Supplementary Table S2: Characteristics of Tomato Arfs and Their Orthologous Genes In

Supplementary Table S2: Characteristics of Tomato Arfs and Their Orthologous Genes In

S1: List of primers used in the study
SlIAA localiation primers
IAA1_F / CACCATGGAGTGTGTTTTGGCTC
IAA1_R / AACTCCACATCCTAATCCTCTT
IAA2-F / CACCATGGAAATGGCTGGAAC
IAA2-R / TAAGCTTGCTAAACCTTTAG
IAA3-F / CACCATGAGAATTTACGAGAAGGA
IAA3-R / TAGACATGCTAGACCTTTAGC
IAA4-F / CACCATGTCTCCGCCGCTCC
IAA4-R / AAAAGGATTCAAGTTTATGAGC
IAA5-F / CACCATGTGTTCAGAGAATAATTCATC
IAA5-R / CATACAAAGTCCTTTGGC
IAA6-F / CACCATGTCTGTACCATTAGAACAT
IAA6-R / CATAGCATAAACATGATCACA
IAA7-F / CACCATGGACTTGAAAACTGAGTT
IAA7-R / GCTCCTGTTCTTGCATTTC
IAA8-F / CACCATGTCATCGGAGACAGC
IAA8-R / ACTCGACGATCTCCCAGGT
IAA9-F / CACCATGGCAACAGAATTGGAA
IAA9-R / TTTCTCTTGAGACATTCCCTT
IAA10_F / CACCATGAGTAGTAATAAGTTGGATTTT
IAA10_R / TCCATTTCTGTTCTTGCACTTC
IAA12-F / CACCATGGAGAAAATTTTGAATC
IAA12-R / TAGTTCACTTGATCCCAAGCC
IAA13-F / CACCATGGAAGAAGAGGATTCT
IAA13-R / AAGATTATAAGTTCGGGTCATT
IAA14-F / CACCATGGAAGGTTATTCACAAA
IAA14-R / GTTCCCAAGCAGAAGTTT
IAA15-F / CACCATGGAGAGAGATTTGAATCT
IAA15-R / GCTTCTGATCTTTTCATTATC
IAA16-F / CACCATGGATTCAAATTCTTCTGA
IAA16-R / ATTGGGGAAGAATGCTTC
IAA17-F / CACCATGGCAACAATCTACGAGA
IAA17-R / TAGGCATCCCAAACCTT
IAA18-F / CACCATGGAACTTGAGCTTGG
IAA18-R / AAACTGTTGAGGAATATGGG
IAA19-F / CACCATGATGGAGCTTCAATTG
IAA19-R / AATAATCTTCATCTCTAATTAATT
IAA21-F / CACCATGGAACTAGAGCTTGGC
IAA21-R / CTTCCATGGTACATCTCCA
IAA22-F / CACCATGAGAGGTACTCTTGGTTT
IAA22-R / TGCTGGAAATAATCCCC
IAA23-F / CACCATGACAAGTATAGTGGGCA
IAA23-R / AACTCCACATCCCAAGC
IAA24_F / CACCATGGATTTGAAAGAAACTGAGT
IAA24_R / GATCCTGCTCTTGCATTTCTC
IAA25-F / CACCATGGAGCAAGATTACAATATG
IAA25-F / CACCATGAGAGTACTCTTGGTAAATAA
SlARF localization primers
ARF2A-F / CACCATGGCTGCTTCGGAG
ARF2A-R / AGATTCTGCTTGACCAGATTC
ARF6A-F / CACCATGAGGTTCCGAATGC
ARF6A-R / GTACTCAAGTGATCCCAGAG
ARF7A-F / CACCATGTTTGAGACAGAAGAATCA
ARF7A-R / CACATTTCCTCCGTCTGA
SlIAA-QPCR primers
IAA1-F / GTGGCCACCAGTAAGAGCTAACA
IAA1-R / TCCCACATTCAGCTTCTGCTT
IAA2-F / GGTGACGTACCTTGGGATATGTTC
IAA2-R / ACCTTTAGCTTCAGATCCTTTCATAATT
IAA3-F / AGCTCCTGCACCAAAAGCA
IAA3-R / CACATGATTTTTCCTGTATGATCGA
IAA4-F / GAAAGGTTCAGATGCCATTGG
IAA4-R / TGAATGAAGAGGTCTAAGGCTCAA
IAA5-F / GATCATCAGAGTTTGTTCTCACATATGA
IAA5-R / AAACATCCCCCATGGAACATC
IAA6-F / GAAAAATGATGATGAAGGGAGAACA
IAA6-R / TGGAGCACCATCCATGCTAA
IAA7-F / TGATTCATGCAAGCGTTTACG
IAA7-R / TGGCTCTTGGTGCTAGTCCAA
IAA8-F / GAAAAACGAAATCTCTACCGGAAA
IAA8-R / GGCGGCCATCCAATTACTT
IAA9-F / TGACGGTGCACCATACTTACGT
IAA9-R / TGATCTCTTCATGATCCTTAGCCTTT
IAA10-F / GGGATGTTTGTTGATTCTTGCA
IAA10-R / GCTAGTCCTATTGCTTCAGTTCCTTT
IAA11-F / CGGCGATGTTCCATGGA
IAA11-R / GCATCAGAGAGTTGTTGGTAACTTTT
IAA12-F / TTCAGAGAGGGAAGGCTATAAAGG
IAA12-R / CATCTCCAACAAGCATCAAATCAC
SlIAA13F / GGGCTAAGGCTATTCCAAG
SlIAA13R / CGATCTGCAAATTCGTTCC
IAA14-F / CCTCCAATTCGTTCCTTTAGGA
IAA14-R / TTGTGTCTCACTTGCAGATTTCAC
IAA15-F / TTGGAGATGTTCCTTGGGAATT
IAA15-R / TCCTCAGTCTCTTGCATGATGAC
NwIAA16-F / TTACAAAGATAGGAATGACCAATGGA
NwIAA16-R / TCACTCGATCTGCAAATTCGTT
NwIAA17-F / TGTTGGTTGGCCACCAGTAA
NwIAA17-R / TCAATTGAATTCTTGGCTTGTACAC
IAA18-F / GTGATGAAAATGATGGACGCTTTAC
IAA18-R / CTCCAGCAAGCATCCAATCTC
IAA19-F / GGAGAACGGCGGCGTTA
IAA19-R / CTCCTTCCATTTTCACTTTCACATACT
IAA20-F / GTGATCTCAGTTGGAAAGATTTCGT
IAA20-R / TCGCCGGCAAAATTCG
IAA21-F / TGAAGAGGCCTTTCATGAGGAT
IAA21-R / GGCCATTCCATATGAACAAAGAC
IAA22-F / GACAAAGATGGAGACTGGATGCT
IAA22-R / GCAAGGTAACAGATGCAGGACATA
IAA23-F / TGTTGCCAAGGCACAAATTG
IAA23-R / GGTTGGATGATGTTTTTCCTGTTAG
IAA24-F / GCAACACTGAAGAAAGTGAGAAGACT
IAA24-R / AGGTGCACCATCCATGCAA
IAA25-F / TCCGAGGTGCAGGCTCTAAC
IAA25-R / TGCTTCTGAGGGATTCTTGGA
IAA26-F / CAAGGCTGGCCAATGTGAA
IAA26-R / TCCGCCAATTTGCTTTCTTTA
SlARF-QPCR primers
Soly96070-RTF / TCTGCTTGTCGGTTATTTGGAA
Soly96070-RTR / TCGCCTTAGACGGCGTATTATT
SolY81240-RTF / TGAAGAGCTGCGGTCTGAAA
SolY81240-RTF / GAGCCTCGAGTGTCATTCAGAA
Soly75150-RTF / TGGCTTGTCGAATTGGTCTCTAA
Soly75150-RTR / CCTTGGTGGTGAGTTGTGTGA
Soly07810-RTF / GGCTCGGTCAAGCAACTTG
Soly07810-RTR / TTCGCGCTGTTTTCATGAAG
Soly86130-RTF / ATACCATGATTCCCAAGCCAAGTA
Soly86130-RTR / GTTGAACTTCCAAGGGTTAGCAA

Supplementary Table S2: Characteristics of tomato ARFs and their orthologous genes in potato, pepper and N. benthemiana. The number represented in parentheses in potato syntelogs depicts the chromosome for that gene.

SGN ID ITAG (2.40) / Zouine et al. (2014) / Kumar et al. (2010) / Wu et al. (2011) / PGSC description (DMG) / SlARF gene in syntenic region / Potato syntelogs / N. benthemiana homologs description / Pepper (C. annum) homologs
Solyc01g103050 / SlARF1 / SlARF1 / SlARF1 / PGSC0003DMG400020711 / None / StARF1 (1) / NbS00032208g0017.1 (NbARF1) / CA00g28540
Solyc02g037530 / SlARF8B / SlARF2 / SlARF8 / PGSC0003DMG401018664 / SlARF8A / None / NbS00001007g0010.1 (NbARF8B-1), NbS00007832g0009.1 (NbARF8B-2) / CA00g12430
Solyc02g077560 / SlARF3 / SlARF3 / SlARF3 / PGSC0003DMG400031769 / None / StARF3 (2) / NbS00002969g0004.1 (NbARF3-1), NbS00043675g0005.1 (NbARF3-2) / CA02g04150
Solyc03g031970 / SlARF8A / SlARF4 / SlARF8-1 / PGSC0003DMG402018664 / SlARF8B / StARF8A(3) / NbS00006928g0008.1 (NbARF8A-1),
NbS00048507g0005.1 (NbARF8A-2) / CA04g02450
Solyc03g118290 / SlARF2A / SlARF5 / SlARF2 / PGSC0003DMG400014179 / SlARF2B / StARF2A(3), StARF2B(12) / NbS00032208g0017.1 (NbARF2A-1), NbS00012296g0005.1 (NbARF2A-2) / CA00g26120
Solyc01g096070 / SlARF18 / SlARF6 / NA / PGSC0003DMG400000118 / None / StARF18(1) / NbS00005482g0006.1 (NbARF18A-1), NbS00013395g0001.1 (NbARF18A-2) / CA00g64660
Solyc05g056040 / SlARF24 / SlARF7 / SlARF13, SlARF13-1 / PGSC0003DMG400023345 / None / StARF24(5); StARF6A(11) / None / None
Solyc07g016180 / SlARF7A / SlARF8 / SlARF19 / PGSC0003DMG400009773 / None / StARF7A(7) / NbS00043991g0008.1 (NbARF7A-1), NbS00002181g0206.1 (NbARF7A-2) / CA07g06550
Solyc07g042260 / SlARF19 / SlARF9 / SlARF7 / PGSC0003DMG400002392 / None / StARF19(7) / NbS00008608g0003.1 (NbARF19-1), NbS00036543g0010.1 (NbARF6B-4) / CA07g05960
Solyc07g043620 / SlARF6B / SlARF10 / SlARF6, SlARF6-1 / PGSC0003DMG400015919 / None / StARF6B(7) / NbS00045280g0004.1 (NbARF6B-1), NbS00032579g0013.1 (NbARF6B-2), NbS00039121g0001.1 (NbARF6B-3) / CA09g14300
Solyc08g008380 / SlARF9B / SlARF11 / SlARF12 / PGSC0003DMG400005794 / SlARF9A / StARF9B(8); StARF9A(8) / None / CA00g24330
Solyc08g082630 / SlARF9A / SlARF12 / SlARF9 / PGSC0003DMG400012261 / SlARF9B / StARF9A(8); StARF9B(8) / NbS00039272g0017.1 (NbARF9A-1), NbS00011021g0013.1 (NbARF9A-2) / CA01g00820
Solyc11g013480 / SlARF17 / SlARF13 / SlARF17 / PGSC0003DMG400027798 / None / StARF17(11) / NbS00056599g0002.1 (NbARF17-1), NbS00010441g0006.1 (NbARF17-2) / CA04g07510
Solyc11g069190 / SlARF4 / SlARF14 / SlARF4 / PGSC0003DMG400008065 / None / StARF4(11) / NbS00001271g0002.1 (NbARF4-1), NbS00017862g0008.1 (NbARF4-2) / CA00g12140
Solyc11g069500 / SlARF10A / SlARF15 / SlARF10 / PGSC0003DMG400008081 / SlARF10B / StARF10A(11) / NbS00028965g0003.1 (NbARF10A-1), NbS00036438g0004.1 (NbARF10A-2) / CA00g12430
Solyc00g196060 / SlARF6A / SlARF16 / NA / PGSC0003DMG400028826 / None / None / NbS00006125g0017.1 (NbARF6A) / CA00g91200
Solyc12g042070 / SlARF2B / SlARF17 / SlARF11 / PGSC0003DMG400014452 / SlARF2A / StARF2B(12), StARF2A(3) / NbS00002744g0004.1 (NbARF2B-1), NbS00004792g0017.1 (NbARF2B-2) / CA12g12020
Solyc04g081240 / SlARF5 / SlARF5 / PGSC0003DMG400003771 / None / StARF5(4) / NbS00019558g0008.1 (NbARF5-1), NbS00021404g0008.1 (NbARF5-2) / CA00g54820
Solyc05g047460 / SlARF7B / SlARF19-1 / PGSC0003DMG400013686 / None / StARF7B(5) / NbS00026230g0012.1 (NbARF7B-1), NbS00030922g0014.1 (NbARF7B-2) / CA05g09990
Solyc06g075150 / SlARF10B / SlARF16 / PGSC0003DMG400024320 / SlARF10A / StARF6A(9) / NbS00005871g0012.1 (NbARF10B-1), NbS00003282g0001.1 (NbARF10B-2) / CA00g38330
Solyc09g007810 / SlARF16A / NA / PGSC0003DMG400021560 / SlARF16B / StARF16A(9), StARF16B(10) / NbS00026905g0003.1 (NbARF16A-1), NbS00059497g0003.1 (NbARF16A-2), NbS00018737g0003.1 (NbARF16A-3) / CA09g02640
Solyc10g086130 / SlARF16B / SlARF14 / PGSC0003DMG400017585 / SlARF16A / StARF16A(9), StARF16B(10) / None / CA10g12340

NA- not identified in Wu et al. (2012). We have followed the same nomenclature as adopted by Zouine et al. (2014).

Supplementary Table S3: Characteristics of tomato Aux/IAA genes and their orthologs in potato, pepper and N. benthemiana. The number represented in parentheses in potato syntelogs depicts the chromosome for that gene

SGN ID ITAG (2.40) / Name [Based on Wu et al. (2012)] / Audran-Delalande et al. (2012) / PGSC description / SlIAA gene in syntenic region / Potato syntelogs / Affymetrix probe ID / N. benthemiana homologs description / Pepper (C. annum) homologs
Solyc06g053840.2.1 / SlIAA1 / SlIAA4 / PGSC0003DMG400016317 / None / None / Les.4095.1.S1_at / NbS00021580g0006.1 (NbIAA1-1), NbC26213611g0002.1 (NbIAA1-2) / CA06g08660
Solyc06g084070.2.1 / SlIAA2 / SlIAA2 / PGSC0003DMG400020139 / SlIAA3 / StIAA2 (6), StIAA3 (9) / Les.3707.1.A1_at / NbS00059570g0003.1 (NbIAA2-1), NbS00059132g0004.1 (NbIAA2-2) / CA00g21440
Solyc09g065850.2.1 / SlIAA3 / SlIAA3 / PGSC0003DMG400019302 / SlIAA2 / StIAA3 (9), StIAA2 (6) / Les.3706.1.A1_at / NbS00015683g0002.1 NbIAA3-1, NbS00015816g0009.1 NbIAA3-2 / CA00g43090
Solyc04g076850.2.1 / SlIAA4 / SlIAA9 / PGSC0003DMG400006393 / None / StIAA9 (4) / Les.1298.1.S1_at / NbS00016281g0006.1 (NbIAA4-1), NbS00003784g0004.1 (NbIAA4-2) / CA00g19170 (CaIAA4a), CA02g01930 (CaIAA4b), CA11g07490 (CaIAA4c), CA01g16530 (CaIAA4d),
CA07g12240 (CaIAA4e)
Solyc12g096980.1.1 / SlIAA5 / SlIAA11 / PGSC0003DMG400029339 / SlIAA25 / StIAA5 (12), StIAA25 (9) / Les.3705.1.S1_at / NbS00015796g0012.1 (NbIAA5) / CA12g19270
Solyc03g120500.2.1 / SlIAA6 / SlIAA27 / PGSC0003DMG400002550 / None / StIAA6 (3), StIAA13 (6) / Les.256.1.A1_at / NbS00028687g0017.1 (NbIAA6-1), NbS00029120g0008.1 (NbIAA6-2), NbS00016959g0109.1 (NbIAA6-3), NbS00018213g0005.1 (NbIAA6-4) / CA03g29400
Solyc06g053830.2.1 / SlIAA7 / SlIAA7 / PGSC0003DMG400016280 / SlIAA24 / StIAA7 (6) / Les.4097.1.A1_at / NbS00052931g0005.1 (NbIAA7-1), NbS00004218g0101.1 (NbIAA7-2) / None
Solyc03g120390.2.1 / SlIAA8 / SlIAA15 / PGSC0003DMG402002635 / None / None / Les.4087.1.S1_at / NbS00033734g0007.1 (NbIAA8-1), NbS00021136g0004.1 (NbIAA8-2), NbS00031776g0002.1 (NbIAA8-3) / CA03g29280
Solyc01g097290.2.1 / SlIAA9 / SlIAA16 / PGSC0003DMG402019457 / None / StIAA9 (1) / Les.3703.1.A1_at / NbS00025916g0003.1 (NbIAA9-1), NbS00057776g0004.1 (NbIAA9-2) / None
Solyc06g008590.2.1 / SlIAA10 / SlIAA17 / PGSC0003DMG400005327 / None / StIAA10 (6) / Les.3702.1.A1_at / None / CA00g66500
Solyc03g120380.2.1 / SlIAA11 / SlIAA19 / PGSC0003DMG400002636 / None / StIAA6 (3), StIAA13 (6) / Les.3701.1.A1_at / NbS00049197g0003.1 (NbIAA11-1), NbS00012015g0002.1 (NbIAA11-2) / CA03g29270 (CaIAA11a), CA06g14500 (CaIAA11b)
Solyc03g005360.1 / SlIAA12 / SlIAA21 / PGSC0003DMG400013445 / None / None / ― / None / None
Solyc03g113410.1.1 / SlIAA13 / NA / PGSC0003DMG400016512 / None / None / ― / NbC25965424g0004.1 (NbIAA13) / CA00g37610
Solyc03g121060.2.1 / SlIAA14 / SlIAA26 / PGSC0003DMG400002608 / None / StIAA14 (3) / LesAffx.3360.2.A1_at / NbS00031268g0002.1 (NbIAA14-1), NbS00000426g0009.1 (NbIAA14-2), NbS00011236g0101.1 (NbIAA14-3) / CA00g46410
Solyc04g054280.1.1 / SlIAA15 / SlIAA23 / PGSC0003DMG400038100 / None / StIAA15 (4) / ― / None / CA00g13500
Solyc05g008850.2.1 / SlIAA16 / SlIAA32 / PGSC0003DMG400030572 / None / None / ― / NbS00055775g0010.1 (NbIAA16-1), NbS00043162g0009.1 (NbIAA16-2) / CA11g00220
Solyc06g008580.2.1 / SlIAA17 / SlIAA22 / PGSC0003DMG400005338 / None / None / ― / None / CA00g66510
Solyc06g066020.2.1 / SlIAA18 / SlIAA36 / PGSC0003DMG400020478 / None / StIAA18 (6) / ― / NbS00004717g0120.1 (NbIAA18) / CA00g51680
Solyc07g008020.2.1 / SlIAA19 / SlIAA35 / PGSC0003DMG400030896 / None / StIAA19 (7) / ― / NbS00055408g0003.1 (NbIAA19-1), NbS00017553g0203.1 (NbIAA19-2) / CA07g03220
Solyc07g019450.2.1 / SlIAA20 / SlIAA33 / PGSC0003DMG400043142 / None / StIAA20 (7) / ― / NbS00007051g0112.1 (NbIAA20) / None
Solyc08g021820.2.1 / SlIAA21 / SlIAA29 / PGSC0003DMG400013765 / None / None / Les.5442.1.S1_at / NbS00031554g0005.1 (NbIAA21-1), NbS00010241g0022.1 (NbIAA21-2) / None
Solyc09g064530.2.1 / SlIAA22 / SlIAA12 / PGSC0003DMG400008586 / None / StIAA22 (9) / ― / NbS00047479g0021.1 (NbIAA22-1), NbS00012460g0040.1 (NbIAA22-2) / CA09g06760
Solyc09g083280.2.1 / SlIAA23 / SlIAA1 / PGSC0003DMG400006108 / None / None / ― / NbS00025247g0001.1 NbIAA23-1, NbS00012728g0018.1 NbIAA23-2 / CA03g05020
Solyc09g083290.2.1 / SlIAA24 / SlIAA14 / PGSC0003DMG400006093 / SlIAA7 / StIAA24 (9) / LesAffx.67531.1.S1_at / NbS00013471g0003.1 (NbIAA24-1), NbS00002382g0004.1 (NbIAA24-2) / CA03g05000
Solyc09g090910.1.1 / SlIAA25 / SlIAA13 / PGSC0003DMG400001498 / SlIAA5 / StIAA25 (9),StIAA5 (12) / ― / NbS00029861g0021.1 (NbIAA25-1), NbS00017768g0005.1 (NbIAA25-2) / CA00g02840
Solyc12g007230.1.1 / SlIAA26 / SlIAA8 / PGSC0003DMG400000375 / None / StIAA26 (12) / LesAffx.58084.1.S1_at / NbS00008944g0109.1 (NbIAA26-1), NbS00021267g0018.1 (NbIAA26-2), NbS00061347g0003.1 (NbIAA26-3) / CA00g82880 (CaIAA26a), CA00g93260 (CaIAA26b)

― means probeset for that gene is not available in tomato GeneChip array

Supplementary file S4: Herein the information of number of exons present in the genomic region of tomato, potato and N. benthemiana Aux/IAAs is listed. In addition protein sequences of eggplant and petunia is presented. * entries in case of PhIAA, SmIAA and CaIAA represents proteins which although exhibited presence of typical Aux/IAA domain but were not taken in phylogenetic analysis.

SGN ID ITAG (2.40) / No. of Exon (s)
>SlIAAs
Solyc01g097290.2.1 / 5
Solyc03g005360.1 / 2
Solyc03g113410.1.1 / 3
Solyc03g120380.2.1 / 3
Solyc03g120390.2.1 / 5
Solyc03g120500.2.1 / 5
Solyc03g121060.2.1 / 5
Solyc04g054280.1.1 / 3
Solyc04g076850.2.1 / 6
Solyc05g008850.2.1 / 4
Solyc06g008580.2.1 / 3
Solyc06g008590.2.1 / 5
Solyc06g053830.2.1 / 5
Solyc06g053840.2.1 / 3
Solyc06g066020.2.1 / 4
Solyc06g084070.2.1 / 3
Solyc07g008020.2.1 / 4
Solyc07g019450.2.1 / 2
Solyc08g021820.2.1 / 4
Solyc09g064530.2.1 / 5
Solyc09g065850.2.1 / 3
Solyc09g083280.2.1 / 3
Solyc09g083290.2.1 / 5
Solyc09g090910.1.1 / 5
Solyc12g007230.1.1 / 5
Solyc12g096980.1.1 / 4
>StIAAs
PGSC0003DMT400050101 / 5
PGSC0003DMT400034978 / 2
PGSC0003DMT400042572 / 3
PGSC0003DMT400006800 / 3
PGSC0003DMT400006798 / 5
PGSC0003DMT400006548 / 5
PGSC0003DMT400006709 / 5
PGSC0003DMT400088529 / 2
PGSC0003DMT400016356 / 3
PGSC0003DMT400006799 / 6
PGSC0003DMT400013662 / 3
PGSC0003DMT400013627 / 5
PGSC0003DMT400041976 / 5
PGSC0003DMT400042074 / 3
PGSC0003DMT400052767 / 3
PGSC0003DMT400051896 / 3
PGSC0003DMT400079375 / 4
PGSC0003DMT400093571 / 1
PGSC0003DMT400035770 / 4
PGSC0003DMT400022133 / 5
PGSC0003DMT400049677 / 3
PGSC0003DMT400015655 / 3
PGSC0003DMT400015610 / 5
PGSC0003DMT400003784 / 5
PGSC0003DMT400001013 / 5
PGSC0003DMT400075427 / 4
>NbIAA
>NbS00025916g0003.1 / 5 exon
>NbS00057776g0004.1 / 5
>NbS00025247g0001.1 / 2
>NbS00021580g0006.1 / 2
>NbS00012728g0018.1 / 2
>NbC26213611g0002.1 / 2
>NbS00049197g0003.1 / 3
>NbS00012015g0002.1 / 3
>NbC25965424g0004.1 / 2
>NbS00033734g0007.1 / 4
>NbS00021136g0004.1 / 5
>NbS00031776g0002.1 / 2
>NbS00029861g0021.1 / 5
>NbS00047479g0021.1 / 5
>NbS00017768g0005.1 / 2
>NbS00028687g0017.1 / 7
>NbS00029120g0008.1 / 5
>NbS00016959g0109.1 / 5
>NbS00018213g0005.1 / 3
>NbS00061347g0003.1 / 4
>NbS00015683g0002.1 / 3
>NbS00031268g0002.1 / 4
>NbS00000426g0009.1 / 4
>NbS00011236g0101.1 / 2
>NbS00016281g0006.1 / 2
>NbS00003784g0004.1 / 6
>NbS00055775g0010.1 / 3
>NbS00043162g0009.1 / 3
>NbS00015816g0009.1 / 3
>NbS00059570g0003.1 / 3
>NbS00059132g0004.1 / 3
>NbS00052931g0005.1 / 3
>NbS00004218g0101.1 / 5
>NbS00021267g0018.1 / 5
>NbS00013471g0003.1 / 4
>NbS00002382g0004.1 / 6
>NbS00012460g0040.1 / 2
>NbS00004717g0120.1 / 4
>NbS00017553g0203.1 / 4
>NbS00007051g0112.1 / 2
>NbS00031554g0005.1 / 3
>NbS00010241g0022.1 / 3
>NbS00015796g0012.1 / 5
>NbS00008944g0109.1 / 6
>Solanum melanogena IAA protein sequences used in the study
>SmTC10554
MDLKETELCLGLPGGGGGGGELLRDNNKINGKRGFSETVDFKLNFHQANDDISCAMEKNK
MKNTPTTITKENGCNKDPIKPPAKAQVVGWPPVRSFRKNVMAHKSNTEETEKNTTAAAFV
KVCMDGAPYLRKVX
>SmTC1095
PSDFLLGNISSSQDVQSQITSASLADSQNFSVQEFADNSGGASSSNVNFDECNLLQNSSW
QQVAPRVRTYTKIQKAGSVGRSIDVSGFKNYEELCFEIERMFGLEGLLNDTRGSGWKLVY
VDFENDVLLVGDDPWEEFVGCVRCIRILSPTEVQQMGEEGMQLLNSAGLQGKMAQHQNFR
TELSTSDL
>SmTC11387
MERRGIYDKDVNDLEATELRLGLPGIIDESESIQSSTSTNTTKNSRKRSSSSVNENEQQD
SPPAPKAQIVGWPPVRSYRKNHVLQTKKPEFDNSSSGMYLKVSMDGAPYLRKIDLKVYKS
YPELLKALQNMFKCTIGVYSEREGYNGSDYAPTYEDKDGDWMLVGDVPWEMFINSCKRLR
IIKGSEAKGLACL
>SmTC13403
MECVLADERDLNLKATELRLGLPGRTEEESDKQIVKNNKRALPEDEDSESNSISDSKTPP
VAKAQIVGWPPVRSNRKNSFPSKKAETECGMYVKVSVDGAPYLRKIDLTLYKCYPELLKA
LEKMFKLSIGEYSEREGYKGSDFAPAYEDKDGDLMLVGDVPFEMFLSSCKRLRIMRGSEA
RGLGCGV
>SmTC14491*
AAEVEITELRLGLVIPSSKKRVYSEIDNDQSSSNVNDDRNNQVVGWPPVCGYRRKNNSNS
NNSNNTNGDARSKKMYVKVSMDGAPFLRKVDLSIHKDYYGFVMNLEKLFQFYGICK
>SmTC1508*
RNYYYLSFSFLVSLSTXYQVDQLQQRLPSNVSSSFLKADFADLNSKFSTSVAPSGVQNML
GSICSEGSSNSLSINRTGQSXDHRAAAPTVMDVKLYAVATKYMLQLIITPNIWEGYYQST
GKLSLGSQNQVLFGGNVDSSGNLLRTTMSNVTTTCADMSSMPLGASGYQNSLYGYVQDSS
ELLHNSGQIDPPNTTHTFVKVYKSGCVGRSLDITQFHSYHELRRELGQMFGIEGFLEDPQ
RSGWQLVFVDRENDILLLGDDPWEAFVNNVWYIKILSPEDVQKLGKEEAESLNCAAVERM
SSTSADDRDLISGMPSLGSLETDCCNALKKRTNSDSRIFSRVRNSNFMPRNRAFLAFI
>SmTC2529*
TRSCTKVHKQGTALGRSVDLAKFNNYDELIAELDGLFDFNGELKARSKSWLVVYTDDEGD
MMLVGDDPWQEFCGMVRKIFIYTKEEVQRMNPGTLNSKGEDTSSVAEGSDAKEVKNQLLP
SESCQEEY
>SmTC346
MESMVAHQKDLNFKATELRLGLPGTEDQESDQEILLSSNSKNNNKRALPQSTHDEEDCES
KSSSDHVKTPPIAKAQIVGWPPVRSNRKNIIQLKKTESESGMYVKVSMDGAPYLRKIDLK
MYKCYAELLKALENMFKLTIGEYSEREGYKGSEFAPAYEDKDGDLMLVGDVPWEMFMSSC
KRLRIMKGSEARGLGCGV
>SmTC4326
MTSVLGVECDKIRLDYEAETELRLGLPGANGNEVESTNKNNGKRVFSETVDLKLNLSSKD
STMDNINQVDNINEKKNNDPAKPPAKAQVVGWPPVRSFRKNVMTVQKNTTGAGESSGTGA
AFVKVSVDGAPYLRKVDLKMYKSYQQLSDALGKMFSSFTIGNCGTQGFKDFMNESKLIDL
LNGSDYVPTYEDRDGDWMLVGDVPWEMFVDSCKRLRIMKGSEAIGLAPRAVEKCKNRS
>SmTC5267
MEGYSRKWLMQREETNHGNCSEEKKLELRLGPPNGDWSCNEKDESLFPFSYISKGNHAQN
FSSFLQLQSTAQNQSLKVQESSQTTADLQNTEKKKAFSQTATVHNSAQKRTAPAPVVGWP
PIRSFRKNLASSSSVKPAAEVQNVVPSKSANKKPMEICQKGLFVKINMDGIPIGRKVDLK
AYDSYDKLSFAVDQLFKGLLAAQNDPFAGGNEKNEDGEKAISGLLDGSGEYTLVYEDNEG
DRMLVGDVPWHMFVFTVKRLRVLKSSDLSTLTRGTKQQPXLT
>SmTC542
PASEKRPANGCRLFGIELHHATIDENSLVPMPLAVMEDHMPLAVMEDQPAPSLYVDSDQN
SEPSYPIPSVSCEPEKSSLRSTHESRSKQIRSCTKVHMQGKAVGRAVDLTRLYSYEDLLK
KLEEMFEIEGELCGSTKKWQVVYTDDEDDMMMVGDDPWHEFCSMVRKIYVYTAEEAKRLS
PKIKLPVDEMKPGKSVSDGATVINEEKA
>SmSmTC6166
MVGEEEKISNKLDFEETELRLGLPGGGRKKSHDDNDTYNANGKRGFVDLKLNLSSDVNNI
KASTLKTPVSKAQVVGWPPVRSFRKNILTSQKIGQESDNILVKVSMDGAPYLRKVDLNMY
KSYQELFDALAKMFSSFTIVQGMKDFMNERKLMDLLNSSDYVPTYEDKDGDWMLVGDVPW
GMFVDSCKRMRIMKGVEAIGLAPRAMEKCKNRIN
>SmTC6482*
GLPIGRKVDLSSHNCYETLAKILEEMFFKSTKTTNCGEKEQATKSCKLLDGSSEFVLTYE
DKDGDWMLVGDVPWEMFLSTVKRLRIMRTTEAKGLGI
>SmTC6912
MSSERANGLPETDISGLNFSETELTLGLPGESRKQISGTKRGIYDGMELSLGSSTSGERR
KEDHSKKEISTGTKPPTKAQVVGWPPVRSHRKNMIEKCKYVKVAVDGAPYLRKVDLEIYD
SYQKLLNALENMFTCLTICNSESECKLMDLANGVEYVPTYEDKDGDWMLVGDVPWKMFVD
TCKRIRLMKSSEAIGLAPRTPGRSSSSS
>SmTC7907
MSPPILGVAEEEGQSNVTLLASSTSLGSICKKGSAFKERNYMGLSDCSSVDSCNISTSSE
DNNGCGLNLKATELRLGLPGSQSPERGAEACPLGSTKVDEKLLFPLHPAKDTAFSVSQKT
VVTGNKRGFSDAMEGKFLSNSGVKAGNTKETSRVQPPKMKDANSQSTVPERPAAVNEASN
RAGSGAPATKAQVVGWPPIRSFRKNTLASASKNNDEVDGKAGSPALFIKVSMDGAPYLRK
VDLRTYSAYQELSSALEKMFSCFTIGQYGSHGALGKDMLSESKLKDLLHGSEYVLTYEDK
DGDWMLVGDVPWEMFIDTCKRLRIMKGSDAIGPGPKGYGKVSEQKLAYLHMIKAIHPALP
VRRGNAKRVKGMDGSWLLGLGQLSMGSRCFT
>SmTC8740*
MSVTLEHDYIGLSEASLMERSSDKISSSSSSSSSVLNLKETELRLGLPGSESHGVSIFGK
DLEDKNLGLNPLSNFTSRTKRGFSDAIDASGKWDLSINCRSEADGEKGNLLFSPKRGNGG
SKPVEEKKSIPHTSKA
>SmTC9593*
YEDKDGDWMLAGDVPWEMFINSCTRLRIMKASEAKGLATL
>Petunia hybrida Aux/IAA protein sequences used in the study
>PhTC13147
TAFGVSLAKRQAQDQEKDFNLLGKPWSLLSSGLSLNLMDSGSKAPGQGGDSTYQMRGDTR
YGGYGELSVHPGHRIDNQQGSWFMPQSVSPYIQLSSHSRDMMHKSAVVQYPDAVKPKEGN
CKLFGIPLTSNVCTDPVMMRKSSLIDSASNMNIGIHPHQSPATDSDQRSEQSKGSKVLDD
GNTAIDQQDKQCHSFHLAARDRDGKSHSSSTRSCTKVHKSGTALGRSVDLAKFSNYDELI
AELDQLFDFNGELKAPSKSWLVVYTDDEGDMMLVGDDPWQEFCSMVRKIFIYTKDEVQRM
NPGTLNSKGEDTSSIAEGSEAKEMKNLQLPSESGQEDS
>PhTC15595
MESIVAHQKDLNLKATELRLGLPGSEEESDQEVLSNSNKRALPESADDEDCESKSSSDVK
IPPVAKTQIVGWPPVRSNRRNNIQPKKTETESGMYVKVSMDGAPYLRKIDLKMYKCYQEL
LKALENMFKLTIGQYSEREGYKGSEFAPAYEDKDGDLMLVGDVPWEMFMSSCKRLRIMKG
SEARGLGCGV
>PhTC15803
EDETELELGLGLSLNSGVGVAKAKKSPWGEYGRILTAKDFPNGFSAGRLCNDGGVSGTKK
RAADFVGSTTDVVGSPPTGSSQVVGWPPIRAYRMNSLVNQSKAQNAEEDKGVGGNDKKEH
SKKKINHGNTKDDAASNKEKGNLGFVKVNMDGLPIGRKVDLKAHTCYETLAETLEDMFFK
STKSGEKEQSGKSAKLLDGSSDFVLTYEDKEGDWMLVGDVPWRDVSEHCEKAKNHEASEA
NGLAPRNLEKQERHKGKPI
>PhTC15838
MSSENFKETELTLGLPGESRKQISGTKRGISDDIELSLGSSTSGERSKNEMSTTATKPPA
KTQVVGWPPVRSYRKNIIEQCKYVKVSVDGAPYLREVDMEMYDSYQKSIKALEYMWTVLT
VCKYSK
>PhTC6797
SFSTTGALLPKPAKISDVAAERAPPSTVPAGDSDQSSDLSMDIKDQKPGHLQLPLKEAQS
KQSFSTRSCTKVQMQGVAVGRAVDLTALKGYDELIKELEEMFEIQGELHPRNKWEIVFTD
DEGDMMLMGDHPWLEFCNVVRRIFICSSQDMKKLSAVNKPLSCADSEVTAL
>PhTC6970
PVDQEGNNDPHNHLLFGVNIDSPSLMQNGIPNLRGVGSDCESTNVPFASSNYLSNTGTDF
QNAVMGTSGCIDESGFMQNSENVGQQSPHNTFVKVYKSGSFGRPLDITKFSSYHELRSEL
AQMFGLEGLLEDPLRSGWQLVFVDRENDVLLLGDDPWPEFVNSVWCIKILSPQDVQQMGK
QGLELLNSVSVSRTSNNYSCDDFANRSETRNMTSGIMSV
>PhTC7035
LDSLGNRSYKPNPRLARVLDILFILHAEHEMNCSTAAARHLASSGVDVYQEAAHSISPPR
STLSQVVGWPPIRTYRMNTLQTKSSLTGEFSPTTEKCKSKKITTDAGSSKSNSLAKEKGL
SKSSLFVKVNMDGVAIGRKVDLNAHSSYENLARTLDNMFLRPSTMVCARSSAKELCLMSE
TTSSFKNYXNGSSEFVLTYEDKEGDWMLVGDVPWEMFISSVKRLRIMKTSDANGL
>PhTC8882
MGAATYEKDLNLKATELRLGLPGIDELEKPSCSTNLGAKFSKKRSSLEMDNSPNGNNDEQ
DSAPAPKAQVVGWPPVRSYRKNVLQAKKPESDVSAGMYVKVSMDGAAYLRKIDLKVYKNY
PELLKALEHMFKCTIGVYSEIEGYNGSD
>PhSGN-U208098
YYWSILLHFHLCPLILSLSLIFTQEDLIKKKSLLLNFQMDLKETELCLGLPGAVADNKVNGKRGFSETVDLKLNFET
IDSSAKDLKEKTKNTPTKETACNKDPVKPPAKAQVVGWPPVRSFRKNAMAQKSNSEETEKTSSAAFVKVCMDGAPYLRKV
DLKMYKSYQELSDALAKMFSSFTMGNYGAQGMIDFMNESKLMDLLNSSEYVPSYEDKDGDWMLVGD
>PhSGN-U209630
SCRRKNVQKNSTAGTGESSGTGAAFVKVSVDGAPYLRKVDLKMYQSYQQLSDALGKMFSSFTIGNCGTHGFKDFMNESKL
IDLLNGSDYVPTYEDKDGDWMLVGDVPWEMFVDSCKRLRIMKGSEAIGLAPRAVEKCKNRSNCSNKLFIVFYFIFLVS
MVKLYILTVEFLNVSFDGLYIIVKKK
>PhSGN-U208112
LVPENSSGMYLKVSMDGAPYLRKVDLKVYKNYPELLKALQNMFKCTIGVYSEREGYNGADYAPTYEDKDGDWMLVGDVPW
DMFINSCRRLRIMKGSEAKGLACQGTRQSLRACLKNGPAGLYFEKDPVSLKQQAYHWDFQETWKFIQIYQVLGRM
NKKDKAEDFDLCDFSFLTAQQRYTSVAWDRSRSTCTNTFSFLLFLEQFAVYLFIKSIYIHTGKIQNFSTKKK
>PhSGN-U212227
SLQIFIVSHQLNKKKKKPIPRNRYCLSFIYVERKMDLNLKETELCLGLPGGGELRGLAENNNESINKKRGFSETVDL
KLNLQSSDSSANMELKEKMKNVPSKETCKKDSAKPPAKAQVVGWPPVRSYRKNIMAQKDNNNTEESEKGGISNNSVAFVK
VSMDGAPYLRKVDLKMYKSYQELSDAPRCQLLYYGLWG
>PhSGN-U210750
EIQLFFKSIPLEHDILDLKETELRLGLPGSESPERKDFEDKNTLNNITSRAKRVFSDGGKKSIPSNENGAPQSSKTQVVG
WPPIRSFRKNTLATTTPKNNDGEGKSSSSCLYVKVSMDGAPYLRKVDIKTCSNYAELSSALEKMFSCFSIGQCASDRLP
>PhSGN-U212201*
TYEDKDGDWMLVGDVPWDMFIETCKRLRIMKGSDAIGLAPRAMEKCRSRNAHLHMIKAIHPALLVGEEVEKGRSHKL
SLFKHQWLVVGPGQHGMGRCLYLITTWFFLYLRNCQLSYLSCLIETPILEFVYNLMCVVNEFFRFSMFKCNVC
SSFVCTDQACGYFDLVRVCTRELCYYSINVSMSRFIGKKK
>PhSGN-U212274*
NNQQNRLSSWMDRLILCSRMRIKKETGCLLEMFHGGMFLSTVKRLRIMRTSEANGLAPRNLEKQERHKGKPIFALAQGK
NKCLEQKNRIGKCKSQEIWLLFSWLHFLFFTIFVSSFLGFFPCNLFQIRSQTPHIVADTPMFCPYLSFSHNVNMGML
FSSKKK
>PhSGN-U212055
ENPKDAQPELSTSMVSQSFGVPDMAFNSIDSTINEDSFMNRGAWAPPPQMPRLRTYTKVYKRGAVGRSIDIARYSGYEEL
KQDLARRFGIEGQLEDRQRIGWKLVYVDHENDVLLVGDDPWEEFVNCVRCIKILSPQEVQQMSLDGDFGSGVQNQACSSS
DGG

Supplementary file S5: Herein the information of number of exons present in the genomic region of tomato, potato and N. benthemiana ARFs is listed. In addition protein sequences of eggplant, and petunia is presented.

SGN-ID
>Solanum lycopersicon / Number of exon
>SlARF24 / 11
>SlARF7A / 13
>SlARF1 / 14
>SlARF8A / 14
>SlARF6A / 7
>SlARF19 / 13
>SlARF6B / 12
>SlARF9A / 14
>SlARF17 / 2
>SlARF9B / 14
>SlARF2B / 14
>SlARF3 / 10
>SlARF2A / 14
>SlARF4 / 12
>SlARF8B / 14
>SlARF10B / 7
>SlARF5 / 14
>SlARF18 / 14
>SlARF16 / 3
>SlARF16B / 2
>SlARF16A / 14
>Solanum tuberosum
>StARF24 / 9
>StARF10A / 4
>StARF4 / 7
>StARF8A / 13
>StARF6A / 14
>StARF19 / 12
>StARF6B / 14
>StARF9A / 15
>StARF17 / 5
>StARF9B / 16
>StARF1 / 14
>StARF2B / 16
>StARF3 / 12
>StARF2A / 13
>StARF8B / 13
>StARF7A / 13
>StARF10B / 7
>StARF5 / 15
>StARF18 / 13
>StARF16A / 3
>StARF16B / 3
>StARF7B / 14
>Nicotiana benthamiana
>NbS00005482g0006.1 / 14
>NbS00013395g0001.1 / 13
>NbS00043991g0008.1 / 14
>NbS00002181g0206.1 / 14
>NbS00001271g0002.1 / 13
>NbS00026230g0012.1 / 13
>NbS00028965g0003.1 / 6
>NbS00036438g0004.1 / 7
>NbS00005871g0012.1 / 8
>NbS00003282g0001.1 / 2
>NbS00026905g0003.1 / 3
>NbS00059497g0003.1 / 3
>NbS00026245g0009.1 / 13
>NbS00012296g0005.1 / 20
>NbS00002744g0004.1 / 10
>NbS00004792g0017.1 / 17
>NbS00006928g0008.1 / 9
>NbS00048507g0005.1 / 16
>NbS00007832g0009.1 / 13
>NbS00001007g0010.1 / 19
>NbS00032579g0013.1 / 12
>NbS00039121g0001.1 / 16
>NbS00045280g0004.1 / 15
>NbS00006125g0017.1 / 14
>NbS00008608g0003.1 / 12
>NbS00036543g0010.1 / 13
>NbS00021404g0008.1 / 14
>NbS00039272g0017.1 / 13
>NbS00010441g0006.1 / 7
>NbS00032208g0017.1 / 14
>NbS00002969g0004.1 / 10
>NbS00043675g0005.1 / 11
>NbS00017862g0008.1 / 8
>NbS00001271g0002.1 / 14
>NbS00018737g0003.1 / 5
>NbS00019558g0008.1 / 14
>NbS00018737g0003.1 / 5
>NbS00026230g0012.1 / 13
>NbS00030922g0014.1 / 14
>NbS00011021g0013.1 / 16
>NbS00056599g0002.1 / 2
>Solanum melanogena ARF protein sequences used in the study
>AJ002140
MASPQPNSESVLELPNNDKSGHKKNKRKQDSVSKRKASATGKKEKKQAVSETIEEPTA
GRKRPKRAAACSDFKEKSVHLSKKSSVIETKKDHCVDEEDVAIR
LTAGLQESQRPCRRLTDFVFHNSEGIPQPFGMSEVDDLFISGLILPLEDSLDKVKAKG
IRCEGFGRIEEWAISGYEDGTPVIWISTETADYDCLKPSGSYKKFYDHFLAKATACVE
VYKKLSKSSGGNPDLSLDELLAGVVRAMTGIKCFSGGVSIRDFVITQGGFIYKELIGL
DDTSKKTDQLFVELPVLASLRDESSKHETLAQPETISSGNGLRIGPKAGNGGDKIVES
GLANGPAPEDEDLKLAKLLHEEEYWCSLKQKKDRNTSSSSSKIYIKINEDEIASDYPL
PAYYKTSNEETDEYIVFDSGVETYHIDELPRSMLHNWALYNSDSRLISLELLPMKACA
DIDVTIFGSGVMTADDGSGYNFDTDANHSSSGGSRSAEIDGMPIYLSAIKEWMIEFGS
SMIFISIRTDMAWYRLGKPLKQYAPWYEPVIKTARLAVSIITLLKEQNRVARLSFGEV
IKRVSEFKKDHPAYISSNVDAVERYVVVHGQIILQQFSEFPDVSIRNCAFAVGLSRKM
EERHHTKWVIKKKKVMQRLEQNLNPRASMAPSVKRKAMQATTTRLINRIWGEYYSNYS
PEVSKEVADCEVKDDEEPDEQEENEEDDVPERNLDVPEKAHTPSSTRRHIKSRSDSKE
INWDGESIGKTASGEQLFKKARVHGHEIAVGDSVLVEHDEPDELGCIYFVEYMFEKLD
GSKMLHGKMMQRGSDTVLGNAANEREVFLINECMNLQLGDVKESIAVNIRMMPWGHQH
RNTNADKLETAKAEDRKRKGLPTEFYCKSFYRPEKGAFFRLPFDKMGLGNGLCYSCEL
QQTDQEKESFKFDMSKSSFVYLGTEYSVDDFVYVSPDHFTAERGGNGTFKAGRNVGLM
AYVVCQLLEIVGPKGSKQAKVDSTNVKVRRFFRPEDISSDKAYSSDIREIYYSEDIHT
VPVEIIKGKCEVRKKYDISSEDVPAMFDHIFFCEYLYDPLNGSLKKLPAQINLILSKI
KLDDATSRKRKGKGKEGVDEVGELNETSPQNRLSTLDIFAGCGGLSEGLQHSGVTDTN
WAIEYEAPAGDAFRLNHPKTKVFIHNCNVILRAVMQKCGDSDDCISTPEASELAAAMD
ESELNSLPLPGQVDFINGGPPCQGFSGMNRFNQSTWSKVQCEMILAFLSFADYYRPKF
FLLENVRNFVSFNQKQTFRLTVASLLEMGYQVRFGILEAGAYGVPQSRKRAFIWAGSP
EEVLPEWPEPMHVFAVPELKIALSETSYYAAVRSTASGAPFRSLTVRDTIGDLPVVGN
GASKTCIEYQGDPVSWFQKKIRGSSITLSDHISKEMNELNLIRCQRIPKRPGADWRDL
EDEKVKLSNGQLVDLIPWCLPNTAKRHNQWKGLFGRLDWDGNFPTSITDPQPMGKVGM
CFHPDQDRIVTVRECARSQGFPDSYQFAGNILHKHRQIGNAVPPPLAYALGRKLKEAV
ESKNRLT
>EU344815
MDKHLSEEDSDNIDWDTEDELEIQDTTFSSCRDLRTNGQYAISG
DGEASSSSVPGQSTFIQKFLVMGFSEESIAKAIEQNGENSDLVLDALLTLKAIEDSPE
EQPSASPHLEPCINSDDSSSEYNENFLDDVYDEDSWSSDSDYCTNSVKQCYVKEESNS
LSEKEQTILFLANMGYPVEEVSIAMERCGPEASVSELTDFICAAQMAREEDPYLPEDV
KPKLNHGSGGYKKRKMFNQLCKSKKPRAIFDEETIRLPKPMIGFGVPTESVSAIVRRT
IPEQAFGPPFFYYENVALAPKGVWDTISRFLYDIEPEFVDSKYFCATARKRGYIHNLP
TENRFPLLPLPPRTINEALPLTKKWWPSWDPRTKLNCLQTAIGSARLTDRIRKAVEAF
DGEPPMRVQKFVLDQCRKWNLVWVGRNKVAPWSQRIGNAIGVPKNHTRGGGISRTDRY
KSLGNSFQVDTVAYHLSVLKDMFPNGMNVLSLFSGIGGAEVALYRLGIQLNNVVSVEK
SEVNRNIVRSWWEQTNQRGNLIDFDDVQQLNGDRLEQLIDSCGGFDLLIGGSPCNNLA
GSNRVSRDGLEGKESSLFYDYVRILDLVKSIMSRQR
>Petunia hybrida ARF protein sequences used in the study
>SGN-U210705
WSQTCMRQQVNAPSSVNPVIACILGVLATGLACYSDQNDVHSVLQTKDKPCGVYVPYDHFMESEKNNYSIGMRFKMRFEGEESPEQRFTA
TIVGIEDADPKRWLESKWRCLKVRWDENSNHSX
>SGN-U212055
ENPKDAQPELSTSMVSQSFGVPDMAFNSIDSTINEDSFMNRGAWAPPPQMPRLRTYTKVYKRGAVGRSIDIARYSGYEELKQDLARRFGI
EGQLEDRQRIGWKLVYVDHENDVLLVGDDPWEEFVNCVRCIKILSPQEVQQMSLDGDFGSGVQNQLVAVRMGG

Supplementary Table S6: Promoter architecture of Solanaceae ARF and Aux/IAA genes. 2-kb upstream region from the starting codon of each gene was used to analyze presence of cis-regulatory elements in PlantCare (bioinformatics.psb.ugent.be/webtools/plantcare/html/ ) and PLACE ( ) web tools. Results obtained only from PlantCare are presented in the table. Gene names and identified cis-elements in their promoters are represented by the same color in the table. All the promoter were found to harbor many light signaling elements and the most frequently present elements have been mentioned in the respective row.

Cis-acting elements / Tomato / Potato / N. benthemiana
Hormone signalling: ABRE (ABA responsiveness), CGTCA-motif (MeJA responsiveness), GARE-motif (GA responsive element),TCA-element (SA responsiveness), TGACG-motif (MeJA-responsiveness), AuxRR-core (Auxin responsive element), P-box (GA responsive element), TATC-box (GA responsive element), ERE (Ethylene response element), TGA-element (Auxin responsive element), CE3 (ABA and VP1 responsiveness), SARE (SA responsiveness), GCC-Box (ethylene responsiveness) , JERE (jasmonate and elicitor-responsive element) / IAA7-9,11,16, 18, 24, ARF7, 10, 13, 15, 17, 19, 20; IAA1, 3, 5, 7-9, 14-16, 22, 26, ARF1, 8B, 3, 2A, 7A, 19, 9B, 4, 10A, 2B; IAA3, 4, 6, 8, 9, 12, 13, 14, ARF1, 2A, 3, 8A, 7A, 9B, 4, 2B, 7B, 16A; IAA1, 2, 4, 6, 9, 10, 12-15, 17, 19, 20, 22-24, ARF1, 8B, 2A, 18, 24, 7A, 19, 6B, 4, 2B, 5, 7B, 10B, 16A, 16B; IAA1, 2, 5, 7-9, 14, 16, 22, 26, ARF1, 8B,3, 2A, 24, 7A, 19, 9B, 4, 10A, 2B; IAA2, 13; IAA4, 7, 11, 13, 25, ARF1, 3, 24, 7A, 6B,9B, 4, 5, 7B; IAA11, 13, 20, 21, 23, ARF10A, 7B; IAA3, 4, 11, 18, 20, 21, ARF7A, 10A,2B, 5, 7B; IAA2, 5, 6, 8, 14, 26, ARF24, 4; IAA8; IAA1; IAA23 / IAA7-9, 12, 16, 17, 22, 24, 26, ARF1, 18, 17, 10A, 2B; IAA3, 5, 6, 9, 13, 16, 20,22, ARF8B, 3, 8A, 2A, 24,7A,9B, 9A, 17, 4, 10A, 6A, 2B, 5, 7B, 16B; IAA1, 4, 6, 8, 9, 12-14, 20, 21, 24, ARF3, 18, 24, 19, 4, 10A, 6A, 2B, 5, 7B, 16A; IAA1-7, 9, 10, 13-17, 18, 19, 21, ARF1, 2A, 24, 19, 17, 4, 10A, 5, 10B, 16A; IAA3, 5, 6, 9, 13, 16,20, 22, ARF8B, 3, 8A, 2A, 24, 7A, 9B, 9A, 4, 10A, 6A, 2B, 16B; IAA13; IAA1, 3, 4, 6, 9, 11, 18, 19, 22, 25, ARF1, 7A, 7B, 16B; IAA7, ARF24, 9B, 16B; IAA4, 5, 11, 12, 17-20, 25, ARF9B, 17, 2B, 5; IAA1, 2, 13, 14, 15, 18, 26, ARF2A, 19, 9B, 4, 10A; IAA8; IAA23 / IAA 3.1, 3.2, 6.1, 7.2, 8.1, 8.2, 9.1, 9.2, 14.3, 22.1, 22.2, 23.2, 24.1, 24.2, 26.1, ARF8A.2, 18.1, 2B.2; IAA1.1, 1.2, 2.1, 3.1, 4.1, 6.1, 6.2, 7.2, 8.1, 8.2, 9.1, 9.2,14.1, 14.2, 14.3, 16.1, 16.2, 20, 21.1, 22.1, 23.2, 25.2, 26.3; IAA2.1, 2.2, 3.1, 3.2, 4.1, 7.1,11.2, 13, 14.1, 16.1, 16.2, 19.2, 20, 22.2, ARF8B.2, 3.1, 3.2, 8A.2, 8A.1, 8A.2, 9A, 4, 10A.2, 2B.2, 16A.2, 16A.3; IAA1.1, 1.2, 2.1, 3.1, 4.1, 6.1, 6.2, 7.2, 8.1, 8.2, 9.1, 9.2, 14.1, 14.2, 14.3, 16.1, 16.2, 20, 21.1, 22.1, 23.2, 25.2, 26.3, ARF1, 8B, 8B.1, 8B.2, 3, 8A.2, 18.1, 7A.1, 7A.1, 9A, 4, 10A.2, 2B.2, 5, 7B.4, 16A.2; IAA 2.1, 3.1, 4.1, 6-1, 6.2, 7.2, 8.1, 8.2, 9.1, 9.2, 11.1, 14.2, 14.3, 16.1, 16.2, 20, 21.1, 22.1, 23.1, 25.1, 25.2, 26.3, ARF8B.1, 8B.2, 8A.2, 2A.1, 2A.2, 18.1, 7A.1, 7A.2, 19.1, 19.2, 10A.2, 2B.2, 16A.2, 16A.3; IAA 6.1, 8.1, 9.1, 14.3, 16.2, 25.1, 25.2, ARF16A.1, 8A.2,IAA1.2, 6.2, 8.1, 11.2, 14.2,19.2, 21.1, 25.1, 25.2, ARF8B, 8B.2, 3.1, 3.2, 2A.1, 2A.2, 7A.1, 10B; IAA1.1, 1.2, 4.1, 6.2, 6.4, 11.2, 13, 16.2, 22.1, 23.1, 23.2, ARF8B, 8B.1, 8B.2, 2A.1, 7A.2, 9A, 7B.4; IAA1.2, 2.2, 3.1 , 6.1, 6.4, 11.2, 14.2, 14.3, 22.1, 22.2,23.1, 23.2, 24.1, 24.2, 26.2, ARF8B.1, 8B.2, 3, 7A.2, 17, 5; IAA4.1, 6.2, 9.1, 9.2, 20, 24.1, 25.1, 26.1, ARF8B, 8B.1, 8B.2, 3.1, 2A.1, 7A.1, 19.2, 17, 4, 10A.2, 2B.2; ARF8A.2; ARF4
Stress responses:HSE (heat shock element), TC-rich repeats (defense and stress responsiveness), MBS (drought-inducibility),LTR (low-temperature response), WUN-motif (wound-responsive element), Box-W1 (fungal elicitor responsive element),DRE (cold- and dehydration-responsiveness),AT-rich sequence (maximal elicitor-mediated activation) / IAA3-6, 8-11, 13-20, 23-25, ARF1, 8A, 18, 24, 19, 6B, 9B, 17, 4, 10A, 5, 10, 16A, 16B; IAA2, 3, 5-9,11-13, 14-18, 20-22, 24-26, ARF1, 8B, 3, 8A, 18, 24, 7A, 19, 6B, 9B, 9A, 17, 2B, 5, 7B, 10B, 16A, 16B; IAA1,6, 7, 11-13, 16, 17, 19-22, 24, ARF1, 8B, 3, 8A, 18,, 24, 7A, 6B, 9A, 17, 4, 2B, 5, 7B, 10B, 16B; IAA3, 6, 13, 17, 18, 25, ARF8B, 3, 24, 17, 7B; IAA10, 22, ARF8A, 18; IAA3, 22-24, ARF1, 2, 4, 7, 8, 17, 19-21; IAA18;ARF8B, 3, 8A, 6A, 10B / IAA1, 3-9, 11, 15, 18-22, ARF1, 3, 2A, 24, 7A, 19, 9B, 17, 4, 10A, 2B, 5, 10B, 16B; IAA1-3, 5-8, 9, 11-16, 18, 19-26, ARF1, 3, 2A, 24, 7A, 19, 9B, 9A, 17, 4, 10A, 6A, 2B, 5, 10B, 16A, 16B; IAA1-4, 9-13, 15-20, 22, 26, ARF1, 3, 24, 7A, 19, 9B, 17, 4, 2B, 10B, 16A, 16B; IAA2, 11,17, 21, 25, ARF3, 17, 10A, 16A, 16B; IAA5, ARF9, 11, 13; IAA1, 3, 6, 11, 15, 17, 19, 22, 23, ARF1, 2A, 7A, 19, 2B, 7B, 10B, 16A, 16B; ARF8B, 8A, 18, 10B / IAA1.1, 1.2, 2.1, 2.2, 3.1, 3.2, 6.1, 4.1, 4.2, 7.1, 7.2, 6.2, 6.4, 8.1, 8.2, 8.3, 9.1, 11.2, 13, 14.2, 14.3, 16.1, 16.2, 19.1, 19.2, 21.1, 21.2, 23.2, 24.1, 24.2, 25.1, 26.1, 26.2, ARF1, 8B.1, 8B.2, 3.1, 2A.1, 7A.1, 19.1, 19.2, 6B.1, 6B.3, 17, 2B.2, 5, 7B-4, 16B.1, 16.2, 16.3; IAA1.1, 1.2, 2.1, 2.2, 3.1, 4.1, 4.2, 6.1, 6.4, 7.1, 8.1, 8.2, 8.3, 9.1, 9.2, 14.2, 14.3, 16.1, 19.2, 20, 21.2, 22.1, 22.2, 24.2, 25.1, 26.1, 26.2, 26.3, ARF1, 8B.1,8B.2, 8A.2, 2A.1, 7A.1, 7A.2, 19.1, 19.2, 6B.3, 9A, 17, 4, 2B.2, 5, 7B.4, 16A.1, 16A.3; IAA 1.1, 1.2, 2.1, 2.2, 3.1, 3.2, 4.1, 4.2, 6.1, 6.4, 8.2, 9.1, 9.2, 11.2, 13, 14.2, 14.3, 16.1, 16.2, 19.1, 19.2, 20, 21.1, 22.2,24.2, 25.2, 26.2, 26.3, ARF1.1, 8B.1, 3.1, 3.2, 2A.2, 18.1, 7A.1, 7A.2, 19.1, 6B.1, 17, 4, 10A.2, 2B.2, 5, 7B.4, 10B, 16A.3; IAA2.2, 3.1, 3.2, 6.4, 8.1, 8.3, 14.1, 14.3, 16.2, 19.2, 23.1, 23.2, 25.1, 26.3, ARF3.1, 7A.2, 6B.1, 9A, 17, 4, 2B.2, 7B.4; IAA7.1, 14.3, 26.1, ARF 4, 10A.2, 16A.1; IAA7.2, 14.2, 16.1, 16.2, 20, 21.1, 22.2, 25.1, 25.2, 26.2, ARF2A.1, 7A.1, 7A.2, 19.2, 9A, 17, 4, 2B.2, 7B.4, 16A.1; ARF7A.1;IAA6.1, 25.1, 26.1
Light signaling elements / AT1-motif, Box 4, Box I, G-Box, Sp1, TCT-motif, GT1-motif, GAG-motif, I-box elements are present in the promoters of almost all the SlARF and SlIAA genes. ACE, ATCT-motif, GATA-motif, MRE, GA-motif, L-box, LAMP-element, chs-CMA1a, MNF1, TCCC-motif, as-2-box elements are present at least in 5 promoters each of SlARF and SlIAA genes. / Box 4, Box I, G-Box, TCT-motif, GT1-motif, GAG-motif, I-box elements are present in the promoters of almost all atheStARF and StIAA genes.AT1-motif, ACE, ATCT-motif, GATA-motif, MRE, GA-motif, L-box, LAMP-element, chs-CMA1a, MNF1, MRE, TCCC-motif and as-2-box elements are present at least in 5 promoters each of StARF and StIAA genes. / AT1-motif, Box 4, Box I, G-Box, Sp1, GT1-motif, GAG-motif, GATA-box, Sp1, I-box elements are present in the promoters of almost all atheNbARF and NbIAA genes. ACE, ATCT-motif, Box III, MRE, GA-motif, L-box, LAMP-element, chs-CMA1a, MNF1, TCT-motif, TCCC-motif, as-2-box elements are present at least in 5 promoters each of NbARF and NbIAA genes.