Table 1 Characters of Clementine Mandarin MADS-Box Genes

Supplementary table 1 Characters of Clementine mandarin MADS-box genes

Name / Gene ID / ORF / Protein length / Molecular weight / PI / Map to EST / Intron / Predicted Function / Type
CcMADS1 / clementine0.9_019908m / 738 / 245 / 28.19 / 9.59 / ﹢ / 6 / AG / AG
CcMADS2 / clementine0.9_021068m / 675 / 224 / 25.69 / 9.44 / ﹢ / 6 / STK / AG
CcMADS3 / clementine0.9_021154m / 672 / 223 / 25.6 / 9.44 / ﹢ / 6 / STK / AG
CcMADS4 / clementine0.9_022612m / 585 / 194 / 22.35 / 9.77 / ﹢ / 4 / AG / AG
CcMADS5 / clementine0.9_024260m / 477 / 158 / 18.46 / 9.89 / ﹢ / 3 / SHF1 / AP1/FUL
CcMADS6 / clementine0.9_019973m / 735 / 244 / 27.76 / 9.08 / ﹢ / 7 / AGL6 / AGL6
CcMADS7 / clementine0.9_027776m / 513 / 170 / 19.49 / 9.04 / ﹢ / 5 / AGL12 / XAL1
CcMADS8 / clementine0.9_020257m / 723 / 240 / 27.18 / 7.73 / ﹣ / 6 / AGL15 / AGL15
CcMADS9 / clementine0.9_031353m / 396 / 131 / 14.72 / 8.85 / ﹢ / 3 / AGL18 / AGL15
CcMADS10 / clementine0.9_029324m / 309 / 102 / 11.89 / 9.73 / ﹢ / 1 / AGL44 / AGL17
CcMADS11 / clementine0.9_020032m / 732 / 243 / 28.41 / 9.28 / ﹢ / 8 / AGL8 / AP1/FUL
CcMADS12 / clementine0.9_020838m / 687 / 228 / 26.56 / 9.31 / ﹢ / 6 / APL1 / AP1/FUL
CcMADS13 / clementine0.9_021724m / 636 / 211 / 24.64 / 9.32 / ﹢ / 6 / APL1 / AP1/FUL
CcMADS14 / clementine0.9_020307m / 717 / 238 / 27.39 / 8.45 / ﹢ / 5 / APL3 / AP3
CcMADS15 / clementine0.9_021103m / 672 / 223 / 25.76 / 9.39 / ﹢ / 6 / APL3 / AP3
CcMADS16 / clementine0.9_021253m / 666 / 221 / 25.87 / 9.51 / ﹢ / 6 / APL3 / AP3
CcMADS17 / clementine0.9_021759m / 636 / 211 / 24.36 / 8.59 / ﹢ / 6 / APL3 / AP3
CcMADS18 / clementine0.9_024077m / 489 / 162 / 18.46 / 9.43 / ﹢ / 3 / APL3 / AP3
CcMADS19 / clementine0.9_030040m / 573 / 190 / 21.23 / 8.45 / ﹢ / 5 / FLC / FLC
CcMADS20 / clementine0.9_021355m / 660 / 219 / 25.66 / 9.11 / ﹢ / 6 / PI / PI
CcMADS21 / clementine0.9_021718m / 636 / 211 / 24.83 / 8.42 / ﹢ / 6 / PI / PI
CcMADS22 / clementine0.9_019281m / 774 / 257 / 29.26 / 8.45 / ﹢ / 7 / SEP3 / SEP
CcMADS23 / clementine0.9_019320m / 771 / 256 / 29.13 / 8.65 / ﹢ / 7 / SEP3 / SEP
CcMADS24 / clementine0.9_019626m / 753 / 250 / 28.59 / 8.99 / ﹢ / 7 / SEP1 / SEP
CcMADS25 / clementine0.9_019726m / 750 / 249 / 28.46 / 8.99 / ﹢ / 6 / SEP1 / SEP
CcMADS26 / clementine0.9_019967m / 738 / 245 / 28 / 7.8 / ﹢ / 7 / SEP2 / SEP
CcMADS27 / clementine0.9_019980m / 735 / 244 / 27.81 / 8.45 / ﹢ / 7 / SEP3 / SEP
CcMADS28 / clementine0.9_019984m / 735 / 244 / 27.88 / 7.8 / ﹢ / 7 / SEP2 / SEP
CcMADS29 / clementine0.9_020021m / 732 / 243 / 27.95 / 9.01 / ﹢ / 7 / SEP 2 / SEP
CcMADS30 / clementine0.9_020090m / 729 / 242 / 27.56 / 8.65 / ﹢ / 7 / SEP3 / SEP
CcMADS31 / clementine0.9_020731m / 693 / 230 / 26.11 / 8.67 / ﹢ / 7 / SEP3 / SEP
CcMADS32 / clementine0.9_022203m / 609 / 202 / 23.28 / 9.4 / ﹢ / 7 / SEP1 / SEP
CcMADS33 / clementine0.9_023878m / 504 / 167 / 19.33 / 9.6 / ﹢ / 6 / SEP3 / SEP
CcMADS34 / clementine0.9_023925m / 501 / 166 / 19.39 / 9.62 / ﹢ / 3 / SEP3 / SEP
CcMADS35 / clementine0.9_019716m / 750 / 249 / 28.91 / 9.54 / ﹢ / 7 / AGL19 / SOC1
CcMADS36 / clementine0.9_021261m / 663 / 220 / 25.19 / 9.24 / ﹢ / 6 / AGL20 / SOC1
CcMADS37 / clementine0.9_021700m / 639 / 212 / 24.89 / 8.53 / ﹢ / 6 / AGL42 / SOC1
CcMADS38 / clementine0.9_021791m / 633 / 210 / 24.69 / 8.53 / ﹢ / 6 / AGL42 / SOC1
CcMADS39 / clementine0.9_021815m / 633 / 210 / 24.51 / 9.23 / ﹢ / 6 / AGL19 / SOC1
CcMADS40 / clementine0.9_022186m / 609 / 202 / 23.52 / 9.11 / ﹢ / 6 / AGL19 / SOC1
CcMADS41 / clementine0.9_023727m / 513 / 170 / 19.66 / 9.85 / ﹢ / 5 / AGL20 / SOC1
CcMADS42 / clementine0.9_021434m / 654 / 217 / 24.67 / 6.18 / ﹢ / 6 / SVP / SVP
CcMADS43 / clementine0.9_019775m / 747 / 248 / 28.67 / 6.62 / ﹢ / 6 / TT16 / TT16
CcMADS44 / clementine0.9_020252m / 723 / 240 / 28.17 / 7.22 / ﹢ / 5 / TT16 / TT16
CcMADS45 / clementine0.9_012775m / 1155 / 384 / 43.28 / 6.4 / ﹢ / 11 / AGL65 / MIKC*
CcMADS46 / clementine0.9_013916m / 1083 / 360 / 40.52 / 6.12 / ﹢ / 10 / AGL65 / MIKC*
CcMADS47 / clementine0.9_014436m / 1053 / 350 / 39.46 / 6.76 / ﹢ / 10 / AGL30 / MIKC*
CcMADS48 / clementine0.9_016536m / 933 / 310 / 35.71 / 5.55 / ﹢ / 10 / AGL104 / MIKC*
CcMADS49 / clementine0.9_032522m / 1047 / 348 / 39.27 / 5.25 / ﹣ / 10 / AGL104 / MIKC*
CcMADS50 / clementine0.9_020619m / 699 / 232 / 26.61 / 5.83 / ﹢ / 0 / AGL62 / Mα
CcMADS51 / clementine0.9_022731m / 576 / 191 / 21.89 / 9.27 / ﹣ / 1 / AGL62 / Mα
CcMADS52 / clementine0.9_023618m / 519 / 172 / 19.12 / 9.05 / ﹢ / 0 / AGL61 / Mα
CcMADS53 / clementine0.9_027868m / 570 / 189 / 21.67 / 9.42 / ﹢ / 1 / AGL61 / Mα
CcMADS54 / clementine0.9_028969m / 381 / 126 / 14.37 / 9.79 / ﹢ / 0 / AGL62 / Mα
CcMADS55 / clementine0.9_029852m / 561 / 186 / 21.48 / 9.28 / ﹣ / 0 / AGL62 / Mα
CcMADS56 / clementine0.9_030320m / 570 / 189 / 21.78 / 9.55 / ﹢ / 1 / AGL61 / Mα
CcMADS57 / clementine0.9_030864m / 552 / 183 / 20.88 / 9.3 / ﹣ / 1 / AGL62 / Mα
CcMADS58 / clementine0.9_030885m / 450 / 149 / 17.48 / 9.38 / ﹣ / 0 / AGL61 / Mα
CcMADS59 / clementine0.9_032410m / 660 / 219 / 24.85 / 5.49 / ﹣ / 0 / AGL62 / Mα
CcMADS60 / clementine0.9_032418m / 531 / 176 / 20.17 / 9.49 / ﹣ / 0 / MADS-box / Mα
CcMADS61 / clementine0.9_032526m / 522 / 173 / 20.27 / 5.7 / ﹣ / 1 / AGL62 / Mα
CcMADS62 / clementine0.9_032708m / 513 / 170 / 18.84 / 9.06 / ﹢ / 0 / AGL29 / Mα
CcMADS63 / clementine0.9_032961m / 672 / 223 / 25.14 / 9.16 / ﹣ / 2 / AGL62 / Mα
CcMADS64 / clementine0.9_033224m / 450 / 149 / 16.49 / 9.3 / ﹢ / 0 / AGL61 / Mα
CcMADS65 / clementine0.9_033714m / 684 / 227 / 25.71 / 8.99 / ﹢ / 0 / AGL62 / Mα
CcMADS66 / clementine0.9_033757m / 684 / 227 / 25.61 / 9.34 / ﹢ / 0 / AGL62 / Mα
CcMADS67 / clementine0.9_034251m / 870 / 289 / 32.31 / 5.94 / ﹣ / 0 / MADS-box / Mα
CcMADS68 / clementine0.9_034435m / 561 / 186 / 21.4 / 9.34 / ﹣ / 1 / AGL57 / Mα
CcMADS69 / clementine0.9_034937m / 579 / 192 / 21.83 / 7.99 / ﹢ / 1 / AGL61 / Mα
CcMADS70 / clementine0.9_035380m / 501 / 166 / 18.74 / 6.85 / ﹣ / 0 / AGL29 / Mα
CcMADS71 / clementine0.9_035692m / 576 / 191 / 21.58 / 6.32 / ﹢ / 0 / AGL61 / Mα
CcMADS72 / clementine0.9_035770m / 525 / 174 / 20.06 / 9.89 / ﹣ / 1 / AGL62 / Mα
CcMADS73 / clementine0.9_035878m / 543 / 180 / 20.22 / 8.77 / ﹣ / 0 / AGL29 / Mα
CcMADS74 / clementine0.9_018087m / 843 / 280 / 30.98 / 9.41 / ﹢ / 1 / AGL81 / Mβ
CcMADS75 / clementine0.9_019069m / 786 / 261 / 29.18 / 8.7 / ﹢ / 0 / AGL81 / Mβ
CcMADS76 / clementine0.9_020900m / 684 / 227 / 25.94 / 9.53 / ﹢ / 1 / AGL81 / Mβ
CcMADS77 / clementine0.9_030762m / 813 / 270 / 31.42 / 8.89 / ﹣ / 0 / AGL81 / Mβ
CcMADS78 / clementine0.9_032015m / 990 / 329 / 38.05 / 9.1 / ﹢ / 0 / AGL81 / Mβ
CcMADS79 / clementine0.9_033067m / 861 / 286 / 32.18 / 5.37 / ﹣ / 0 / AGL81 / Mβ
CcMADS80 / clementine0.9_028401m / 702 / 233 / 27.06 / 9.5 / ﹣ / 0 / AGL80 / Mγ
CcMADS81 / clementine0.9_029754m / 714 / 237 / 27.2 / 9.3 / ﹣ / 0 / AGL80 / Mγ
CcMADS82 / clementine0.9_030818m / 714 / 237 / 27.19 / 9.37 / 0 / AGL80 / Mγ
CcMADS83 / clementine0.9_031499m / 534 / 177 / 20.35 / 9.76 / ﹣ / 0 / AGL87 / Mγ
CcMADS84 / clementine0.9_034705m / 1341 / 446 / 48.44 / 6.88 / ﹣ / 0 / AGL48 / Mγ

Supplementary table 2 Characters of Sweet orange MADS-box genes

Name / Gene ID / Chromosomal location / Common / ORF / Protein length / Molecular weight / PI / Intron / Map to EST / Predicted Function / Type
CsMADS1 / orange1.1g036452m / chrUn:4679846..4684337 / no / 735 / 360 / 41.3 / 9.19 / 9 / ﹢ / AG / AG
CsMADS2 / orange1.1g037149m / chr9:16011858..16017818 / Clementine
0.9_019973m / 687 / 244 / 27.76 / 9.08 / 7 / ﹢ / AGL6 / AGL6
CsMADS3 / orange1.1g046479m / chr5:18037676..18043336 / no / 606 / 228 / 26.12 / 9.18 / 7 / ﹢ / AGL6 / AGL6
CsMADS4 / orange1.1g028961m / chr7:826783..831548 / no / 768 / 201 / 22.9 / 7.68 / 6 / ﹢ / AGL 12 / XAL1
CsMADS5 / orange1.1g025240m / chr2:2055241..2051512 / no / 1083 / 255 / 28.88 / 8.29 / 7 / ﹢ / AGL15 / AGL15
CsMADS6 / orange1.1g039982m / chrUn:35063856..35066941 / no / 762 / 253 / 28.88 / 7.69 / 7 / ﹢ / AGL15 / AGL15
CsMADS7 / orange1.1g024093m / chr4:3740320..3742615 / no / 819 / 272 / 31.31 / 8.09 / 4 / ﹢ / AP3 / AP3
CsMADS8 / orange1.1g027470m / chr1:27100646..27103679 / no / 672 / 223 / 25.81 / 9.39 / 5 / ﹢ / AP3 / AP3
CsMADS9 / orange1.1g028296m / chr4:3740320..3742607 / no / 636 / 211 / 24.33 / 8.27 / 4 / ﹢ / AP3 / AP3
CsMADS10 / orange1.1g031283m / chr4:3740320..3741715 / no / 489 / 162 / 18.44 / 9.32 / 3 / ﹢ / AP3 / AP3
CsMADS11 / orange1.1g040046m / chr3:27150820..27152982 / no / 666 / 221 / 25.9 / 9.53 / 6 / ﹢ / AP3 / AP3
CsMADS12 / orange1.1g040096m / chr3:23275424..23278074 / no / 639 / 212 / 24.94 / 8.42 / 6 / ﹢ / PI / PI
CsMADS13 / orange1.1g042044m / chr3:23270421..23273328 / no / 657 / 218 / 25.57 / 9.11 / 6 / ﹢ / PI / PI
CsMADS14 / orange1.1g024640m / chr5:9253721..9256475 / no / 798 / 265 / 30.23 / 8.9 / 7 / ﹢ / SEP1 / SEP
CsMADS15 / orange1.1g026043m / chr7:7763967..7775808 / no / 735 / 244 / 27.91 / 8.36 / 8 / ﹢ / SEP2 / SEP
CsMADS16 / orange1.1g026143m / chr6:19406316..19411587 / no / 732 / 243 / 27.89 / 9.01 / 7 / ﹢ / SEP2 / SEP
CsMADS17 / orange1.1g027656m / chrUn:4690986..4695981 / Clementine
0.9_021261m / 663 / 220 / 25.19 / 9.24 / 9 / ﹢ / AGL20 / SOC1
CsMADS18 / orange1.1g028363m / chr5:6921959..6931427 / Clementine
0.9_021815m / 633 / 210 / 24.51 / 9.23 / 7 / ﹢ / AGL19 / SOC1
CsMADS19 / orange1.1g028641m / chrUn:4690986..4695981 / no / 621 / 206 / 23.59 / 9.4 / 6 / ﹢ / AGL20 / SOC1
CsMADS20 / orange1.1g028858m / chr5:6921959..6931427 / Clementine
0.9_022186m / 609 / 202 / 23.52 / 9.11 / 7 / ﹢ / AGL19 / SOC1
CsMADS21 / orange1.1g030748m / chrUn:4690986..4695981 / no / 519 / 172 / 19.44 / 9.07 / 8 / ﹢ / AGL14 / SOC1
CsMADS22 / orange1.1g030981m / chr5:6921959..6931427 / no / 507 / 168 / 19.63 / 9.74 / 7 / ﹢ / AGL19 / SOC1
CsMADS23 / orange1.1g031002m / chrUn:4690986..4695981 / no / 504 / 167 / 19.32 / 9.88 / 6 / ﹢ / AGL20 / SOC1
CsMADS24 / orange1.1g031392m / chr5:6921959..6931427 / no / 483 / 160 / 18.64 / 9.65 / 6 / ﹢ / AGL19 / SOC1
CsMADS25 / orange1.1g027190m / chr3:21012281..21018014 / no / 684 / 227 / 25.36 / 8.6 / 8 / ﹢ / SVP / SVP
CsMADS26 / orange1.1g030090m / chr3:21012281..21018014 / no / 552 / 183 / 21.15 / 9.68 / 7 / ﹢ / SVP / SVP
CsMADS27 / orange1.1g036652m / chr7:9576581..9578975 / Clementine
0.9_020252m / 723 / 240 / 28.17 / 7.22 / 5 / ﹢ / TT16 / TT16
CsMADS28 / orange1.1g040075m / chr2:8482093..8484711 / no / 765 / 254 / 29.37 / 6.62 / 5 / ﹢ / TT16 / TT16
CsMADS29 / orange1.1g017511m / chr5:7635524..7643874 / no / 1113 / 370 / 41.89 / PI 6.17 / 10 / ﹢ / AGL65 / MIKC*
CsMADS30 / orange1.1g017948m / chr5:7635524..7643874 / no / 1092 / 363 / 40.85 / 6.02 / 10 / ﹢ / AGL65 / MIKC*
CsMADS31 / orange1.1g018115m / chr5:7635524..7643874 / no / 1083 / 360 / 40.63 / 6.12 / 10 / ﹢ / AGL65 / MIKC*
CsMADS32 / orange1.1g018780m / chr7:1651092..1655826 / no / 1053 / 350 / 39.5 / 6.76 / 9 / ﹢ / AGL30 / MIKC*
CsMADS33 / orange1.1g018825m / chr7:1651092..1655826 / no / 1053 / 350 / 39.46 / 6.76 / 9 / ﹢ / AGL30 / MIKC*
CsMADS34 / orange1.1g027395m / chr2:19333093..19335273 / no / 675 / 224 / 25.9 / 7.05 / 9 / ﹢ / AGL66 / MIKC*
CsMADS35 / orange1.1g039560m / chr3:22151556..22164045 / no / 1035 / 344 / 38.75 / 5.17 / 10 / ﹣ / AGL104 / MIKC*
CsMADS36 / orange1.1g046530m / chr3:19650735..19654653 / no / 933 / 310 / 35.66 / 5.46 / 10 / ﹢ / AGL104 / MIKC*
CsMADS37 / orange1.1g029592m / chr1:24042667..24045016 / Clementine
0.9_035692m / 576 / 191 / 21.58 / 6.32 / 1 / ﹣ / AGL61 / Mα
CsMADS38 / orange1.1g036705m / chr8:1734293..1734985 / no / 639 / 212 / 24.19 / 9.61 / 1 / ﹢ / AGL62 / Mα
CsMADS39 / orange1.1g037442m / chr2:1690410..1690952 / no / 543 / 180 / 20.26 / 8.44 / 0 / ﹣ / AGL29 / Mα
CsMADS40 / orange1.1g039654m / chr8:1737091..1738500 / no / 678 / 225 / 25.21 / 9.28 / 1 / ﹣ / AGL62 / Mα
CsMADS41 / orange1.1g042235m / chr5:10146015..10147073 / no / 882 / 293 / 32.56 / 5.78 / 0 / ﹣ / AGL97 / Mα
CsMADS42 / orange1.1g043113m / chrUn:34688065..34688514 / no / 519 / 172 / 20.03 / 9.14 / 1 / ﹣ / AGL57 / Mα
CsMADS43 / orange1.1g044532m / chrUn:34674253..34674885 / no / 444 / 147 / 16.8 / 9.93 / 2 / ﹣ / AGL61 / Mα
CsMADS44 / orange1.1g044792m / chr1:19947020..19947682 / no / 660 / 219 / 24.92 / 5.49 / 0 / ﹣ / AGL62 / Mα
CsMADS45 / orange1.1g048296m / chr2:1243320..1244383 / no / 522 / 173 / 20.24 / 5.82 / 0 / ﹣ / AGL28 / Mα
CsMADS46 / orange1.1g024884m / chr6:18439116..18442037 / no / 786 / 261 / 29.06 / 9.01 / 1 / ﹢ / AGL82 / Mβ
CsMADS47 / orange1.1g040948m / chrUn:8514572..8515731 / no / 861 / 286 / 32.2 / 5.57 / 0 / ﹣ / AGL103 / Mβ
CsMADS48 / orange1.1g041581m / chr8:21165156..21165971 / no / 816 / 271 / 31.53 / 8.89 / 0 / ﹣ / AGL82 / Mβ
CsMADS49 / orange1.1g043963m / chr1:4374316..4375752 / no / 948 / 315 / 36.29 / 9.31 / 1 / ﹢ / AGL82 / Mβ
CsMADS50 / orange1.1g038848m / chr6:14966564..14968057 / no / 1341 / 446 / 48.62 / 7.76 / 0 / ﹣ / AGL48 / Mγ
CsMADS51 / orange1.1g040635m / chr3:25381879..25382412 / no / 534 / 177 / 20.41 / 9.76 / 0 / ﹣ / AGL87 / Mγ
CsMADS52 / orange1.1g040642m / chr5:16802165..16802866 / no / 702 / 233 / 27.12 / 9.52 / 0 / ﹣ / AGL80 / Mγ

Supplementary table 3 Clementine mandarin SSR analysis

Gene ID / Motif / No.of Repeats / Type
clementine0.9_012775m.g-1 / ac / 9 / Intron
clementine0.9_013916m.g-1 / ac / 9 / Intron
clementine0.9_021068m.g-2 / ac / 18 / Intron
clementine0.9_021154m.g-2 / ac / 18 / Intron
clementine0.9_014436m.g-1 / ag / 9 / Intron
clementine0.9_019626m.g-1 / ag / 9 / UTR
clementine0.9_019726m.g-1 / ag / 9 / UTR
clementine0.9_019908m.g-1 / ag / 8 / Intron
clementine0.9_020021m.g-1 / ag / 11 / Intron
clementine0.9_021700m.g-2 / ag / 7 / Intron
clementine0.9_021791m.g-2 / ag / 7 / Intron
clementine0.9_022203m.g-1 / ag / 9 / Intron
clementine0.9_022612m.g-1 / ag / 8 / Intron
clementine0.9_030864m.g / ag / 8 / Intron
clementine0.9_012775m.g-2 / at / 11 / Intron
clementine0.9_013916m.g-2 / at / 11 / Intron
clementine0.9_016536m.g-3 / at / 10 / Intron
clementine0.9_019716m.g-1 / at / 12 / Intron
clementine0.9_019973m.g-3 / at / 8 / Intron
clementine0.9_020032m.g / at / 11 / Intron
clementine0.9_021700m.g-1 / at / 10 / Intron
clementine0.9_021791m.g-1 / at / 10 / Intron
clementine0.9_021815m.g-1 / at / 12 / Intron
clementine0.9_022186m.g-1 / at / 12 / Intron
clementine0.9_020838m.g-1 / ct / 15 / Intron
clementine0.9_021724m.g-1 / ct / 15 / Intron
clementine0.9_019973m.g-2 / gc / 7 / Intron
clementine0.9_019626m.g-2 / gt / 6 / Intron
clementine0.9_019726m.g-2 / gt / 6 / Intron
clementine0.9_022203m.g-2 / gt / 6 / UTR
clementine0.9_016536m.g-1 / ta / 8 / Intron
clementine0.9_019775m.g-1 / ta / 6 / CDS
clementine0.9_021068m.g-3 / ta / 13 / Intron
clementine0.9_021154m.g-3 / ta / 13 / Intron
clementine0.9_021355m.g-1 / ta / 8 / Intron
clementine0.9_024260m.g-2 / ta / 8 / Intron
clementine0.9_031353m.g-1 / ta / 9 / Intron
clementine0.9_018087m.g / tc / 6 / Intron
clementine0.9_019281m.g-1 / tc / 10 / Intron
clementine0.9_019320m.g-1 / tc / 10 / Intron
clementine0.9_019980m.g-1 / tc / 10 / Intron
clementine0.9_020090m.g-1 / tc / 10 / Intron
clementine0.9_020731m.g-1 / tc / 10 / Intron
clementine0.9_023878m.g-1 / tc / 10 / Intron
clementine0.9_023925m.g-1 / tc / 10 / Intron
clementine0.9_024260m.g-1 / tc / 6 / Intron
clementine0.9_019626m.g-3 / tg / 11 / Intron
clementine0.9_019716m.g-2 / tg / 9 / Intron
clementine0.9_019726m.g-3 / tg / 11 / Intron
clementine0.9_019967m.g / tg / 8 / Intron
clementine0.9_019973m.g-1 / tg / 7 / Intron
clementine0.9_019984m.g / tg / 8 / Intron
clementine0.9_021815m.g-2 / tg / 9 / Intron
clementine0.9_022186m.g-2 / tg / 9 / Intron
clementine0.9_022203m.g-3 / tg / 11 / Intron
clementine0.9_020021m.g-2 / tat / 6 / Intron
clementine0.9_022731m.g / gct / 5 / CDS
clementine0.9_035380m.g / gga / 6 / CDS
clementine0.9_032522m.g / ata / 5 / Intron
clementine0.9_021355m.g-2 / att / 5 / Intron
clementine0.9_021434m.g / att / 6 / Intron
clementine0.9_031353m.g-2 / att / 6 / Intron
clementine0.9_016536m.g-2 / ca / 12 / Intron
clementine0.9_020252m.g / ca / 11 / Intron
clementine0.9_021068m.g-1 / ca / 8 / Intron
clementine0.9_021154m.g-1 / ca / 8 / Intron
clementine0.9_021068m.g-4 / cat / 5 / Intron
clementine0.9_021154m.g-4 / cat / 5 / Intron
clementine0.9_019775m.g-2 / agc / 6 / Intron
clementine0.9_019281m.g-2 / ctg / 5 / Intron
clementine0.9_019320m.g-2 / ctg / 5 / Intron
clementine0.9_019980m.g-2 / ctg / 5 / Intron
clementine0.9_020090m.g-2 / ctg / 5 / Intron
clementine0.9_020731m.g-2 / ctg / 5 / Intron
clementine0.9_023878m.g-2 / ctg / 5 / Intron
clementine0.9_023925m.g-2 / ctg / 5 / Intron
clementine0.9_019908m.g-2 / tta / 13 / Intron
clementine0.9_021261m.g / tta / 5 / Intron
clementine0.9_022612m.g-2 / tta / 13 / Intron
clementine0.9_023727m.g / tta / 5 / Intron
clementine0.9_024260m.g-3 / ccac / 5 / Intron
clementine0.9_031353m.g-3 / ttgg / 5 / Intron
clementine0.9_020838m.g-2 / ttta / 5 / Intron
clementine0.9_023885m.g / aaat / 5 / Intron
clementine0.9_021724m.g-2 / ttta / 5 / Intron

Supplementary table 4. Sweet orange SSR analysis

Gene ID / Motif / No.of Repeats / type
orage1.1g017511m.g-1 / ac / 9 / Intron
orage1.1g017948m.g-1 / ac / 9 / Intron
orage1.1g018115m.g-1 / ac / 9 / Intron
orage1.1g036452m.g-3 / ac / 10 / Intron
orage1.1g018780m.g / ag / 10 / Intron
orage1.1g018825m.g / ag / 10 / Intron
orage1.1g024640m.g-1 / ag / 8 / UTR
orage1.1g026143m.g / ag / 11 / Intron
orage1.1g036452m.g-1 / ag / 10 / Intron
orage1.1g046479m.g-1 / ag / 7 / Intron
orage1.1g017511m.g-2 / at / 11 / Intron
orage1.1g017948m.g-2 / at / 11 / Intron
orage1.1g018115m.g-2 / at / 11 / Intron
orage1.1g018135m.g / at / 11 / Intron
orage1.1g024640m.g-4 / at / 8 / Intron
orage1.1g037149m.g-3 / at / 8 / Intron
orage1.1g042044m.g-1 / at / 7 / Intron
orage1.1g042235m.g / at / 6 / Intron
orage1.1g036652m.g / ca / 11 / Intron
orage1.1g037149m.g-2 / gc / 7 / Intron
orage1.1g024640m.g-2 / gt / 6 / Intron
orage1.1g027190m.g-1 / gt / 6 / Intron
orage1.1g039982m.g-1 / gt / 6 / Intron
orage1.1g046530m.g / ta / 7 / Intron
orage1.1g024884m.g / tc / 6 / Intron
orage1.1g024640m.g-3 / tg / 11 / Intron
orage1.1g036452m.g-2 / tg / 6 / Intron
orage1.1g037149m.g-1 / tg / 7 / Intron
orage1.1g040948m.g / taa / 7 / CDS
orage1.1g040075m.g / agc / 6 / CDS
orage1.1g039560m.g / ata / 5 / Intron
orage1.1g024640m.g-5 / att / 5 / Intron
orage1.1g039982m.g-2 / att / 6 / Intron
orage1.1g042044m.g-2 / att / 5 / Intron
orage1.1g027190m.g-2 / tta / 5 / Intron
orage1.1g030748m.g / tta / 5 / Intron
orage1.1g031002m.g / tta / 5 / Intron
orage1.1g031012m.g / tta / 5 / Intron
orage1.1g036452m.g-4 / tta / 5 / Intron
orage1.1g046479m.g-2 / tta / 6 / Intron
orage1.1g027190m.g-3 / aaat / 5 / Intron
orage1.1g039982m.g-3 / ttgg / 5 / Intron

Expression primers

clementine0.9_012775m Sense:5-TGAAGCCTGATGCTGAGAT-3 Antisense:5-CTATTTGTTTGCTGGTGGTA-3

clementine0.9_014436m Sense:5-GTTTGCTCAACTAACTCCG-3 Antisense:5-TTCCTGAACATTCCACATC-3

clementine0.9_018087m Sense:5-GCTCGCTTGGCAACCTTTA-3 Antisense:5-CCTCGTCTTACTTTCATCG-3

clementine0.9_019281m Sense:5-CTTTCCGTTCTTTGTGATG-3 Antisense:5-CCTTTGTTTGAGGGTCTTAT-3

clementine0.9_019716m Sense:5-CGAGTTATCGGTTCTTTGTG-3 Antisense:5-CTTATTGCTCCTCTGACGCT-3

clementine0.9_019726mSense:5-CAGAGGAACCTTCTTGGAG-3 Antisense:5-CTGGGTAGCGATTGTATGT-3

clementine0.9_019775m Sense:5-ATGGGACGGGGAAAGATAG-3 Antisense:5-CCAAAGGTGGGGAAATGAA-3

clementine0.9_019908m Sense:5-CGCCTTTATGAGTATTCCA-3 Antisense:5-CATTCTCGGCTATCTTTGC-3

clementine0.9_019967m Sense:5-GGGAAGGGGAAAAGTAGAG-3 Antisense:5-CCGAATGAGCAGGTTGGTT-3

clementine0.9_019973m Sense:5-TGGCGGCATAAACAAAACC-3 Antisense:5-TCCTTTACACTCAGCGGTC-3

clementine0.9_020257m Sense:5-ACGCAAACAGTAGGCAAGT-3 Antisense:5-CATCAGAGGCAACATCAGG-3

clementine0.9_020307m Sense:5-ATGGGTAGAGGAAAGATGG-3 Antisense:5-GTGGAAGGGCTGATGTATT-3

clementine0.9_020619mSense:5-CCGCCATCCTGACTTTGAC -3 Antisense:5-CTTGCCACCAGAACCTACC-3

clementine0.9_021068m Sense:5-TTTGTGATGCTGAAGTTGCC-3 Antisense:5-TTTGCTGACTCCTGCTGATA-3

clementine0.9_021103m Sense:5-ATAAGCCCTACAACCACGA-3 Antisense:5-CCATTGCGGATTGATAGTC-3

clementine0.9_021261m Sense:5-GATGCTGAGGTTGCCGTTAT-3 Antisense:5-TTTGTTCCGTTGGCTGTTG-3

clementine0.9_021355m Sense:5-CTCATCATTTTCGCCACT-3 Antisense:5-TTGTTCTCCAAAGCCATC-3

clementine0.9_021434mSense:5-TTGCGATGCCGATGTTGCT-3 Antisense:5-GCTTGAGGGAGGTGTCTGA-3

clementine0.9_021700mSense:5-GACGCTGAAGTTGCTGTTA-3 Antisense:5-TAACCTGGCATTGTCTTCC-3

clementine0.9_024260mSense:5-TCCGTTCTTTGTGATGCTG-3 Antisense:5-GCGAATGCGTTCAACTCCA-3

clementine0.9_027776mSense:5-CTCGTGGAAAGGTTCAGATG-3 Antisense:5-CAAGGAATGGTTGAGTCTGC-3

clementine0.9_029324mSense:5-GTTGAAGAAGGCGAAAGAG-3 Antisense:5-ACGCACATCCGAAAAGTAG-3

clementine0.9_030040m Sense:5-GAATCTACTCAACGATACACTG-3Antisense:5-TATCTAAGCAAAGGGAGGG-3

clementine0.9_030885m Sense:5-TGACTCTAACTGGCTCTGA-3 Antisense:5-TGACCTACAACCAACGAAT-3

clementine0.9_032015m Sense:5-GCTTGAAGAAGAAGGCACA-3 Antisense:5-CTTGGAAGAGCAGGAAACT-3

clementine0.9_032961mSense:5-GAAGGTGGAGATGGTGAAG-3 Antisense:5-GGAGATTTGAGGAGGGTTT-3

clementine0.9_033757mSense:5-GATGAGTGAGATAAGGAAAGC-3 Antisense:5-AGAAGCAGGAATCCCAAGA-3

orange1.1g046479m Sense:5-TAGACAACGAAAGACGGAT-3 Antisense:5-ACTAAGCAGGACTAATGGC-3

SSR primers

clementine0.9_021068mSense: 5-TCAACTTCGATCTGCTGCTA-3 Antisense: 5-CGTTGAAAGCCACTGTGAAA-3

clementine0.9_014436mSense: 5-TTCCAACCAGTTTCGGAGATGA-3Antisense: 5-CCAAGCAAAAGGGAAAGCAATA-3

clementine0.9_020021mSense: 5-CATCCTAAGAAATCTGGGTT-3 Antisense: 5-GACCTAAAAGGCGTAGTAAC-3

clementine0.9_019775mSense: 5-AATGTTGGAGGAGGAGAATG-3 Antisense: 5-GAACGGCTGATAATGAGGAA-3

clementine0.9_013916m Sense: 5-CTATCGGAGCAATCCTGGTA-3 Antisense: 5-CTTAGTCTGACATGGCGTAG-3

clementine0.9_021700mSense: 5-CGTTCTATGCTTCTGTCCTTT-3 Antisense: 5-CGCAACACCATAATACCAAAC-3

clementine0.9_021815mSense: 5-CATACACGCACTAGGCTAAA-3 Antisense: 5-CGTCATTGATATTCAAGGTTC-3

clementine0.9_016536mSense: 5-CTGGTCAAATAAGCCGAAGA-3 Antisense: 5-GCATTAGTGATTGCTCCTGT-3

clementine0.9_020252m Sense: 5-TAGGAGCGAATGCTGGAGGA-3 Antisense: 5-TGAAGATGGTGATAAGGGTG-3

clementine0.9_020090mSense: 5-ACAAAGTCTGATAGAGGGAG-3 Antisense: 5-TAACTGCGGGAAGATGAAAC-3

clementine0.9_022731mSense: 5-CGCCAGGTGAGAATTAACGAG-3 Antisense: 5-TTGGACCCGCAGCCTCAGATA-3

clementine0.9_020090mSense: 5-GTCTTTGTGATGCTGAGGTT-3 Antisense: 5-GAAGAGGGAAACAGTGAAGC-3

clementine0.9_022203mSense: 5-GGGGCTTTTGAACATTAGATTG-3Antisense: 5-AAGTTAGGTAGCTCCATAGTCG-3

clementine0.9_022612mSense: 5-CGGTTTCTTTCCATTACTGAC-3 Antisense: 5-GCGGGATATTTGAATTTTAGC-3

clementine0.9_020838mSense: 5-CACTGTAGTTACGCCGAATA-3 Antisense: 5-GGTTATAGCCAGTGAGTTCC-3