Table S1. Candidate genes of leaf shape determination in Arabidopsis and physical location of their homologues in G. raimondii genome and homologous sequences in cotton gene index.

Leaf shape candidate gene / Gossypiumraimondii / Gossypiumhirsutum
Arabidopsis Protein / Family/Role / G. raimondii Gene / Chr / Physical Position (Mb) / Amino Acid Similarity (%) / EST/TC / Score / E-value
KNAT6 / Class 1 KNOX / Gorai.004G236400.1 / 4 / 57.47 / 58.1 / TC261486 / 4674 / 3.10E-206
KNAT1 / Class 1 KNOX / Gorai.005G098100.1 / 5 / 15.04 / 60.0 / TC255316 / 4801 / 3.60E-212
KNAT6 / Class 1 KNOX / Gorai.005G180500.1 / 5 / 52.99 / 84.7 / TC254507 / 5879 / 9.20E-261
KNAT6 / Class 1 KNOX / Gorai.007G306500.1 / 7 / 52.00 / 52.8 / AI054970 / 1224 / 7.80E-50
KNAT6 / Class 1 KNOX / Gorai.008G296800.1 / 8 / 56.95 / 68.0 / DW500145 / 1486 / 9.40E-62
STM / Class 1 KNOX / Gorai.009G181500.1 / 9 / 13.95 / 61.5 / TC273462 / 4895 / 3.00E-162
KNAT1 / Class 1 KNOX / Gorai.009G223200.1 / 9 / 17.38 / 67.5 / TC254362 / 3598 / 3.30E-171
KNAT6 / Class 1 KNOX / Gorai.009G336900.1 / 9 / 36.51 / 73.8 / ES843392 / 4451 / 3.80E-196
KNAT1 / Class 1 KNOX / Gorai.010G029000.1 / 10 / 2.37 / 72.0 / TC254362 / 6874 / 0
STM / Class 1 KNOX / Gorai.010G183800.1 / 10 / 53.31 / 62.0 / TC254864 / 4409 / 2.30E-194
KNAT6 / Class 1 KNOX / Gorai.013G129400.1 / 13 / 33.75 / 52.6 / TC268433 / 1892 / 3.00E-80
KNATM / Modified KNOX / Gorai.008G291600.1 / 8 / 56.59 / 42.5 / TC261475 / 198 / 0.79
AS1 / ARP / Gorai.012G104100.1 / 12 / 23.31 / 61.0 / TC248918 / 7171 / 0
AS2 / LOB Domain / Gorai.007G350300 / 7 / 58.03 / 67.6 / ES819678 / 532 / 2.30E-18
BOP1 / BTB/POZ Domain / Gorai.006G133600.1 / 6 / 38.79 / 82.2 / TC234590 / 2951 / 2.40E-128
BOP2 / BTB/POZ Domain / Gorai.002G226700.1 / 2 / 58.35 / 78.9 / TC234590 / 3902 / 2.70E-171
CLF / PRC2 / Gorai.007G215200.1 / 7 / 23.78 / 72.2 / ES803358 / 5237 / 9.60E-232
CLF / PRC2 / Gorai.011G106100.1 / 11 / 12.34 / 71.6 / ES803358 / 4421 / 6.90E-195
SWN / PRC2 / Gorai.008G139100.1 / 8 / 38.98 / 64.9 / TC273368 / 1337 / 0
FIE / PRC2 / Gorai.013G163900.1 / 13 / 44.49 / 71.7 / TC236369 / 4869 / 3.20E-228
EMF2 / Polycomb-Group / Gorai.001G051500.1 / 1 / 4.88 / 70.9 / TC240563 / 6555 / 2.20E-191
EMF2 / Polycomb-Group / Gorai.003G112000.1 / 3 / 34.29 / 72.7 / TC252943 / 6678 / 5.8e-297
LHP / PRC1-Like / Gorai.007G347200.1 / 7 / 57.75 / 46.8 / TC239922 / 3331 / 1.80E-145
AtRING1a / PRC1-Like / Gorai.008G154600.1 / 8 / 41.35 / 55.8 / ES793846 / 214 / 0.64
AtRING1a / PRC1-Like / Gorai.010G155500.1 / 10 / 42.88 / 46.6 / None / N/A / N/A
YAB1/FIL / YABBY TF / Gorai.001G174800.1 / 1 / 25.60 / 74.5 / TC232172 / 4770 / 1.00E-210
YAB1/FIL / YABBY TF / Gorai.007G089700.1 / 7 / 6.52 / 71.3 / TC277424 / 3453 / 5.50E-151
YAB1/FIL / YABBY TF / Gorai.008G236500.1 / 8 / 52.22 / 78.7 / TC277225 / 2964 / 5.00E-129
PIN1 / Auxin Efflux Carrier / Gorai.006G191800.1 / 6 / 44.88 / 83.3 / TC243046 / 7636 / 0
PIN1 / Auxin Efflux Carrier / Gorai.007G003800.1 / 7 / 0.31 / 80.1 / TC243046 / 3604 / 6.10E-228
PIN1 / Auxin Efflux Carrier / Gorai.007G352200.1 / 7 / 58.24 / 80.2 / TC243046 / 1891 / 2.00E-151
PIN1 / Auxin Efflux Carrier / Gorai.008G290000.1 / 8 / 56.48 / 83.9 / TC278560 / 6025 / 2.10E-167
PID / Ser/Threo Kinase / Gorai.005G267200.1 / 5 / 63.97 / 71.4 / TC259159 / 8446 / 0
PID / Ser/Threo Kinase / Gorai.008G047700.1 / 8 / 6.57 / 74.8 / TC256184 / 7405 / 0
ARF6 / Auxin Response Factor / Gorai.006G008700.1 / 6 / 1.84 / 76.8 / TC250097 / 6308 / 3.70E-280
ARF6 / Auxin Response Factor / Gorai.008G097200.1 / 8 / 26.75 / 77.5 / TC278390 / 4742 / 1.10E-286
ARF6 / Auxin Response Factor / Gorai.009G152700.1 / 9 / 11.62 / 83.4 / TC246198 / 5305 / 7.50E-235
ARF6 / Auxin Response Factor / Gorai.011G048200.1 / 11 / 3.74 / 82.0 / TC231817 / 5500 / 8.90E-244
ARF8 / Auxin Response Factor / Gorai.001G204500.1 / 1 / 39.74 / 75.7 / DT463674 / 3833 / 3.40E-168
ARF8 / Auxin Response Factor / Gorai.008G054600.1 / 8 / 7.98 / 75.5 / TC241907 / 3605 / 7.90E-158
SAW1/BLH2 / BEL1-Like / Gorai.003G018100.1 / 3 / 1.33 / 48.1 / CO114222 / 2578 / 2.20E-111
SAW1/BLH2 / BEL1-Like / Gorai.007G207200.1 / 7 / 21.77 / 58.6 / TC244589 / 4489 / 6.90E-189
SAW1/BLH2 / BEL1-Like / Gorai.008G070800.1 / 8 / 12.16 / 60.0 / TC274830 / 5356 / 4.30E-237
BLR/PNY/BLH9 / BEL1-Like / Gorai.002G255800.1 / 2 / 61.80 / 52.9 / TC267809 / 4337 / 5.50E-191
BLR/PNY/BLH9 / BEL1-Like / Gorai.012G108300.1 / 12 / 24.32 / 41.1 / TC244159 / 5082 / 9.30E-225
PNF/BLH8 / BEL1-Like / Gorai.009G109300.1 / 9 / 7.98 / 23.4 / TC234021 / 4077 / 3.20E-179
PNF/BLH8 / BEL1-Like / Gorai.003G143600.1 / 3 / 40.89 / 39.2 / TC259268 / 6551 / 3.70E-291
ATH1 / BEL1-Like / Gorai.001G023100.1 / 1 / 2.18 / 40.4 / DW486245 / 3592 / 2.90E-157
CUC2 / NAC / Gorai.002G067300.1 / 2 / 7.85 / 71.0 / TC246269 / 1386 / 7.00E-58
CUC2 / NAC / Gorai.007G323900.1 / 7 / 54.20 / 69.7 / TC258660 / 1310 / 3.30E-54
CUC2 / NAC / Gorai.013G171300.1 / 13 / 45.79 / 69.6 / TC258660 / 1212 / 8.90E-50
CUC3 / NAC / Gorai.002G113300.1 / 2 / 16.00 / 49.5 / TC268975 / 1215 / 4.90E-50
CUC3 / NAC / Gorai.009G186000.1 / 9 / 14.30 / 46.1 / TC268975 / 4758 / 4.60E-120
JAG / Zn Finger TF / Gorai.005G191500.1 / 5 / 55.83 / 57.5 / ES794796 / 2050 / 3.50E-104
JAG / Zn Finger TF / Gorai.012G122600.1 / 12 / 28.07 / 51.7 / ES794796 / 1004 / 5.30E-54
IPT7 / Cytokinin Biosynthesis / Gorai.011G169700.1 / 11 / 35.59 / 71.4 / TC233950 / 1213 / 7.70E-50
IPT7 / Cytokinin Biosynthesis / Gorai.004G259100.1 / 4 / 59.50 / 64.1 / None / N/A / N/A
GA20ox1 / Gibberellin Biosynth. / Gorai.006G005500.1 / 6 / 1.04 / 66.4 / TC256212 / 4318 / 3.10E-190
GA20ox1 / Gibberellin Biosynth. / Gorai.006G196600.1 / 6 / 45.34 / 77.6 / TC269286 / 10656 / 0
GA2ox1 / Gibberellin Redox / Gorai.002G038900.1 / 2 / 3.11 / 71.6 / TC244437 / 5402 / 1.60E-267
GA2ox1 / Gibberellin Redox / Gorai.013G176900.1 / 13 / 46.76 / 72.9 / TC263827 / 48989 / 1.30E-219
COMT1 / Lignin Biosynthesis / Gorai.002G222400.1 / 2 / 57.71 / 67.3 / TC258071 / 6850 / 0
COMT1 / Lignin Biosynthesis / Gorai.004G125600.1 / 4 / 32.81 / 90.1 / TC243681 / 6779 / 1.80E-301
COMT1 / Lignin Biosynthesis / Gorai.004G251400.1 / 4 / 58.91 / 62.8 / TC232188 / 4719 / 2.00E-208
COMT1 / Lignin Biosynthesis / Gorai.006G126800.1 / 6 / 37.91 / 69.8 / TC245932 / 4335 / 5.00E-220
COMT1 / Lignin Biosynthesis / Gorai.008G131700.1 / 8 / 37.72 / 69.8 / TC236546 / 4088 / 1.00E-179
COMT1 / Lignin Biosynthesis / Gorai.008G264900.1 / 8 / 54.41 / 83.7 / TC232474 / 6911 / 0
CCoAOMT / Lignin Biosynthesis / Gorai.005G237100.1 / 5 / 61.87 / 89.2 / TC261091 / 1285 / 2.30E-119
CCoAOMT / Lignin Biosynthesis / Gorai.008G024000.1 / 8 / 2.75 / 74.2 / TC264798 / 5661 / 6.70E-251
CCoAOMT / Lignin Biosynthesis / Gorai.012G149800.1 / 12 / 32.36 / 94.8 / TC232412 / 4711 / 4.80E-208
CCoAOMT / Lignin Biosynthesis / Gorai.013G045300.1 / 13 / 3.96 / 94.0 / TC261091 / 4816 / 1.10E-212
LMI1/ATHB51 / HD-Zip 1 / Gorai.002G244000.1 / 2 / 60.81 / 42.4 / TC252073 / 1580 / 2.00E-66
LMI1/ATHB51 / HD-Zip 1 / Gorai.002G244200.1 / 2 / 60.84 / 55.5 / TC252073 / 3779 / 9.80E-166
TCP4 / TCP / Gorai.002G064500.1 / 2 / 7.55 / 61.7 / TC237216 / 10554 / 0
TCP15 / TCP / Gorai.008G181600.1 / 8 / 45.92 / 48.8 / TC237103 / 5668 / 3.20E-251
TCP2 / TCP / Gorai.009G153900.1 / 9 / 11.75 / 43.9 / TC270454 / 7716 / 0
TCP4 / TCP / Gorai.009G373000.1 / 9 / 50.50 / 65.8 / TC245172 / 8452 / 0
TCP2 / TCP / Gorai.011G046000.1 / 11 / 3.52 / 44.7 / TC240768 / 5531 / 4.20E-245
TCP15 / TCP / Gorai.013G084500.1 / 13 / 12.16 / 46.6 / TC262572 / 5161 / 2.50E-228
TCP5 / TCP / Gorai.001G076700.1 / 1 / 7.89 / 30.1 / TC236882 / 861 / 1.40E-41
TCP13 / TCP / Gorai.006G009800.1 / 6 / 2.18 / 46.0 / TC265966 / 4251 / 4.30E-187
TCP5 / TCP / Gorai.008G199700.1 / 8 / 48.46 / 24.5 / TC236882 / 4677 / 2.30E-206
TCP13 / TCP / Gorai.012G048500.1 / 12 / 6.24 / 31.1 / TC255975 / 6108 / 4.10E-271
TCP20 / TCP / Gorai.006G043800.1 / 6 / 13.02 / 67.4 / TC249024 / 3159 / 1.90E-153
TCP20 / TCP / Gorai.008G157300.1 / 8 / 42.00 / 56.7 / TC231811 / 5243 / 5.40E-232
TCP20 / TCP / Gorai.011G086900.1 / 11 / 9.06 / 64.7 / TC272182 / 4642 / 8.60E-205
IAA4 / Auxin Response / Gorai.005G046400.1 / 5 / 4.40 / 80.5 / TC237283 / 4687 / 7.60E-207
IAA4 / Auxin Response / Gorai.006G245900.1 / 6 / 49.08 / 77.7 / TC265149 / 2146 / 8.70E-92
IAA4 / Auxin Response / Gorai.007G277000.1 / 7 / 47.40 / 80.3 / TC257537 / 5021 / 6.10E-222
IAA4 / Auxin Response / Gorai.013G200800.1 / 13 / 51.19 / 74.3 / TC239351 / 2881 / 4.90E-174