Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi3g116 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g117 . . . . . Bpe12g00110 Bma05g00415 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00465 Csa07g00082 . . . Blo13g00524 . . . . . . . . . . . . . Cpe16g00299 Cpe05g01313 . . . . . . . Cla02g01128 Cam02g1203 Cec02g1206 Cco02g1256 Clacu02g1192 Cmu02g1154 Cre02g1464 . Csa02g01357 . .
Vvi3g118 . Blo15g00650 . . . . . . . . . . Car02g00206 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00468 . Chy11g00289 . . . . . . . . . . Cmo02g00320 . . . . . . Cpe05g01314 Bhi10g01884 . . . Hepe08g0266 . . Cla02g01129 Cam02g1204 Cec02g1214 Cco02g1257 Clacu02g1194 Cmu02g1155 Cre02g1466 . Csa02g01359 . Cme11g00412
Vvi3g119 . . . . . . . . Cmo19g00735 Cmo11g01727 . . . . Sed05g2232 Cpe04g00579 Cpe15g00581 Bhi05g01740 Tan02g0707 Cmetu01g1169 . Hepe02g0441 . . Cla02g00443 Cam02g0452 Cec02g0450 Cco02g0469 Clacu02g0453 Cmu02g0448 Cre02g0781 Cone12ag1216 Cone8ag1268 . . . Csa07g00083 . Cme01g01281 Blo04g00555 . . Bda14g00604 Bpe15g00826 . Bma03g00595 . . . . Cma11g01391 . . Car19g00555 . . . . . . . . . . . . . . . . Lsi11g01183 . Chy01g00695 .
Vvi3g120 . . . . . Bpe12g00111 . . . Cmo11g01728 Cma02g00325 Cma20g00766 Car02g00205 Car20g00670 Sed05g2231 Cpe04g00580 . Bhi05g01738 Tan02g0706 Cmetu01g1657 . . . . Cla02g00442 Cam02g0451 . . . . . . . . . Lsi10g00469 Csa07g00084 Chy11g00288 Cme01g01280 Blo04g00556 . Bda15g01044 Bda14g00605 Bpe15g00825 . Bma03g00596 Bma08g00764 Sed01g0218 Cmo02g00319 Cmo20g00764 . . . . Cpe16g00301 Cpe05g01315 Bhi10g01883 Tan05g1181 Cmetu11g0510 . Hepe08g0267 . . Cla02g01138 Cam02g1214 Cec02g1222 Cco02g1266 Clacu02g1196 Cmu02g1165 Cre02g1472 Lsi11g01184 Csa02g01360 Chy01g00694 Cme11g00411
Vvi3g121 . . . . . . . . . . . Cma20g00765 . Car20g00669 . . . . . . . . . . . . . . . . . . Cone8ag1269 . . . . Chy11g00287 . . . . . . . . . Sed01g0216 . Cmo20g00762 . . . . Cpe16g00302 . Bhi10g01882 Tan05g1180 Cmetu11g1766 . Hepe08g0268 . . Cla02g01139 Cam02g1215 Cec02g1223 Cco02g1267 Clacu02g1197 Cmu02g1166 Cre02g1473 . Csa02g01362 . Cme11g00410
Vvi3g122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma11g01390 . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g123 . . . . . . . . Cmo19g00736 Cmo11g01729 . . . . . . Cpe15g00582 . . . . . . . . . . . . . . Cone12ag1217 Cone8ag1270 . . . Csa07g00085 Chy11g00286 . Blo04g00557 . . . . . Bma03g00597 . . . . . . . Car19g00556 . . Bhi10g01881 Tan05g1178 . . Hepe08g0269 . . Cla02g01140 Cam02g1217 Cec02g1224 Cco02g1270 Clacu02g1199 Cmu02g1168 Cre02g1475 . Csa02g01363 . Cme11g00409
Vvi3g124 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1219 Cone8ag1272 . . Lsi10g00470 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01185 . . .
Vvi3g125 . . . . . . . . . . . . . . Sed05g2230 . . Bhi05g01736 Tan02g0704 Cmetu01g0664 . Hepe02g0439 . . Cla02g00441 Cam02g0450 Cec02g0449 Cco02g0468 Clacu02g0452 Cmu02g0447 Cre02g0780 . . . . . Csa07g00086 Chy11g00285 Cme01g01279 . Blo13g00523 . . . . . . Sed01g0214 . . . . . . . . Bhi10g01880 Tan05g1177 Cmetu11g0691 . Hepe08g0270 . . . . . . . . . . Csa02g01364 Chy01g00693 Cme11g00407
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 4557673 4560209 + Bda027358.1 Bda14g00604 604
14 4562470 4563585 + Bda027359.1 Bda14g00605 605
15 19473111 19474253 - Bda013032.1 Bda15g01044 1044
5 55951428 55955481 - XM_039031975.1 Bhi05g01736 1736
5 55956310 55957959 - XM_039031976.1 Bhi05g01738 1738
5 55959736 55963253 - XM_039031028.1 Bhi05g01740 1740
10 46921479 46924300 - XM_039044985.1 Bhi10g01880 1880
10 47003184 47008017 - XM_039046649.1 Bhi10g01881 1881
10 47014254 47017950 - XM_039044901.1 Bhi10g01882 1882
10 47037250 47039681 - XM_039046159.1 Bhi10g01883 1883
10 47070718 47157018 - XM_039046836.1 Bhi10g01884 1884
4 4784193 4786776 + BLOR13467 Blo04g00555 555
4 4800139 4803269 + BLOR13468 Blo04g00556 556
4 4814883 4816791 + BLOR13469 Blo04g00557 557
13 26798381 26805487 - BLOR05804 Blo13g00523 523
13 26806381 26808042 - BLOR05805 Blo13g00524 524
15 18239540 18255518 - BLOR07044 Blo15g00650 650
3 4932277 4934878 + Bma016886.1 Bma03g00595 595
3 4935866 4936981 + Bma016887.1 Bma03g00596 596
3 4938178 4940108 + Bma016888.1 Bma03g00597 597
5 13116945 13118165 + Bma021254.1 Bma05g00415 415
8 44659284 44660411 - Bma028141.1 Bma08g00764 764
12 796295 797718 + Bpe005350.1 Bpe12g00110 110
12 798647 799777 + Bpe005351.1 Bpe12g00111 111
15 18337642 18338757 - Bpe001750.1 Bpe15g00825 825
15 18342184 18344742 - Bpe001751.1 Bpe15g00826 826
2 5216685 5219882 - CaPI482276_02g004500.1 Cam02g0450 450
2 5223378 5227699 - CaPI482276_02g004510.1 Cam02g0451 451
2 5227743 5230393 - CaPI482276_02g004520.1 Cam02g0452 452
2 23961230 23964633 + CaPI482276_02g012030.1 Cam02g1203 1203
2 23990691 23991670 + CaPI482276_02g012040.1 Cam02g1204 1204
2 24107461 24109378 + CaPI482276_02g012140.1 Cam02g1214 1214
2 24116543 24118951 + CaPI482276_02g012150.1 Cam02g1215 1215
2 24133979 24136170 + CaPI482276_02g012170.1 Cam02g1217 1217
2 1239491 1241977 - Carg19795-RA Car02g00205 205
2 1243095 1263586 - Carg19796-RA Car02g00206 206
19 7093815 7096979 + Carg19364-RA Car19g00555 555
19 7098110 7101868 + Carg19363-RA Car19g00556 556
20 3761567 3762929 - Carg16189-RA Car20g00669 669
20 3767115 3769357 - Carg16190-RA Car20g00670 670
2 4221301 4224533 - CcPI632755_02g004680.1 Cco02g0468 468
2 4227575 4235235 - CcPI632755_02g004690.1 Cco02g0469 469
2 23920859 23923987 + CcPI632755_02g012560.1 Cco02g1256 1256
2 23948280 23951105 + CcPI632755_02g012570.1 Cco02g1257 1257
2 24054962 24056879 + CcPI632755_02g012660.1 Cco02g1266 1266
2 24063239 24065714 + CcPI632755_02g012670.1 Cco02g1267 1267
2 24087080 24090177 + CcPI632755_02g012700.1 Cco02g1270 1270
2 4238601 4241877 - CePI673135_02g004490.1 Cec02g0449 449
2 4245441 4252490 - CePI673135_02g004500.1 Cec02g0450 450
2 28351665 28354730 + CePI673135_02g012060.1 Cec02g1206 1206
2 28457437 28468035 + CePI673135_02g012140.1 Cec02g1214 1214
2 28567979 28569893 + CePI673135_02g012220.1 Cec02g1222 1222
2 28577434 28579899 + CePI673135_02g012230.1 Cec02g1223 1223
2 28582039 28598130 + CePI673135_02g012240.1 Cec02g1224 1224
1 5063813 5067044 - Chy1G006930.1 Chy01g00693 693
1 5067234 5070171 - Chy1G006940.1 Chy01g00694 694
1 5075841 5078530 - Chy1G006950.1 Chy01g00695 695
11 2608523 2610929 - Chy11G188650.1 Chy11g00285 285
11 2612105 2615153 - Chy11G188660.1 Chy11g00286 286
11 2616800 2617955 - Chy11G188670.1 Chy11g00287 287
11 2625435 2627355 - Chy11G188680.1 Chy11g00288 288
11 2631594 2655854 - Chy11G188690.1 Chy11g00289 289
2 4098031 4102131 - ClG42_02g0045200.10 Clacu02g0452 452
2 4105567 4112642 - ClG42_02g0045300.10 Clacu02g0453 453
2 24133380 24136237 + ClG42_02g0119200.10 Clacu02g1192 1192
2 24162757 24219884 + ClG42_02g0119400.10 Clacu02g1194 1194
2 24279867 24281785 + ClG42_02g0119600.10 Clacu02g1196 1196
2 24288910 24291308 + ClG42_02g0119700.10 Clacu02g1197 1197
2 24306127 24309469 + ClG42_02g0119900.10 Clacu02g1199 1199
2 4351416 4355516 - ClCG02G004260.2 Cla02g00441 441
2 4358727 4360360 - ClCG02G004270.1 Cla02g00442 442
2 4363128 4366413 - ClCG02G004280.2 Cla02g00443 443
2 24392590 24395319 + ClCG02G011540.1 Cla02g01128 1128
2 24421615 24505965 + ClCG02G011550.2 Cla02g01129 1129
2 24544299 24546472 + ClCG02G011610.1 Cla02g01138 1138
2 24554364 24556762 + ClCG02G011620.1 Cla02g01139 1139
2 24559273 24573942 + ClCG02G011630.1 Cla02g01140 1140
2 1568498 1572533 - CmaCh02G003250.1 Cma02g00325 325
11 9161690 9174661 - CmaCh11G013900.1 Cma11g01390 1390
11 9175944 9180209 - CmaCh11G013910.1 Cma11g01391 1391
20 3613767 3615147 - CmaCh20G007650.1 Cma20g00765 765
20 3618353 3620899 - CmaCh20G007660.1 Cma20g00766 766
1 16154677 16158443 - MELO3C013372.2.1 Cme01g01279 1279
1 16162001 16163754 - MELO3C013373.2.1 Cme01g01280 1280
1 16168085 16173119 - MELO3C013374.2.1 Cme01g01281 1281
11 4078248 4080745 - MELO3C020793.2.1 Cme11g00407 407
11 4081713 4085666 - MELO3C020792.2.1 Cme11g00409 409
11 4088233 4089744 - MELO3C020791.2.1 Cme11g00410 410
11 4100462 4101762 - MELO3C020790.2.1 Cme11g00411 411
11 4107885 4163243 - MELO3C020789.2.1 Cme11g00412 412
1 5372493 5376166 - PI0025771.1 Cmetu01g0664 664
1 5392043 5395318 - PI0015077.1 Cmetu01g1169 1169
1 5377326 5379322 - PI0001031.1 Cmetu01g1657 1657
11 28347956 28350446 + PI0002353.1 Cmetu11g0510 510
11 28369668 28372543 + PI0015130.1 Cmetu11g0691 691
11 28357579 28360563 + PI0020340.1 Cmetu11g1766 1766
2 1634465 1636823 - CmoCh02G003190.1 Cmo02g00319 319
2 1637978 1660047 - CmoCh02G003200.1 Cmo02g00320 320
11 12220042 12224141 + CmoCh11G017270.1 Cmo11g01727 1727
11 12225354 12226742 + CmoCh11G017280.1 Cmo11g01728 1728
11 12227119 12232233 + CmoCh11G017290.1 Cmo11g01729 1729
19 7581746 7585759 + CmoCh19G007350.1 Cmo19g00735 735
19 7586416 7590305 + CmoCh19G007360.1 Cmo19g00736 736
20 3831421 3832731 - CmoCh20G007620.1 Cmo20g00762 762
20 3837167 3839361 - CmoCh20G007640.1 Cmo20g00764 764
2 4094048 4098149 - CmPI595203_02g004470.1 Cmu02g0447 447
2 4101585 4108668 - CmPI595203_02g004480.1 Cmu02g0448 448
2 24002468 24005325 + CmPI595203_02g011540.1 Cmu02g1154 1154
2 24031850 24032829 + CmPI595203_02g011550.1 Cmu02g1155 1155
2 24148932 24150850 + CmPI595203_02g011650.1 Cmu02g1165 1165
2 24157973 24160370 + CmPI595203_02g011660.1 Cmu02g1166 1166
2 24175193 24178538 + CmPI595203_02g011680.1 Cmu02g1168 1168
8 10493979 10497121 + Conep08aG0130600.1 Cone8ag1268 1268
8 10501596 10504088 + Conep08aG0130700.1 Cone8ag1269 1269
8 10504568 10506554 + Conep08aG0130800.1 Cone8ag1270 1270
8 10508549 10510930 + Conep08aG0131000.1 Cone8ag1272 1272
12 9468910 9471884 + Conep12aG0125600.1 Cone12ag1216 1216
12 9476041 9478881 + Conep12aG0125700.1 Cone12ag1217 1217
12 9481350 9483742 + Conep12aG0125900.1 Cone12ag1219 1219
4 6190990 6195621 + Cp4.1LG04g05080.1 Cpe04g00579 579
4 6195809 6203149 + Cp4.1LG04g05040.1 Cpe04g00580 580
5 9218000 9219718 + Cp4.1LG05g13110.1 Cpe05g01313 1313
5 9220984 9242932 + Cp4.1LG05g13100.1 Cpe05g01314 1314
5 9243915 9246704 + Cp4.1LG05g13070.1 Cpe05g01315 1315
15 6623131 6627138 + Cp4.1LG15g05770.1 Cpe15g00581 581
15 6627809 6631564 + Cp4.1LG15g05780.1 Cpe15g00582 582
16 4940508 4943156 + Cp4.1LG16g02990.1 Cpe16g00299 299
16 4947554 4950020 + Cp4.1LG16g02980.1 Cpe16g00301 301
16 4953749 4954976 + Cp4.1LG16g03050.1 Cpe16g00302 302
2 4658606 4661808 - CrPI670011_02g007800.1 Cre02g0780 780
2 4665527 4672640 - CrPI670011_02g007810.1 Cre02g0781 781
2 26486626 26489619 + CrPI670011_02g014640.1 Cre02g1464 1464
2 26556204 26563550 + CrPI670011_02g014660.1 Cre02g1466 1466
2 26656928 26658847 + CrPI670011_02g014720.1 Cre02g1472 1472
2 26666454 26668894 + CrPI670011_02g014730.1 Cre02g1473 1473
2 26683992 26685433 + CrPI670011_02g014750.1 Cre02g1475 1475
2 13044509 13047459 + CsaV3_2G015730.1 Csa02g01357 1357
2 13052548 13096363 + CsaV3_2G015750.1 Csa02g01359 1359
2 13099403 13103036 + CsaV3_2G015760.1 Csa02g01360 1360
2 13110456 13111845 + CsaV3_2G015780.1 Csa02g01362 1362
2 13113555 13117587 + CsaV3_2G015790.1 Csa02g01363 1363
2 13118481 13120876 + CsaV3_2G015800.1 Csa02g01364 1364
7 779944 786503 + CsaV3_7G000820.1 Csa07g00082 82
7 789418 792829 + CsaV3_7G000830.1 Csa07g00083 83
7 796525 798886 + CsaV3_7G000840.1 Csa07g00084 84
7 799707 803019 + CsaV3_7G000850.1 Csa07g00085 85
7 804272 806223 + CsaV3_7G000860.1 Csa07g00086 86
2 4225175 4233834 - Hsped.02g04390.1 Hepe02g0439 439
2 4247662 4251226 - Hsped.02g04410.1 Hepe02g0441 441
8 2415351 2448985 + Hsped.08g02660.1 Hepe08g0266 266
8 2452039 2454782 + Hsped.08g02670.1 Hepe08g0267 267
8 2457751 2459955 + Hsped.08g02680.1 Hepe08g0268 268
8 2460926 2465661 + Hsped.08g02690.1 Hepe08g0269 269
8 2466824 2469465 + Hsped.08g02700.1 Hepe08g0270 270
10 6737001 6740026 + Lsi10G004660.1 Lsi10g00465 465
10 6798125 6800623 + Lsi10G004680.1 Lsi10g00468 468
10 6804811 6807008 + Lsi10G004690.1 Lsi10g00469 469
10 6817630 6842461 + Lsi10G004700.1 Lsi10g00470 470
11 20318328 20321718 + Lsi11G011830.1 Lsi11g01183 1183
11 20325688 20327252 + Lsi11G011840.1 Lsi11g01184 1184
11 20327281 20342175 + Lsi11G011850.1 Lsi11g01185 1185
1 1714255 1718338 - Sed0012086.1 Sed01g0214 214
1 1733847 1736457 - Sed0004865.1 Sed01g0216 216
1 1751905 1753967 - Sed0026833.1 Sed01g0218 218
5 35044384 35049632 - Sed0008875.1 Sed05g2230 2230
5 35050580 35051975 - Sed0008982.1 Sed05g2231 2231
5 35052426 35057262 - Sed0006196.1 Sed05g2232 2232
2 6593063 6596922 - Tan0010121.1 Tan02g0704 704
2 6598725 6600037 - Tan0012237.1 Tan02g0706 706
2 6603424 6607226 - Tan0005242.1 Tan02g0707 707
5 11372286 11375994 - Tan0010682.1 Tan05g1177 1177
5 11395154 11418149 - Tan0000493.1 Tan05g1178 1178
5 11464033 11468053 - Tan0018262.1 Tan05g1180 1180
5 11495604 11498107 - Tan0000846.1 Tan05g1181 1181
3 1292142 1293614 - Vvi3g116 Vvi3g116 116
3 1298168 1302974 + Vvi3g117 Vvi3g117 117
3 1303981 1347184 + Vvi3g118 Vvi3g118 118
3 1349911 1356647 + Vvi3g119 Vvi3g119 119
3 1357403 1360565 + Vvi3g120 Vvi3g120 120
3 1362166 1363697 + Vvi3g121 Vvi3g121 121
3 1364747 1369637 + Vvi3g122 Vvi3g122 122
3 1372251 1381336 + Vvi3g123 Vvi3g123 123
3 1383645 1391290 + Vvi3g124 Vvi3g124 124
3 1393092 1396092 + Vvi3g125 Vvi3g125 125
       

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