAAATCTGCGGAGGAAGTGAAAAGGCACTATGAAATCCTCATAGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Acanthocalyx_alba_2B ----------------------------------------------------------------------------------------------------------------------ACAACATTGCGAGGGCGGTG---GGTGGAAAATCAGCAGAGGAAGTGAAAAGGCACTACGAAATCCTCATAGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Acanthocalyx_alba_3 ------------------------------------------------------------------------------------------------------------------TGGCAGAATATCGCGAGGGCTGTG---GGTGGAAAATCGGCAGAAGAAGTGAAAAGGCATTACGAGATTTTAATTGCGGATCTCAAGCGTATTGAGTCCGGCGGTGTGCCTTTCCCCAACTAT------------------------------------------------------ Antirrhinum_majus_AmRL1 ---------------------------------------------------------------------------AGGGCATTGGCGGTTTACGATCAAGAAACCCCCGATCGATGGGCCAATGTGGCGAGGGCCGTTGGAGCTGGACGTACCGTGGAAGAAGTGAAGAGGCACTATGAGATACTTTTGGAAGACATTGGATACATAGAAAGTGGCAAAGTGGCATATCCTAACTATAGG--------------------------------------------------- Antirrhinum_majus_RADIALIS ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCCAAGGCTGTT---GAAGGCAAAACTGCCGAGGAAGTGGAGAGGCATTATCAACTCCTTGTGAAAGACGTCAAGCATATCGAGAACGGACATGTTCCCTACCCCAACTACAAA--------------------------------------------------- Antirrhinum_majus_RL2 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCCAGGGCCGTT---GGTGGCAAAACAGCTGAGGAAGTGAAGAGGCATTACGAAATCCTTGTGCAGGATGTCAAGCATATCGAGAATGGCCGTGTGCCGTTCCCCAACTACAGG--------------------------------------------------- Antirrhinum_majus_RL3 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCCAGGGCCATT---GGTGGCAAAACCGCTGAGGAAGTGAAGAGGCATTATGAAATCCTTGCGGAGGATGTCAAGCATATCGAGAATGGCCGTGTGCCGTACCCCAACTACAGG--------------------------------------------------- Antirrhinum_majus_RL4 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCCAGGGCCGTT---GGTGGCAAAACCGCTGAGGAAGTGAAGAGGCATTACGAAATCCTTGTGCAGGATGTCAAGCATATCGAGAATGGA--------------------------------------------------------------------------- Arabidopsis_thaliana_AtRL1 ------------------------------------------------------------------------------------GCGGTGTATGACAAGGATACCCCTGACCGGTGGTACAATGTAGCCAGGGCCGTT---GGTGGCAAAACGGCTGAGGAGGTGAAGAGGCATTACGAAATCCTTGTGGAGGATGTCAAGCATATC------------------------------------------------------------------------------------ Arabidopsis_thaliana_AtRL2 ------------------------------------------------------------------------------------GCGGTATTTGATAAGGACACTCCCGACCGTTGGCAGAATATTGCCAAGGCAGTG---GGAGGAAAATCTGCTGAGGAAGTGAAAAGGCATTATGAAATCCTCATAGAAGACCTTAGGCACATA------------------------------------------------------------------------------------ Arabidopsis_thaliana_AtRL3 ATGGCATCCAGCTCAATG---TCCTCCCGCAGCTCTGGCTCATCCTGGACTGCCAAGCAAAACAAAGCCTTTGAAGAGGCGCTTGCAGTGTATGACAAGGACACCCCTGACCGCTGGTACAATGTTGCCAGGGCTGTT---GGTGGGAAAACCGTGGAGGAAGTGAAGAGGCACTATGAGATCCTTGTTGAGGATATCAAGAGCATCGACTCAGACAAAGTGCCCTTCCCCAATTACAAG------ACTACCGGAGCTAGTGGCCGGTCCAAC---ATGAGCGACCAGGAA Arabidopsis_thaliana_AtRL4 ATGGCATCCAATTCTCTCAACTCTTCACGTAACTGTAGTTCCTCTTGGACCCCCAAGCAAAACAAACTATTCGAAAAGGCCCTGGCTTTGTATGACAAGGACACCCCTGACCGCTGGCATAATGTTGCCAAAGCTGTG---GGTGGGAAATCTGCAGAGGAAGTGGAGAGGCACTATGAAATTCTCATCAAGGATGTCAGGGAAATTGAGTCTGGTCGGGTTCCATTCCCTAATTACAGGTCA---AGT---GGA---------AACAGCAAC------------------ Arabidopsis_thaliana_AtRL5 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCCAGAGCTGTT---GGCGGCAAAACAGCAGACGAAGTTAAGAGGCATTATGAGCTTCTTGTGGAGGATGTTAAGCATATCGAAAATGGACGCGTACCATACCCTAACTACAGG--------------------------------------------------- Arabidopsis_thaliana_AtRL6 ------------------------------------------------------------------------------------GCGGTTTATGACAAAGATACCCCTGACAGGTGGTACAATGTGGCTAGAGCTGTA---GGTGGAAAAACAGCTGAGGAAGTTAAGAGGCATTATGAGCTTCTGGTGGAAGATGTTAAACATATCGAAAATGGACGCGTACCGTACCCTAACTACAGA--------------------------------------------------- Bournea_leiophylla_RAD ------------------------------------------------------------------------------------------------------------------TGGCAGAATATTGCGAGGGCAGTG---GGTGGGAAATCTGCGGAGGAAGTGAAAAGGCATTATGAAATCCTCATAGAAGACCTTAGGCACATTGAGTCTGGCAATGTCCCGTACCCCAACTACAGA--------------------------------------------------- Centranthus_ruber_2Ba ----------------------------------------------------------------------------------------------------------------------ACAATGTGGCCAAGGCTGTT---GACGGCGAAACTGCCGAGGAAGTGCAGAGGCATTATGAACTCCTTGTGAAGGACGTCAAACAT--------------------------------------------------------------------------------------- Centranthus_ruber_2Bb -------------------------------------------------------------------------------------------------------CTCCCGACCGTTGGCAGAATATTGCCAAGGCAGTG---GGTGGAAAATCTGCAGAGGAAGTGAAAAGGCATTATGAAATCCTCATAGAAGACCTTAGGCACATCGAGTCT------------------------------------------------------------------------------ Cryptothladia_chinensis_1A ------------------------------------------------------------------------------------------------------------------------AACATAGCCAGGGCAGTT---AGCGGAAAATCCGCGGAGGAAGTAAGGCGGCATTACGAGGTTCTAGAGAAGGACATTATGCAGATTGAAACTGATCAGGTTCCTATTCCAAATTATGGAGCC---ATTGCCACCAAATCTAGAGGCTACGGC---------AATGAGCAA Cryptothladia_chinensis_1Ba ATGGCATCAGGCTCAATG---TCTTCTTATGGCTCTGGCTCA---TGGACTGTTAAGCAGAACAAAGCCTTTGAGCGTGCTCTAGCAGTCTATGACCAAGACACTCCGGACCGTTGGCACAATGTTGCTAGAGCTGTT---GGTGGTAAAACACCAGAAGAAGCTAAGAGACAGTATGACCTTCTAGTTCGTGACATCGAAAGCATCGAGAATGGTCACGTGCCATTCCCTGACTACAAGACT---ACTACAGGAAAC---AGCAACAGAGGCAGGCTGCGTGATGAGGAA Cryptothladia_chinensis_1Bb ----------------------------------------------------------------------------------------------------------------------ACAACATTGCGAGGGCGGTT---GGTGGAAAATCAGTGGAGGAAGTGAAAAGGCACTACGAAATCCTCATCGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Cryptothladia_chinensis_2A ----------------------------------------------------------------------------------------------------------------------ACAACATTGCGAGAGCGGTG---GGTGGAAAATCTGCGGAGGAAGTGAAAAGGCACTATGAAATCCTCGTAGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Cryptothladia_chinensis_2Ba ----------------------------------------------------------------------------------------------------------------------ACAACATTGCAAGGGCGGTT---GGTGGAAAATCGGCCGAGGAGGTGAAAAGGCACTATGAAATCCTTGTCGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Cryptothladia_chinensis_2Bb ----------------------------------------------------------------------------------------------------------------------AGAATATTGCGAGGGCAGTG---GGTGGAAAATCGGCAGAGGAAGTTAGAAGGCATTATGAAATCCTCATTGAAGACCTTAGGCAT--------------------------------------------------------------------------------------- Cryptothladia_chinensis_3 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCTAGAGCTGTT---GGAGGCAAAACAGCGGAGGAAGTTAAGAGGCACTATGAGCTTCTGGTGGAGGATGTTAAGCATATCGAACATGGACGCGTACCGTACCCTAACTACAGG--------------------------------------------------- Diervilla_sessilifolia_1B ATGGCATCAAGCTCAATG---TCTTCTCAGAGCTCTGGCTCG---TGGACTGCTAAGCAGAACAAAGCCTTTGAGCAGGCTCTAGCAACCTATGACCAGGACACTCCTAACCGTTGGCAAAATGTTGCCAAAGTCGTG---GGTGGAAAAACAACAGAGGAGGTAAAGAGACACTACGAACTCTTAGTGCAAGACATCAACAGCATAGAGAACGGTCATGTTCCATTCCCAAACTACAGGACT---AGTGGAGGC------TGCACTAATGGCAGGCTTAGTCAGGAGGAA Diervilla_sessilifolia_2A ----------------------------------------------------------------------------------------------------------------------A{CT}AATGTGGCCAAGGCTGTT---GGTGGCAAAACCCCCGAAGAGGTGAAGAAGCAGTACGAACTCCTCGTTCAAG{AG}CGTTAAGCAT--------------------------------------------------------------------------------------- Diervilla_sessilifolia_2B ------------------------------------------------------------------------------------GCGGTATATGATAAGGACACTCCCGACCGTTGGCAGAATATTGCCAGGGCAGTG---GGTGGAAAATCTGCTGAGGAAGTGAAAAGGCATTATGAAATCCTCATAGAAGACCTTAGGCACATC------------------------------------------------------------------------------------ Dipelta_floribunda_1A ATGGCATCAAGCTCCGTG---TCCTCTCGCGGTTCGGGCTCG---TGGACTGCTCAGCAGAACAAAGCCTTTGAAAGGGCTTTGGCTGTTTATGACAGGGACACACCCGACCGTTGGCATAATGTAGCCAGGGCAGTT---GGTGGAAAAACTGCTGAAGAAGTGAAAAGGCATTACGAAATCCTCGTGGAGGATGTCAAGCATATTGAGTCAGGCCGAGTTCCCTTCCCTAATTACAGGACT------ACCGGGGCA---AATGGCCACTCAAAG---ACTGGTGAGGAA Dipelta_floribunda_1B ---------------------------------------------TGGACCGCGAAGGAAAACAAGGCGTTCGAGCAGGCATTAGCAGTTTATGACAAGGACACTCCTGATCGTTGGGTCAACGTGGCTAAGGCTGTG---CCTGGACGAACCGTTGAAGAAGTGAAGAGACATTATGAAATTCTTGTGGAGGATGTGAAGAGTATCGAGAGTGGGAAAGTACCATTCCCTAATTACAGG--------------------------------------------------- Dipelta_floribunda_2B ----------------------------------------------------------------------------------------------------------------------ATAATGTGGCCAAGGCTGTT---GGTGGCAAAACCCCTGATGAGGTGAAGAGGCATTATGAACTCCTCGTTGAAGATGTCAAGCAT--------------------------------------------------------------------------------------- Dipsacus_pilosus_2Ba ----------------------------------------------------------------------------------TAGCGCTATTTGATAAGGACACTCCCGACCGTTGGCATAACGTGGCGAAGGCCGTT---GGTGGAAAATCAGAGGAGGAAGTAAAAAGGCATTACGAGATTCTTGTGAAGGATATTATGCGAATTGAATCCGGC--------------------------------------------------------------------------- Dipsacus_pilosus_2Bb ---------------------------------------------------------------------------------------------------------------------------------------------GGTGGAAAAAC{AG}G{CT}{CT}GAGGAAGTTAAGAGGCATTATCAACTCCTTGTTGAGGATGTCAATCATATCGAGAATGGC--------------------------------------------------------------------------- Dipsacus_pilosus_2Bc ------------------------------------------------------------------------------------GCGGTGTATGACAAAGATACCCCTGACAGGTGGTATAATGTAGCCAAGGCCGTT---AGTGGAAAAACAGCCGAGGAAGTTAAGAGGCATTATGAACTCCTTGTGGAGGATGTCAAGCATATC------------------------------------------------------------------------------------ Fedia_cornucopiae_2Ba ---------------------------------------------------------------------------------------------------------------------------------------------GGGGGAAAAACGCCTCAGGAAGTTAAGTGGCATTATCAACTACTTGTCGCAGATGTCAAGCGTATCGAGAATGGC--------------------------------------------------------------------------- Fedia_cornucopiae_2Bb ----------------------------------------------------------------------------------TAGCGCTATTTGATAAGGACACTCCCGACCGTTGGTACAATGTGGCCAGGGCCGTT---GGTGGCAAAACCGCTGAGGAAGTGAAGACGCATTACGAAATCCTTGTGCAGGATGTCAAGCATATCGAGAATGG{AC}--------------------------------------------------------------------------- Fedia_cornucopiae_2Bc ------------------------------------------------------------AACAAGGCGTTTGAGAGAGCGCTGGCAGTGTATGACAAAGATACACCTGACAGGTGGTACAATGTAGCCAAGGCTGTT---GGAGGAAAAACGCCTGAGGAAGTTAAGCGGCATTACGAACTACTTGTAGAGGATGTTAAGCATATCGAGAATGGC--------------------------------------------------------------------------- Gratiola_officinalis_RAD --------------------------------------------------------------------------------------------------------------------------TGTGGCCAAGGCTGTT---GAAGGCAAAACTGCCGAGGAAGTGGAGAGGCATTATCAACTCCTTGTGAAGGACGTCAAGCATATCGAGAACGGACATGTTCCCTACC-------------------------------------------------------------- Heptacodium_miconioides_1A ----------------------------------------------------------------------------------------------------------------------ACAACATTGCGAGGGCACTG---GGTGGAAAATCCATGGAGGAAGTGAAAAGGCAATATGAAATCCTCATAGAGGACCTCAGGCAC--------------------------------------------------------------------------------------- Heptacodium_miconioides_1B -----------------------------------------------------------------------------------------------------------------------------------------------TGGAAAATCAGCAGAAGAAGTGAAGAGGCATTACGAGGTCCTAGAGACTAC------------------------------------------------------------------------------------------------- Heptacodium_miconioides_2A ----------------------------------------------------------------------------------------------------------------------ATAATGTGGCTAGAGCAGTT---GGCGGCAAAACAGCTGAGGAAGTGAAGAGGCATTACGAAATCCTTGTGGAGGATGTCAAGCAT--------------------------------------------------------------------------------------- Heptacodium_miconioides_2B ATGGCTTCCAACTCAATGAGCTCTAGCGCTTCT------------TGGACACGTAAGGAGAACAAATTATTTGAAAGGGCGTTGGCTACATATGACCAGGACACTCCTGACCGTTGGCATAACGTTGCAAGAGCCGTT---GGCGGCAAATCAGCTGAAGAAGTAAGGCGACACTACGAGCTCCTCATTAGGGATGTCAATGACATTGAGTCAGGGCGTTATCCACATCCCAATTACCGTTCA------------------AAT---GGAAACAACCAC------------ Kolkwitzia_amabilis_2A ----------------------------------------------------------------------------------------------------------------------ACAACATTGCAAGGGCAGTG---GGTGGAAAATC{AT}GCTGAGGAGGTGAAAAGGCACTATGAAATCCTCATAGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Kolkwitzia_amabilis_2B ----------------------------------------------------------------------------------------------------------------------A{CT}AATGTGGCTAGAGCTGTT---GGCGGCAAAACAGCCGAGGAAGTGAAGAGGCATTACGAAATCCTTGTGGAGGATGTCAAGCAT--------------------------------------------------------------------------------------- Lonicera_maackii_1A ATGGCCTCTAGTTCTATG---AGCTCG---------AGCTCTTCTTGGACGTCTAAGCAAAACAAGATGTTCGAGAGGGCTTTAGCCGTTTACGATAAAGACACTCCCGACCGTTGGCAAAACGTGGCTAAAGCAGTT---GGAAGTAAATCTGCAGAGGAAGTTAAACGTCACTACGACATCCTCGTTGAAGATCTCATGAACATCGAACAAGACTTAGTACCTTTGCCTAAATACAAAACC---GTCGATGTTGGAAGTAAATCTAGAGGC---ATCGATGATTTTGAT Lonicera_morrowii_2A ----------------------------------------------------------------------------------------------------------------------AGAATATTGCGAGGGCAGTG---GGCGGAAA{CT}TCGGC{AT}GAGGAAGTAAAAATGCATTATGAAATCCTCATCGAGGACCTTATAGGC--------------------------------------------------------------------------------------- Lonicera_x_bella_1A ATGGCTTCTAGTTCAATGAGCACCTCATCA---------------TGGACAGCTAGAGAGGACAAGCAATTCGAAATGGCGTTGGCGAAATTCGACAAGGACACTCCTGACCGTTGGCAAAAAATTGCAAGGGCAGTT---GGTGGGAAATCAACTGAAGAAGTAAAGCGACACTATGAATTGCTCCTTAGGGATGTGAATGACATTGAGTCAGGACGCTATCCACAACCTAGGTACCGTAAC---------------------------ACT---AAT------------ Lonicera_x_bella_1B ----------------------------------------------------------------------------------------------------------------------ATAACGTGGCCACGGCCGTG---GGTGGAAAATCAGCAGAAGAAGTGAAGAGGCATTACGAG--------------------------------------------------------------------------------------------------------------- Lonicera_x_bella_2A ----------------------------------------------------------------------------------------------------------------------ATAATGTGGCTAGAGCTGTT---GGCGGCAAAACAGCCGAGGAAGTGAAGAGGCATTACGAAATCCTTGTGGAGGATGTCAAGCAT--------------------------------------------------------------------------------------- Lonicera_x_bella_2B ----------------------------------------------------------------------------------------------------------------------ACAATGTGGCTAGAGCTGTT---GGCGGCAAAACCGCTGAGGAAGTGAAGAGGCATTACGAAATCCTTGTGGAGGATGTCAAGCAT--------------------------------------------------------------------------------------- Lonicera_x_bella_3 ------------------------------------------------------------------------------------------------------------------TGGCAAAATATTGCGAGGGCAGTA---GGGGGGAAATCTGTAGAGGAAGTGAAAAGGCACTATGAAATCCTCGTAGCAGACCTTAGGCACATTGAGTCCGGCAATGTCCCGTACCCAAACTACAGA--------------------------------------------------- Morina_longifolia_1B ---------------------------------------------TGGACGCCGAAGCAAAACAAACTATTCGAGAAGGCATTAGCTAAGTACGATAAGGACACTCCCGACCGATGGCAAAACATCGCTAGGGCCGTC---GGGGGCAAATCCGCCGAGGAAGTAAAAAGGCACTATGAGATTCTTGTGGAGGATCTCAAGCACATTGAATCTGGAAATGTCCCATATCCTAAATACGTA--------------------------------------------------- Morina_longifolia_2A ----------------------------------------------------------------------------------------------------------------------AGAATATTTTGAGGGCAGTG---GGTGGAAAATCGGCTGAGGAAGTGAAAAGGCATTATGAAATCCTCATTGAAGACCTTAGGCAT--------------------------------------------------------------------------------------- Morina_longifolia_2Ba ----------------------------------------------------------------------------------------------------------------------A{CT}AATGTGGCCAAGGCTGTT---GGTGGCAAAACTGCCGAGGAAGTCAAGAGGCATTATGAGCTCCTCGTGGAGGACGTCAAGCAT--------------------------------------------------------------------------------------- Morina_longifolia_2Bb ----------------------------------------------------------------------------------------------------------------------ATAATGTGGCCAGGGCCGTT---GGCGGCAAAACGGCTGAGGAGGTGAAGAGGCAATACGAAATCCTTGTGGAGGATGTCAAGCAT--------------------------------------------------------------------------------------- Morina_longifolia_3 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCTAGAGCTGTT---GGAGGCAAAACAGCGGAGGAAGTTAAGAGGC??TATGAGCTTCTGGTGGAGGATGTTAAGCATATCGAACATGGACGCGTACCGTACCCTAACTACAGG--------------------------------------------------- Populus_trichocarpa_eugene3.00020323 ------------------------------------------------------------------------------------------------------------------TGGTAGAATGTGGCTAGAGTTATT---GGTGGAAAAACAGCTGAGGAAGTTAAGAGGCATTATGAGCTTTTGGTGGAAGATGTTAAGCATATCGAAAATGGACACGTACCCCAACTAC----------------------------------------------------------- Populus_trichocarpa_fgenesh4_pm.C_LG_IV000458 ----------------------------------------------------------------------------------------------------------------------AGAATATTGCAAGGGTGGTG---GGTGGAAAATCTGCAGAGGAAGTGAAGAGGCACTACGAAGTCCTCGTAGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Populus_trichocarpa_gw1.57.329.1 ATGGCATCAGGG---------TCTCGCATGGGCTCTGGC---TTATGGACTTCAAAGCAAAACAAACTGTTTGAAAAGGCTCTAGCCTTGTATGACAAGGACACCCCAGACCGTTGGCAGAATGTAGCCAAGGCTGTG---GGTGGGAAGTCTGCCGAGGAAGTGAAGAGACACTATGAGATCCTCATTGAGGACCTCAAACATATCGAATCGGGCCATGTTCCGATTCCTAATTACAAG------TCCACTGGA---AGCAAC---AGC------ATTGGTGATCAAGAA Populus_trichocarpa_gw1.V.1367.1 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCTAGAGCTGTT---GGTGGCAAAACAGCTGAGGAAGTTAAGAGGCATTATGAGCTTCTGGTGGAGGATGTTAAGCATATCGAAAATGGACGTGTACCCTACCCTAACTACAGG--------------------------------------------------- Sambucus_canadensis_1A ------TCTTCA---------------AATGGCTCCGGCTCCTCTTGGACAGCCAAACAAAATAAGCTATTCGAGAAGGCCCTGGCTGTATACGACAAAGACACCCCAGACCGCTGGCAAAATGTGGCCAAGGCCGTG---GGTGGCAAGTCTCCTGAAGAAGTTAAGAGGCACTATGATCGTCTCGTGGAAGATCTCGTGTACATAGAATCCGGCCAAGCCCCTCTGCCGAATTACAAG------CCCTCTGGC---AGCAATTGGAGC------------TGGGAAGAA Sambucus_canadensis_2A ----------------------------------------------------------------------------------------------------------------------ACAACATTGCAAGGGCAGTG---GGTGGAAAATCAGCCGAGGAGGTGAAAAGGCACTACGAAATCCTCATAGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Sixalix_atropurpurea_1A ATGGCATCAAGTTCGATGACATCTAGTTCA---------------TGGACACAAAAGCAAAATAAGCAGTTCGAGGAGGCTTTAGCCATGTACGGTAATGATACACCGGACTGCTGGCAAAATATAGCCCGAAAAGTT---GGTGGAAAATCGGCTGAGGAAATAAGGAGGCATTATGAGGTGTTAGTTAAGGAAATTATGAAGATTGAAACTGATCAAGTTCCAATTCCAAATTATAATAAA---GTGAAGGGG---TCCAACAGCAGA------------GGATATGGC Sixalix_atropurpurea_2Ba ----------------------------------------------------------------------------------TAGCGCTATTTGATAAGGACACTCCCGACCGTTGGCATAACGTGGCGAAGGCCGTG---GGTGGAAAATCAGAGGAGGAAGTAAAGAGGCATTACGAGATCCTTGTGAAGGATATTATGCGAATAGAATCCGGC--------------------------------------------------------------------------- Sixalix_atropurpurea_2Bb ------------------------------------------------------------------------------------GCCGTGTATGATAAAGATACACCCGACCGTTGGCAGAACATTGCACGCGCAGTA---GGTGGAAAATCAGCAGAAGAAGTGAAAAGACATTACGAAATCCTCATTCAAGATCTTAGGCATATC------------------------------------------------------------------------------------ Symphoricarpos_occidentalis_1A ATGGCGTCAAACTCA------------AGAAGTTCAATCTCACCATGGACGTTTAGTCAAAACAAGATGTTCGAGAGGGCCTTGGCAGTTTACGACAAGGACACACCCGACCGATGGCACAATGTGGCAAAAGCTGTC---GGAGGGAAAACTGTAGAAGAAGTGAAGCGCCACTATGACATTCTCGTCGAGGATCTCATCAACATCGAGACTGGTCGTGTCCCTTTGCCCAATTACAAGACC---TTCGAATCTAACTCAAGAAGCATCAAT---------GACTTTGAC Symphoricarpos_orbiculatus_1B ----------------------------------------------------------------------------------------------------------------------ACAATGTGGCCAAGGCTGTT---GAAGGCAAAACTGCCGAGGAAGTGGAGAGGCATTACGAG--------------------------------------------------------------------------------------------------------------- Symphoricarpos_orbiculatus_2A ----------------------------------------------------------------------------------------------------------------------ATAATGTGGCCAAGGCTGTT---GGTGGCAAAACCCCCGAGGAGGTGAAAAGGCATTACGAACTTCTTGTTGAGGATGTTAAGCAT--------------------------------------------------------------------------------------- Symphoricarpos_orbiculatus_2B ----------------------------------------------------------------------------------------------------------------------ATAACGTGGCGAAGGCCGTG---GGTGGAAAATCAGAGGAGGAAGTAAAAAGGCATTACGAGATTCTTGTGAAGGATATTATGCGA--------------------------------------------------------------------------------------- Symphoricarpos_orbiculatus_3 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCCAGAGCTGTT---GGCGGCAAAACAGCTGAGGAGGTTAAGAGGCATTATGAGCTTCTTGTGGAGGATGTTAAGCATATCGAAAATGGACGCGTACCATGCCCAAACTACAGG--------------------------------------------------- Valerianella_eriocarpa_1A ATGGCATCAAGCTCCATGACATCTTCACGTGGCTCGTCCTCCTTGTGGACGCCTAAGCAAAATAGACAATTTGAGGAGGCGTTGACCATGTTCGATAAGGACACACCCGACCGTTGGCAAAACATAGCGAGACGAATT---GATGGGAAATCAGCCGAGCAAGTGAGGAGGTATTATGAGGAACTACTCAAGGACATTACTCGTATTGAAAATGACCAAGTGCCAATTCCAAATTACAAAACCAATAACCGAGGATAT---ATATGGCAA--------------------- Valerianella_eriocarpa_2B ----------------------------------------------------------------------------------TAGCGCTATTTGATAAGGACACTCCCGACCGTTGGTACAATGTCGCCAAGGCTGTT---GGTGGCAAAACCGCTGAAGAAGTGAAGAGGCATTATGAACTACTTGTGGAGGATGTCAAGCATATCGAGAATGGC--------------------------------------------------------------------------- Valerianella_locusta_2B ------------------------------------------------------------AACAAGGCGTTTGAAAGGGCACTGGCTGTGTATGACAAGGACACACCTGACCGGTGGTACAATGTGGCCAGGGCCGTT---GGTGGCAAAACAGCTGAGGAAGTGAAGAGGCATTAC{AG}AAATCCTTGTGCGGGATGTCAAGCATATCGAGAATGGC--------------------------------------------------------------------------- Veronica_montana_RAD ------------------------------------------------------------------------------------------------------------------TGGTACAATGTGGCCAAGGCTGTC---GAAGGCAAAACTGCCGAGGAAGTGGAGAGGCATTATGAACTCCTTGTGAAGGATGTGAAGCATATCGAGAACGGACATGTTCCCTACCCCAACTACAAA--------------------------------------------------- Viburnum_acerifolium_1B ATGGCTTATTTC------ACGTCTTCACATGGTTCTAGCTCCTCTTGGACGCCCAAACAAAACAAGCTGTTTGAGAAGGCACTGGCTGTCTATGACAAAGACACCCCAGACCGCTGGCAAAATGTGGCCAAGGCTGTG---GGTGGCAAGTCGGCAGAAGAAGTTAAGATGCACTACGATCGTCTTGTGGAGGATCTTACATATATAGAATCCGGCCAAGCTCCACTGCCAAACTACAAG------CCCTCTGGG---AGCAAT---AGTACG------------------ Viburnum_acerifolium_2A ----------------------------------------------------------------------------------------------------------------------ACAATGTGGCTAGAGCTGTT---GGCGGCAAAACCGCTGAGGAAGTGAAGAGGCATTACGAAATCCTTGTGAAGGATGTCAAGCAT--------------------------------------------------------------------------------------- Viburnum_acerifolium_2B ----------------------------------------------------------------------------------------------------------------------ACAACATTGCAAGGGCAGTG---GGTGGAAAATCGGCTGAGGATGTTAAAAGGCACTATGAAATCCTCATAGAGGATCTTAGGCAC--------------------------------------------------------------------------------------- Vitis_vinifera_GSVIVT01031975001 ----------------------------------------------------------------------------------------------------------------------ACAATGTTGCCAAGGCCGTT---GG{GT}GG{AC}AAAACTGCCGAGGAAGTGAAGAGGCATTAC{GT}AG--------------------------------------------------------------------------------------------------------------- Vitis_vinifera_GSVIVT01031982001 ------------------------------------------------------------------------------------------------------------------TGGTACAATGTCGCCAAGGCGGTT---GGCGGAAAAACTGCTGAGGAAGTGAAGAGGCATTATGAGGTCCTTGTGGAGGATGTGAAACATATCGAGAATGGACGTGTCCCCTTCCCCAACTACAGG--------------------------------------------------- Vitis.vinifera_GSVIVT01018944001 ATGGCATCCAACTCTATGACTTCTTCACGTACCTCTGGCTCCTCTTGGACACCCAAGCAAAACAAACTATTTGAAAAGGCACTGGCAAAGTATGACAAGGACACCCCTGACCGCTGGCAGAATATTGCCAAGGCCGTG---GGTGGGAAATCTGCGGAGGAAGTGAAAAGGCACTATGAAATCCTCATAGAGGATGTCAAGCACATCGAGTCCGGCAAAGTTCCATTTCCCAATTACAGG--------------------------------------------------- Weigela_hortensis_1B ----------------------------------------------------------------------------------------------------------------------ACAATGTGGCCAAGGCTGTT---GGTGGCAAAACTGCCGAGGAAGTCAAGAGGCATTATGAGCTCCTCGTGGAGGACGTCAAGCAT--------------------------------------------------------------------------------------- Weigela_hortensis_2A ----------------------------------------------------------------------------------------------------------------------ACAACATTGCAAGGGCAGTG---GGTGGAAAATCAGCCGAGG{AG}GGTGAAAAGGCACTACGAAATCCTTATAGAGGACCTTAGGCAC--------------------------------------------------------------------------------------- Weigela_hortensis_2B ------------------------------------------------------------------------------------GCGGTGTTTGACAAAGATACCCCTGACCGTTGGTACAATGTAGCTAAGGCCGTT---GGTGGAACAACGGCTCAGGAAGTTAAGTGGCGTTACCAACTACTTGAGGAAGATGTTAAGCGAATT------------------------------------------------------------------------------------ ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'RADIALIS-like genes') = 1: 1-289\3, 2: 2-290\3, 3: 3-291\3; CODONPOSSET CodonPositions (CHARACTERS = 'RADIALIS-like genes') = 1: 1-289\3, 2: 2-290\3, 3: 3-291\3; END; BEGIN TREES; TITLE RADIALI_Streebaserun; LINK TAXA = Taxa1; TRANSLATE 1 Populus_trichocarpa_eugene3.00020323, 2 Populus_trichocarpa_gw1.V.1367.1, 3 Arabidopsis_thaliana_AtRL6, 4 Arabidopsis_thaliana_AtRL5, 5 Antirrhinum_majus_RL2, 6 Antirrhinum_majus_RL4, 7 Antirrhinum_majus_RL3, 8 Symphoricarpos_orbiculatus_3, 9 Lonicera_x_bella_3, 10 Acanthocalyx_alba_3, 11 Cryptothladia_chinensis_3, 12 Morina_longifolia_3, 13 Vitis_vinifera_GSVIVT01031982001, 14 Arabidopsis_thaliana_AtRL2, 15 Arabidopsis_thaliana_AtRL1, 16 Vitis_vinifera_GSVIVT01031975001, 17 Populus_trichocarpa_fgenesh4_pm.C_LG_IV000458, 18 Bournea_leiophylla_RAD, 19 Veronica_montana_RAD, 20 Antirrhinum_majus_RADIALIS, 21 Gratiola_officinalis_RAD, 22 Diervilla_sessilifolia_2B, 23 Weigela_hortensis_2B, 24 Sixalix_atropurpurea_2Bb, 25 Dipsacus_pilosus_2Bc, 26 Dipsacus_pilosus_2Ba, 27 Sixalix_atropurpurea_2Ba, 28 Dipsacus_pilosus_2Bb, 29 Fedia_cornucopiae_2Bc, 30 Fedia_cornucopiae_2Ba, 31 Fedia_cornucopiae_2Bb, 32 Valerianella_eriocarpa_2B, 33 Valerianella_locusta_2B, 34 Centranthus_ruber_2Bb, 35 Centranthus_ruber_2Ba, 36 Heptacodium_miconioides_1A, 37 Kolkwitzia_amabilis_2B, 38 Dipelta_floribunda_2B, 39 Lonicera_x_bella_2B, 40 Symphoricarpos_orbiculatus_2B, 41 Weigela_hortensis_2A, 42 Diervilla_sessilifolia_2A, 43 Heptacodium_miconioides_2A, 44 Kolkwitzia_amabilis_2A, 45 Lonicera_morrowii_2A, 46 Lonicera_x_bella_2A, 47 Symphoricarpos_orbiculatus_2A, 48 Viburnum_acerifolium_2A, 49 Sambucus_canadensis_2A, 50 Viburnum_acerifolium_2B, 51 Morina_longifolia_2A, 52 Acanthocalyx_alba_2A, 53 Cryptothladia_chinensis_2A, 54 Morina_longifolia_2Bb, 55 Cryptothladia_chinensis_2Bb, 56 Cryptothladia_chinensis_2Ba, 57 Morina_longifolia_2Ba, 58 Acanthocalyx_alba_2B, 59 Symphoricarpos_orbiculatus_1B, 60 Lonicera_x_bella_1B, 61 Heptacodium_miconioides_1B, 62 Weigela_hortensis_1B, 63 Cryptothladia_chinensis_1Bb, 64 Acanthocalyx_alba_1B, 65 Antirrhinum_majus_AmRL1, 66 Dipelta_floribunda_1B, 67 Morina_longifolia_1B, 68 Cryptothladia_chinensis_1Ba, 69 Diervilla_sessilifolia_1B, 70 Acanthocalyx_alba_1A, 71 Cryptothladia_chinensis_1A, 72 Sixalix_atropurpurea_1A, 73 Valerianella_eriocarpa_1A, 74 Dipelta_floribunda_1A, 75 Symphoricarpos_occidentalis_1A, 76 Lonicera_maackii_1A, 77 Lonicera_x_bella_1A, 78 Heptacodium_miconioides_2B, 79 Sambucus_canadensis_1A, 80 Viburnum_acerifolium_1B, 81 Vitis.vinifera_GSVIVT01018944001, 82 Populus_trichocarpa_gw1.57.329.1, 83 Arabidopsis_thaliana_AtRL3, 84 Arabidopsis_thaliana_AtRL4; TREE Fig._2 = [&R] ((((((1,2),(3,4)),(((5,(6,7)),(8,9)),(10,(11,12)))),13),(((14,15),16),(17,((((18,19),20),21),(((22,23),(((((((24,25),26),27),28),(((29,(30,31)),(32,33)),(34,35))),36),(37,38))),((39,40),((((41,42),(((43,(44,(45,46))),47),48)),((49,50),((51,52),53))),(54,(55,((56,57),58)))))))))),((((((59,60),61),(62,(((63,64),(((65,66),67),68)),69))),(((70,((71,(72,73)),74)),((75,(76,77)),(78,79))),80)),81),(82,(83,84)))); END;