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
Vvi18g440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0520 . . . . Blo17g00113 Blo18g00128 . Bda13g01394 . Bpe14g00461 Bma01g01397 Bma02g00133 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g441 . . . . . . . . . . . . . . . . . Bhi04g00776 Tan02g2409 . . . . Lcy13g1546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00979 . . .
Vvi18g442 . . Bda01g00893 Bda03g00486 . Bpe04g00439 . . Cmo05g00534 Cmo12g00129 Cma01g01616 Cma09g00568 Car01g01232 Car12g00154 Sed04g0158 Cpe06g00431 Cpe07g00142 Bhi04g00777 Tan02g2410 Cmetu03g2141 . Hepe10g0481 . Lcy13g1545 Cla08g01123 Cam08g1580 Cec08g1150 Cco08g1276 Clacu08g1281 . Cre08g1063 . . . . Lsi04g02246 Csa03g04457 Chy04g00245 Cme03g01852 Blo17g00112 Blo18g00127 . Bda13g01393 Bpe02g01128 Bpe14g00462 Bma01g01396 Bma02g00132 Sed05g1594 Cmo01g01661 Cmo09g00555 Cma12g00167 Cma05g00507 Car05g00457 Car09g00495 Cpe11g00447 Cpe02g00365 Bhi09g02451 Tan01g3801 Cmetu04g2791 . Hepe01g2137 Mch11g0676 . Cla11g01392 Cam11g1448 Cec11g1476 Cco11g1473 Clacu11g1607 Cmu11g1426 Cre11g1846 Lsi08g00980 Csa02g02163 Chy03g01354 Cme04g00274
Vvi18g443 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g444 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01126 Cam08g1582 Cec08g1152 Cco08g1279 Clacu08g1283 . Cre08g1065 . . . . . . . Cme03g01849 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00983 Csa02g02165 Chy03g01352 .
Vvi18g445 . . . Bda03g00483 . Bpe04g00436 . . . . Cma01g01622 Cma09g00570 Car01g01236 . . Cpe06g00433 . . . . . . . . . . . . . . . Cone4ag1323 . . . . Csa03g04459 Chy04g00242 . . . . . . . . . Sed13g2145 Cmo01g01665 Cmo09g00557 . . . Car09g00497 . Cpe02g00362 Bhi09g02455 Tan01g3804 Cmetu04g1099 . Hepe01g2140 Mch11g0679 . Cla11g01395 Cam11g1451 Cec11g1479 Cco11g1476 Clacu11g1610 Cmu11g1429 Cre11g1849 . . . Cme04g00270
Vvi18g446 . . . . . . . . Cmo05g00538 Cmo12g00132 . . . Car12g00158 . Cpe06g00434 Cpe07g00146 Bhi04g00781 . . . . . . Cla08g01128 Cam08g1584 Cec08g1154 Cco08g1280 Clacu08g1284 . Cre08g1066 Cone4ag1322 Cone7ag1265 Cone17ag1204 Cone20ag0523 Lsi04g02249 Csa03g04460 Chy04g00241 Cme03g01846 Blo17g00111 . . Bda13g01388 . Bpe14g00463 . Bma02g00131 . . Cmo09g00558 Cma12g00171 Cma05g00510 Car05g00461 Car09g00498 Cpe11g00451 . Bhi09g02458 . . . . . . Cla11g01396 Cam11g1452 Cec11g1480 Cco11g1477 Clacu11g1611 Cmu11g1430 Cre11g1850 Lsi08g00985 Csa02g02168 Chy03g01349 Cme04g00269
Vvi18g447 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g448 . . . . . . . . . . Cma01g01624 . . . . . . . . . . . . . . . . . . . . . . Cone17ag1203 Cone20ag0525 . . . . . Blo18g00125 . . Bpe02g01131 . . . . Cmo01g01668 . . . . . . Cpe02g00359 . . . . . . . . . . . . . . . . . .
Vvi18g449 . . . . . . . . . . Cma01g01625 . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02252 Csa03g04463 Chy04g00238 . . . . . . . . . . Cmo01g01669 . . . . . . Cpe02g00358 Bhi09g02462 Tan01g3812 . . Hepe01g2145 . . Cla11g01398 Cam11g1455 Cec11g1483 Cco11g1480 Clacu11g1614 Cmu11g1433 Cre11g1853 . . . Cme04g00266
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 41914948 41916239 + Bda003030.2 Bda01g00893 893
3 4154807 4157689 + Bda016453.1 Bda03g00483 483
3 4165513 4166729 - Bda016455.1 Bda03g00486 486
13 36542080 36545875 + Bda000212.1 Bda13g01388 1388
13 36620851 36622501 - Bda000218.1 Bda13g01393 1393
13 36624073 36625900 + Bda000219.1 Bda13g01394 1394
4 19076200 19080187 - XM_039030844.1 Bhi04g00776 776
4 19155547 19157558 + XM_039030815.1 Bhi04g00777 777
4 19212523 19217377 - XM_039030338.1 Bhi04g00781 781
9 66744274 66746818 + XM_039043054.1 Bhi09g02451 2451
9 66769581 66774612 - XM_039041574.1 Bhi09g02455 2455
9 66790521 66793080 - XM_039043348.1 Bhi09g02458 2458
9 66925101 66926258 - XM_039040347.1 Bhi09g02462 2462
17 1032466 1035859 + BLOR15932 Blo17g00111 111
17 1037196 1038833 - BLOR15933 Blo17g00112 112
17 1040288 1045833 + BLOR15934 Blo17g00113 113
18 1161424 1162942 + BLOR08613 Blo18g00125 125
18 1175609 1176963 - BLOR08615 Blo18g00127 127
18 1180443 1187446 + BLOR08616 Blo18g00128 128
1 22059947 22061231 - Bma001743.2 Bma01g01396 1396
1 22062121 22064398 + Bma001744.2 Bma01g01397 1397
2 1214796 1218312 + Bma014587.1 Bma02g00131 131
2 1219654 1221313 - Bma014588.1 Bma02g00132 132
2 1222658 1224496 + Bma014589.1 Bma02g00133 133
2 14903829 14905113 + Bpe008986.1 Bpe02g01128 1128
2 14917832 14919012 - Bpe008989.1 Bpe02g01131 1131
4 2818377 2821271 + Bpe015123.3 Bpe04g00436 436
4 2832304 2833686 - Bpe015125.1 Bpe04g00439 439
14 4163458 4167617 - Bpe007111.1 Bpe14g00461 461
14 4169254 4170874 + Bpe007112.1 Bpe14g00462 462
14 4172207 4175876 - Bpe007113.1 Bpe14g00463 463
8 21977294 21978943 + CaPI482276_08g015800.1 Cam08g1580 1580
8 21991037 21994855 + CaPI482276_08g015820.1 Cam08g1582 1582
8 21999419 22007032 - CaPI482276_08g015840.1 Cam08g1584 1584
11 27210148 27212137 + CaPI482276_11g014480.1 Cam11g1448 1448
11 27228814 27234214 - CaPI482276_11g014510.1 Cam11g1451 1451
11 27235916 27240306 - CaPI482276_11g014520.1 Cam11g1452 1452
11 27273164 27275161 - CaPI482276_11g014550.1 Cam11g1455 1455
1 11298726 11301825 + Carg25636-RA Car01g01232 1232
1 11327794 11332986 - Carg25640-RA Car01g01236 1236
5 2622520 2624675 + Carg08198-RA Car05g00457 457
5 2632454 2636647 - Carg08202-RA Car05g00461 461
9 2767971 2770813 + Carg02977-RA Car09g00495 495
9 2776628 2781028 - Carg02979-RA Car09g00497 497
9 2782126 2786284 - Carg02980-RA Car09g00498 498
12 881107 883116 + Carg20531-RA Car12g00154 154
12 892521 897940 - Carg20527-RA Car12g00158 158
8 24564769 24566394 + CcPI632755_08g012760.1 Cco08g1276 1276
8 24578713 24585539 + CcPI632755_08g012790.1 Cco08g1279 1279
8 24586015 24593638 - CcPI632755_08g012800.1 Cco08g1280 1280
11 27549261 27551248 + CcPI632755_11g014730.1 Cco11g1473 1473
11 27568360 27573810 - CcPI632755_11g014760.1 Cco11g1476 1476
11 27575453 27579830 - CcPI632755_11g014770.1 Cco11g1477 1477
11 27610251 27623584 - CcPI632755_11g014800.1 Cco11g1480 1480
8 23406902 23408549 + CePI673135_08g011500.1 Cec08g1150 1150
8 23414526 23428534 + CePI673135_08g011520.1 Cec08g1152 1152
8 23436457 23436881 - CePI673135_08g011540.1 Cec08g1154 1154
11 28968405 28970389 + CePI673135_11g014760.1 Cec11g1476 1476
11 28997310 29003139 - CePI673135_11g014790.1 Cec11g1479 1479
11 29004854 29009365 - CePI673135_11g014800.1 Cec11g1480 1480
11 29044288 29056162 - CePI673135_11g014830.1 Cec11g1483 1483
3 16424034 16429434 + Chy3G063290.1 Chy03g01349 1349
3 16434433 16436927 - Chy3G063320.1 Chy03g01352 1352
3 16443954 16445657 - Chy3G063340.1 Chy03g01354 1354
4 2150756 2151604 + Chy4G069560.1 Chy04g00238 238
4 2171638 2174989 + Chy4G069590.1 Chy04g00241 241
4 2176874 2180293 + Chy4G069600.1 Chy04g00242 242
4 2195752 2197683 - Chy4G069630.1 Chy04g00245 245
8 22750550 22752195 + ClG42_08g0128100.10 Clacu08g1281 1281
8 22766272 22773772 + ClG42_08g0128300.10 Clacu08g1283 1283
8 22774556 22782792 - ClG42_08g0128400.10 Clacu08g1284 1284
11 27240050 27242053 + ClG42_11g0160700.10 Clacu11g1607 1607
11 27258738 27264212 - ClG42_11g0161000.10 Clacu11g1610 1610
11 27265855 27270374 - ClG42_11g0161100.10 Clacu11g1611 1611
11 27301265 27304038 - ClG42_11g0161400.10 Clacu11g1614 1614
8 23987753 23989567 + ClCG08G011250.2 Cla08g01123 1123
8 24002712 24010973 + ClCG08G011280.2 Cla08g01126 1126
8 24015061 24019680 - ClCG08G011300.1 Cla08g01128 1128
11 27459767 27465588 + ClCG11G014230.2 Cla11g01392 1392
11 27481888 27488777 - ClCG11G014260.1 Cla11g01395 1395
11 27490219 27495138 - ClCG11G014270.1 Cla11g01396 1396
11 27527705 27528550 - ClCG11G014300.1 Cla11g01398 1398
1 11112714 11115366 + CmaCh01G016160.1 Cma01g01616 1616
1 11132416 11137228 - CmaCh01G016220.1 Cma01g01622 1622
1 11145323 11147642 - CmaCh01G016240.1 Cma01g01624 1624
1 11149036 11155579 - CmaCh01G016250.1 Cma01g01625 1625
5 2430586 2432735 + CmaCh05G005070.1 Cma05g00507 507
5 2437939 2444335 - CmaCh05G005100.1 Cma05g00510 510
9 2573521 2579130 + CmaCh09G005680.1 Cma09g00568 568
9 2580963 2590552 - CmaCh09G005700.1 Cma09g00570 570
12 742588 744758 + CmaCh12G001670.1 Cma12g00167 167
12 751637 758896 - CmaCh12G001710.1 Cma12g00171 171
3 26780046 26784508 + MELO3C011046.2.1 Cme03g01846 1846
3 26790940 26793756 - MELO3C011043.2.1 Cme03g01849 1849
3 26800080 26802271 - MELO3C011041.2.1 Cme03g01852 1852
4 2119143 2120525 + MELO3C003554.2.1 Cme04g00266 266
4 2145980 2147355 + MELO3C003558.2.1 Cme04g00269 269
4 2149265 2153174 + MELO3C003559.2.1 Cme04g00270 270
4 2168966 2172524 - MELO3C003562.2.1 Cme04g00274 274
3 2587591 2589352 + PI0013221.1 Cmetu03g2141 2141
4 31208956 31213017 - PI0004832.1 Cmetu04g1099 1099
4 31192206 31194095 + PI0014099.1 Cmetu04g2791 2791
1 12565115 12568232 + CmoCh01G016610.1 Cmo01g01661 1661
1 12602839 12607826 - CmoCh01G016650.1 Cmo01g01665 1665
1 12616153 12619563 - CmoCh01G016680.1 Cmo01g01668 1668
1 12619660 12624640 - CmoCh01G016690.1 Cmo01g01669 1669
5 2590599 2592504 + CmoCh05G005340.1 Cmo05g00534 534
5 2600394 2605001 - CmoCh05G005380.1 Cmo05g00538 538
9 2651002 2653846 + CmoCh09G005550.1 Cmo09g00555 555
9 2661068 2665159 - CmoCh09G005570.1 Cmo09g00557 557
9 2666190 2671053 - CmoCh09G005580.1 Cmo09g00558 558
12 795393 797387 + CmoCh12G001290.1 Cmo12g00129 129
12 806957 812208 - CmoCh12G001320.1 Cmo12g00132 132
11 26491755 26493750 + CmPI595203_11g014260.1 Cmu11g1426 1426
11 26510467 26515941 - CmPI595203_11g014290.1 Cmu11g1429 1429
11 26517730 26522118 - CmPI595203_11g014300.1 Cmu11g1430 1430
11 26553002 26556799 - CmPI595203_11g014330.1 Cmu11g1433 1433
4 10854820 10858737 + Conep04aG0136800.1 Cone4ag1322 1322
4 10859176 10861914 + Conep04aG0136900.1 Cone4ag1323 1323
7 9403619 9407571 + Conep07aG0130200.1 Cone7ag1265 1265
17 8778200 8780060 + Conep17aG0123300.1 Cone17ag1203 1203
17 8786378 8788876 + Conep17aG0123400.1 Cone17ag1204 1204
20 2810772 2814450 - Conep20aG0053600.1 Cone20ag0520 520
20 2841867 2845846 - Conep20aG0053900.1 Cone20ag0523 523
20 2853971 2855003 - Conep20aG0054100.1 Cone20ag0525 525
2 1958699 1964549 + Cp4.1LG02g05150.1 Cpe02g00358 358
2 1965502 1967892 + Cp4.1LG02g05160.1 Cpe02g00359 359
2 1976325 1990513 + Cp4.1LG02g05140.1 Cpe02g00362 362
2 2010903 2014013 - Cp4.1LG02g05080.1 Cpe02g00365 365
6 2467354 2470238 + Cp4.1LG06g04360.1 Cpe06g00431 431
6 2476673 2480771 - Cp4.1LG06g04290.1 Cpe06g00433 433
6 2481940 2486493 - Cp4.1LG06g04300.1 Cpe06g00434 434
7 797418 800181 + Cp4.1LG07g01440.1 Cpe07g00142 142
7 811137 816572 - Cp4.1LG07g01490.1 Cpe07g00146 146
11 2537299 2539520 + Cp4.1LG11g04480.1 Cpe11g00447 447
11 2547357 2551710 - Cp4.1LG11g04540.1 Cpe11g00451 451
8 23757153 23758800 + CrPI670011_08g010630.1 Cre08g1063 1063
8 23770211 23778235 + CrPI670011_08g010650.1 Cre08g1065 1065
8 23778745 23786364 - CrPI670011_08g010660.1 Cre08g1066 1066
11 30105296 30107307 + CrPI670011_11g018460.1 Cre11g1846 1846
11 30123344 30129094 - CrPI670011_11g018490.1 Cre11g1849 1849
11 30130877 30135280 - CrPI670011_11g018500.1 Cre11g1850 1850
11 30166727 30177532 - CrPI670011_11g018530.1 Cre11g1853 1853
2 19525778 19528220 + CsaV3_2G029820.1 Csa02g02163 2163
2 19534358 19536950 + CsaV3_2G029840.1 Csa02g02165 2165
2 19542553 19547441 - CsaV3_2G029870.1 Csa02g02168 2168
3 38853484 38855417 + CsaV3_3G047630.1 Csa03g04457 4457
3 38869082 38873054 - CsaV3_3G047650.1 Csa03g04459 4459
3 38873450 38878345 - CsaV3_3G047660.1 Csa03g04460 4460
3 38896045 38898470 - CsaV3_3G047690.1 Csa03g04463 4463
1 86024202 86028445 + Hsped.01g21370.1 Hepe01g2137 2137
1 86042380 86046900 - Hsped.01g21400.1 Hepe01g2140 2140
1 86074724 86076389 - Hsped.01g21450.1 Hepe01g2145 2145
10 5581578 5583418 - Hsped.10g04810.1 Hepe10g0481 481
13 34264363 34266734 - Maker00033880 Lcy13g1545 1545
13 34281146 34282125 + Maker00033795 Lcy13g1546 1546
4 29500335 29503268 + Lsi04G022460.1 Lsi04g02246 2246
4 29518794 29531221 - Lsi04G022490.1 Lsi04g02249 2249
4 29557379 29559167 - Lsi04G022520.1 Lsi04g02252 2252
8 18266276 18266860 - Lsi08G009790.1 Lsi08g00979 979
8 18276685 18278948 + Lsi08G009800.1 Lsi08g00980 980
8 18288648 18292319 + Lsi08G009830.1 Lsi08g00983 983
8 18296828 18305444 - Lsi08G009850.1 Lsi08g00985 985
11 4418215 4421478 + MC11g0567 Mch11g0676 676
11 4428698 4437436 - MC11g0570 Mch11g0679 679
4 1074549 1077145 + Sed0008660.1 Sed04g0158 158
5 29693563 29697118 - Sed0012216.1 Sed05g1594 1594
13 26061970 26069291 - Sed0018010.3 Sed13g2145 2145
1 102912002 102914908 + Tan0008294.1 Tan01g3801 3801
1 102934423 102944253 - Tan0007682.1 Tan01g3804 3804
1 102987785 102988894 - Tan0002920.3 Tan01g3812 3812
2 92690454 92691016 - Tan0003498.1 Tan02g2409 2409
2 92708655 92711062 + Tan0011989.1 Tan02g2410 2410
18 4733207 4737587 - Vvi18g440 Vvi18g440 440
18 4738322 4739988 - Vvi18g441 Vvi18g441 441
18 4742537 4745017 + Vvi18g442 Vvi18g442 442
18 4745556 4752639 + Vvi18g443 Vvi18g443 443
18 4760149 4762878 + Vvi18g444 Vvi18g444 444
18 4765815 4772366 - Vvi18g445 Vvi18g445 445
18 4773001 4780140 - Vvi18g446 Vvi18g446 446
18 4788237 4789038 - Vvi18g447 Vvi18g447 447
18 4791464 4794870 - Vvi18g448 Vvi18g448 448
18 4806871 4808947 - Vvi18g449 Vvi18g449 449
       

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