Table S1. R2R3MYB Gene Family Classification

Table S1. R2R3MYB gene family classification

Clade / SlMYB / Gene / Synonyms / (Putative) Function / Ref
S1 / 4 / Solyc08g008480.2.1
S1 / 6 / Solyc12g096200.1.1
S1 / 8 / Solyc08g005870.1.1
S1 / 9 / Solyc08g082890.2.1
S2 / 11 / Solyc12g049350.1.1 / PREDICTED：Flavonol biosynthesis / S1; S2
S2 / 12 / Solyc01g079620.2.1 / SlMYB12 / Flavonol biosynthesis / S3
S2 / 111 / Solyc06g009710.2.1 / PREDICTED：Flavonol biosynthesis / S1;S2
S3 / 3 / Solyc06g065100.2.1
S3 / 7 / Solyc01g111500.2.1
S3 / 32 / Solyc10g055410.1.1 / THM27 / PREDICTED：Phenylpropanoid pathway / S4;S5
S3 / 54 / Solyc12g049300.1.1
S3 / 76 / Solyc05g008250.1.1
S4 / 30 / Solyc06g069850.2.1 / PREDICTED：Abiotic stress response；Hypocotyle elongation, brassinosteroid pathway / S6;S7
S4 / 31 / Solyc03g116100.2.1 / PREDICTED：Abiotic stress response；Hypocotyle elongation; Brassinosteroid pathway / S6;S7
S4 / 60 / Solyc10g081490.1.1 / PREDICTED：Drought, ABA-mediated(stomatal closure) / S8
S4 / 94 / Solyc02g087960.2.1 / PREDICTED：Abiotic and biotic stress response / S9
S4 / 96 / Solyc02g067340.2.1 / THM6 / Carotenoid metabolism / S5;S10
S5 / 0 / Solyc03g005570.2.1
S5 / 10 / Solyc05g055030.1.1
S5 / 13 / Solyc06g083900.2.1
S5 / 14 / Solyc06g053610.2.1 / THM18 / S5
S5 / 15 / Solyc09g090130.2.1
S6 / 51 / Solyc03g093940.1.1
S6 / 52 / Solyc03g093890.2.1
S6 / 95 / Solyc06g034000.1.1
S6 / 105 / Solyc06g033870.1.1
S7 / 66 / Solyc07g054960.1.1
S7 / 68 / Solyc12g005640.1.1
S7 / 72 / Solyc07g055000.1.1
S7 / 81 / Solyc07g053240.2.1
S7 / 83 / Solyc07g053230.2.1
S7 / 85 / Solyc07g054980.1.1
S8 / 34 / Solyc08g065910.1.1
S8 / 36 / Solyc07g006750.2.1
S8 / 37 / Solyc06g074910.2.1
S8 / 38 / Solyc09g008250.2.1
S8 / 48 / Solyc06g074920.1.1
S8 / 84 / Solyc02g091980.1.1
S8 / 87 / Solyc04g077260.2.1 / PREDICTED: Root development; Pattern of lateral meristem initiation; Responses to high temperature / S11;S12
S8 / 89 / Solyc11g069030.1.1 / Blind / Formation of lateral meristems / S13
S8 / 90 / Solyc12g008670.1.1
S9 / 35 / Solyc03g059200.1.1 / PREDICTED：Stamen development / S14
S9 / 80 / Solyc10g005760.1.1 / PREDICTED：Stamen development / S14
S10 / 20 / Solyc04g014470.2.1 / PREDICTED：Secondary cell wall biogenesis; Salt tolerance / S15;S16
S10 / 40 / Solyc05g014290.2.1
S10 / 42 / Solyc08g079270.2.1
S10 / 43 / Solyc11g011050.1.1 / PREDICTED：Secondary cell wall biogenesis; Salt tolerance / S15;S16
S10 / 99 / Solyc02g093740.2.1
S11 / 39 / Solyc08g076710.2.1
S11 / 107 / Solyc08g076700.1.1
S12 / 41 / Solyc07g054840.2.1 / PREDICTED：Abiotic and biotic stress response / S17;S18
S12 / 49 / Solyc10g008700.1.1 / PREDICTED：Abiotic and biotic stress response / S17;S18
S12 / 74 / Solyc10g005460.2.1 / PREDICTED：Abiotic and biotic stress response / S17;S18
S12 / 102 / Solyc02g079280.2.1 / PREDICTED：Abiotic and biotic stress response / S17;S18
S13 / 53 / Solyc04g056310.2.1
S13 / 92 / Solyc05g051550.1.1
S13 / 93 / Solyc04g074170.1.1 / PREDICTED：Light-responsive expression / S19
S14 / 16 / Solyc02g088190.2.1 / PREDICTED：Cell fate；Petal morphogenesis
S14 / 17 / Solyc05g048830.2.1
S14 / 18 / Solyc01g094360.2.1
S14 / 23 / Solyc04g005600.1.1 / PREDICTED：Cell fate；Petal morphogenesis / S20;S21
S14 / 25 / Solyc05g007690.1.1 / PREDICTED：Cell fate；Petal morphogenesis / S20;S21
S14 / 64 / Solyc05g007710.2.1 / ShMYB1 / Trichome initiation / S20;S21
S14 / 106 / Solyc01g010910.1.1 / PREDICTED：Cell fate；Petal morphogenesis / S20;S21
S15 / 26 / Solyc03g121740.1.1
S15 / 56 / Solyc02g082040.2.1
S15 / 67 / Solyc10g005240.2.1
S15 / 103 / Solyc08g081500.1.1 / THM1 / S5
S16 / 19 / Solyc03g025870.2.1
S16 / 46 / Solyc11g065840.1.1 / PREDICTED：Secondary wall biosynthesis / S22
S16 / 47 / Solyc01g087130.2.1 / PREDICTED：Secondary wall biosynthesis / S22
S17 / 50 / Solyc06g071690.2.1
S17 / 55 / Solyc10g044680.1.1
S17 / 61 / Solyc01g102340.2.1
S17 / 86 / Solyc03g112390.2.1
S18 / 5 / Solyc01g005660.1.1 / PREDICTED：Proanthocyanindins biosynthesis / S23
S18 / 82 / Solyc07g008010.2.1
S19 / 75 / Solyc10g086250.1.1 / PREDICTED：Anthocyanin biosynthesis / S24;S25;S26
S19 / 113 / Solyc10g086260.1.1 / ANT1 / Anthocyanin biosynthesis / S26
S19 / 114 / Solyc10g086290.1.1 / PREDICTED：Anthocyanin biosynthesis / S24;S25;S26
S20 / 28 / Solyc10g086270.1.1
S20 / 29 / Solyc02g089190.1.1
S20 / 71 / Solyc05g053150.1.1
S20 / 79 / Solyc09g090790.2.1
S21 / 33 / Solyc06g073640.2.1
S21 / 65 / Solyc01g009070.2.1 / GAMyb-like1 / GA signal responds / S27
S21 / 97 / Solyc11g072060.1.1
S22 / 2 / Solyc01g057910.2.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 21 / Solyc02g067760.2.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 24 / Solyc06g009480.1.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 45 / Solyc12g099140.1.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 57 / Solyc06g009410.1.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 62 / Solyc03g119370.1.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 78 / Solyc12g099120.1.1 / AIM1 / Abiotic and biotic stress response / S32
S22 / 108 / Solyc12g099130.1.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 112 / Solyc05g053330.2.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S22 / 116 / Solyc05g009230.1.1 / PREDICTED：Stamen development; Abiotic and biotic stress response / S28;S29;S30;S31;S32
S23 / 22 / Solyc09g008390.1.1 / PREDICTED：Anthocyanin biosynthesis / S33
S23 / 27 / Solyc10g083900.1.1 / PREDICTED：Anthocyanin biosynthesis / S33
S24 / 104 / Solyc01g090530.1.1 / PREDICTED：Stamen development / S34
S24 / 120 / Solyc10g019260.1.1 / PREDICTED：Stamen development / S34
S25 / 98 / Solyc06g071520.1.1 / PREDICTED：Synergid cell differentiation; Embryogenesis / S35;S36;S37;S38
S25 / 100 / Solyc09g055650.1.1 / PREDICTED：Synergid cell differentiation; Embryogenesis / S35;S36;S37;S38
S25 / 118 / Solyc03g112890.1.1 / PREDICTED：Synergid cell differentiation; Embryogenesis / S35;S36;S37;S38
S25 / 119 / Solyc06g076840.1.1 / PREDICTED：Synergid cell differentiation; Embryogenesis / S35;S36;S37;S38
S26 / 69 / Solyc10g081320.1.1 / PREDICTED：Axillary meristem regulation / S39;S40
S26 / 115 / Solyc04g064540.2.1 / PREDICTED：Axillary meristem regulation / S39;S40
S26 / 117 / Solyc05g007870.1.1 / Tf / Axillary meristem regulation / S39
S27 / 1 / Solyc09g011780.2.1
S27 / 44 / Solyc02g092930.1.1 / PREDICTED：Abiotic stress response;Gorwth regulation / S41;S42
S27 / 70 / Solyc04g078420.1.1 / PREDICTED：Abiotic stress response;Gorwth regulation / S41;S42
S27 / 73 / Solyc04g050000.1.1
S27 / 77 / Solyc04g079360.1.1 / PREDICTED：Abiotic stress response;Gorwth regulation / S41;S42
S27 / 109 / Solyc05g052850.2.1
S28 / 58 / Solyc11g073120.1.1 / PREDICTED：Root growth; Cell cycle / S43
S28 / 59 / Solyc06g005330.2.1 / PREDICTED：Root growth; Cell cycle / S43
S29 / 88 / Solyc04g005710.1.1 / PREDICTED：Stomata cell differentiation / S44;S45
S29 / 110 / Solyc05g007160.2.1
63 / Solyc10g005550.1.1
101 / Solyc07g052300.2.1
91 / Solyc09g010840.1.1 / PREDICTED：Axillary meristem regulation / S46

Supplementary references

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S2 Mehrtens F, Kranz H, Bednarek P, Weisshaar B (2005) The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol 138: 1083-1096

S3 BallesterAR, Molthoff J, de Vos R, HekkertBt, Orzaez D, Fernández-Moreno JP, Tripodi P, Grandillo S, Martin C, Heldens J, Ykema M, Granell A, Bovy A (2010) Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit color. Plant Physiol 152:71-84

S4 Mintz-Oron S, Mandel T, Rogachev I, Feldberg L, Lotan O, Yativ M, Wang Z, Jetter R, Venger I, Adato A, Aharoni A (2008) Gene expression and metabolism in tomato fruit surface tissues. Plant Physiol 147:823-851

S5 Lin Q, Hamilton WD, Merryweather A (1996) Cloning and initial characterization of 14 myb-related cDNAs from tomato (Lycopersiconesculentum cv. Ailsa Craig). Plant MolBiol 30:1009-1020

S6 Raffaele S, Vailleau F, Léger A, Joubès J, Miersch O, Huard C, Blée E, Mongrand S, Domergue F, Roby D (2008) A MYB transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in Arabidopsis. Plant Cell 20:752-767

S7 Li L, Yu X, Thompson A, Guo M, Yoshida S, Asami T, Chory J, Yin Y (2009) Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J 58:275-286

S8 Cominelli E, Galbiati M, Vavasseur A, Conti L, Sala T, Vuylsteke M, Leonhardt N, Dellaporta SL, Tonelli C (2005) A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. CurrBiol 15:1196-1200

S9 Seo PJ, Xiang F, Qiao M, Park JY, Lee YN, Kim SG, Lee YH, Park WJ, Park CM (2009) The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis. Plant Physiol 151:275-289

S10 ShuchiSmita, Ravi Rajwanshi, SangramKeshariLenka, AmitKatiyar, ViswanathanChinnusamy, KailashChanderBansal (2013) Comparative Analysis of Fruit Transcriptome in Tomato (Solanumlycopersicum) Genotypes with Contrasting Lycopene Contents. Plant MolBiol Rep 31:1384–1396

S11 Müller D, Schmitz G, Theres K (2006) Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis. Plant Cell 18:586-597

S12 Feng CP, Andreasson E, Maslak A, Mock HP, Mattsson O, Mundy J (2004) Arabidopsis MYB68 in development and responses to environmental cues. Plant Sci 167:1099–1107

S13 Schmitz G, Tillmann E, Carriero F, Fiore C, Cellini F, Theres K (2002) The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems. ProcNatlAcadSci U S A 991064-1069

S14 Zhang ZB, Zhu J, Gao JF, Wang C, Li H, Li H, Zhang HQ, Zhang S, Wang DM, Wang QX, Huang H, Xia HJ, Yang ZN (2007) Transcription factor AtMYB103 is required for anther development by regulating tapetum development, callose dissolution and exine formation in Arabidopsis. Plant J 52:528-538

S15 Cui MH, Yoo KS, Hyoung S, Nguyen HT, Kim YY, Kim HJ, Ok SH, Yoo SD, Shin JS (2013) An Arabidopsis R2R3-MYB transcription factor, AtMYB20, negatively regulates type 2C serine/threonine protein phosphatases to enhance salt tolerance. FEBS Lett 587:1773-1778

S16 Zhong R, Ye ZH (2012) MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes. Plant Cell Physiol 53:368-380

S17 Lippold F, Sanchez DH, Musialak M, Schlereth A, Scheible WR, Hincha DK, Udvardi MK (2009) AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis. Plant Physiol 149:1761-1772

S18 De Vos M, Denekamp M, Dicke M, Vuylsteke M, Van Loon L, Smeekens SC, Pieterse CM (2006) The Arabidopsis thaliana Transcription Factor AtMYB102 Functions in Defense Against the Insect Herbivore Pierisrapae. Plant Signal Behav 1:305-311

S19 Feng S, Martinez C, Gusmaroli G, Wang Y, Zhou J, Wang F, Chen L, Yu L, Iglesias-Pedraz JM, Kircher S, Schäfer E, Fu X, Fan LM, Deng XW (2008) Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451:475-479

S20 Baumann K, Perez-Rodriguez M, Bradley D, Venail J, Bailey P, Jin H, Koes R, Roberts K, Martin C (2007) Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development 134:1691-1701

S21 Jakoby MJ, Falkenhan D, Mader MT, Brininstool G, Wischnitzki E, Platz N, Hudson A, Hülskamp M, Larkin J, Schnittger A (2008) Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106. Plant Physiol 148:1583-1602

S22 Zhong R, Richardson EA, Ye ZH (2007) The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell 19:2776-2792

S23 Gonzalez A, Mendenhall J, Huo Y, Lloyd A (2009) TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation. DevBiol 325:412-421

S24 Borevitz JO, Xia Y, Blount J, Dixon RA, Lamb C (2000) Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell 12:2383-2394

S25 Gonzalez A, Zhao M, Leavitt JM, Lloyd AM (2008) Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J 53:814-827

S26 Mathews H, Clendennen SK, Caldwell CG, Liu XL, Connors K, Matheis N, Schuster DK, Menasco DJ, Wagoner W, Lightner J, Wagner DR (2003) Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport. Plant Cell 15:1689-1703

S27 Gong X, Bewley DJ (2008) A GAMYB-like gene in tomato and its expression during seed germination. Planta 228:563-672

S28 Mandaokar A, Browse J (2009) MYB108 acts together with MYB24 to regulate jasmonate-mediated stamen maturation in Arabidopsis. Plant Physiol 149:851-862

S29 Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15:63-78

S30 Devaiah BN, Madhuvanthi R, Karthikeyan AS, Raghothama KG (2009) Phosphate starvation responses and gibberellic acid biosynthesis are regulated by the MYB62 transcription factor in Arabidopsis. Mol Plant 2:43-58

S31 Cheng H, Song S, Xiao L, Soo HM, Cheng Z, Xie D, Peng J (2009) Gibberellin acts through jasmonate to control the expression of MYB21, MYB24, and MYB57 to promote stamen filament growth in Arabidopsis. PLoS Genet 5:e1000440

S32 Abuqamar S, Luo H, Laluk K, Mickelbart MV, Mengiste T (2009) Crosstalk between biotic and abiotic stress responses in tomato is mediated by the AIM1 transcription factor. Plant J 58:347-360

S33 Velten J, Cakir C, Youn E, Chen J, Cazzonelli CI (2012) Transgene silencing and transgene-derived siRNA production in tobacco plants homozygous for an introduced AtMYB90 construct. PLoS One 7:e30141

S34 Rotman N, Durbarry A, Wardle A, Yang WC, Chaboud A, Faure JE, Berger F, Twell D (2005) A novel class of MYB factors controls sperm-cell formation in plants. CurrBiol 15:244-248

S35 Kasahara RD, Portereiko MF, Sandaklie-Nikolova L, Rabiger DS, Drews GN (2005) MYB98 is required for pollen tube guidance and synergid cell differentiation in Arabidopsis. Plant Cell 17:2981-2992

S36 Shinozaki K, Yamaguchi-Shinozaki K, Urao T, Koizumi M (1992) Nucleotide sequence of a gene from Arabidopsis thaliana encoding a myb homologue. Plant MolBiol 19:493-499

S37 Wang X, Niu QW, Teng C, Li C, Mu J, Chua NH, Zuo J (2009) Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis. Cell Res 19:224-235

S38 Zhang Y, Cao G, Qu LJ, Gu H (2009) Involvement of an R2R3-MYB transcription factor gene AtMYB118 in embryogenesis in Arabidopsis. Plant Cell Rep 28:337-346

S39 Naz AA, Raman S, Martinez CC, Sinha NR, Schmitz G, Theres K (2013) Trifoliate encodes an MYB transcription factor that modulates leaf and shoot architecture in tomato. ProcNatlAcadSci U S A 110:2401-2406

S40 Lee DK, Geisler M, Springer PS (2009) LATERAL ORGAN FUSION1 and LATERAL ORGAN FUSION2 function in lateral organ separation and axillary meristem formation in Arabidopsis. Development 136:2423-2432

S41 Jung C, Seo JS, Han SW, Koo YJ, Kim CH, Song SI, Nahm BH, Choi YD, Cheong JJ (2008) Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol 146:623-635

S42 Shin R, Burch AY, Huppert KA, Tiwari SB, Murphy AS, Guilfoyle TJ, Schachtman DP (2007) The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. Plant Cell 19:2440-2453

S43 Mu RL, Cao YR, Liu YF, Lei G, Zou HF, Liao Y, Wang HW, Zhang WK, Ma B, Du JZ, Yuan M, Zhang JS, Chen SY (2009) An R2R3-type transcription factor gene AtMYB59 regulates root growth and cell cycle progression in Arabidopsis. Cell Res 19:1291-1304

S44 Lai LB, Nadeau JA, Lucas J, Lee EK, Nakagawa T, Zhao L, Geisler M, Sack FD (2005) The Arabidopsis R2R3 MYB proteins FOUR LIPS and MYB88 restrict divisions late in the stomatal cell lineage. Plant Cell 17:2754-2767

S45 Xie Z, Lee E, Lucas JR, Morohashi K, Li D, Murray JA, Sack FD, Grotewold E (2010) Regulation of cell proliferation in the stomatal lineage by the Arabidopsis MYB FOUR LIPS via direct targeting of core cell cycle genes. Plant Cell 22:2306-2321

S46 Byrne ME, Barley R, Curtis M, Arroyo JM, Dunham M, Hudson A, Martienssen RA (2000) Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature 408:967-971