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
Vvi5g499 . . Bda03g00884 Bda08g00237 Bpe04g00829 . Bma04g00782 Bma05g01108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00901 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g500 . . . . . Bpe14g01186 . . Cmo08g01119 Cmo17g00220 . . . . . . . . . . . . . . Cla06g00586 Cam06g0624 Cec06g0627 Cco06g0632 Clacu06g0611 Cmu06g0604 Cre06g1372 . . Cone7ag0251 Cone4ag0245 . . . . . Blo07g00218 Bda11g00576 Bda13g00127 . Bpe13g00607 Bma02g00850 Bma06g01555 Sed04g1906 . . Cma08g01141 Cma17g00233 Car08g01025 Car17g00212 Cpe12g00196 Cpe17g00148 Bhi12g01706 Tan06g2520 Cmetu01g2519 Lac12g2277 Hepe03g0201 . Lcy13g0285 . . . . . . . Lsi09g01318 . . Cme01g01567
Vvi5g501 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g502 . . . . . . . . Cmo08g01117 Cmo17g00219 . . . . . . . . . . . . . . Cla06g00587 Cam06g0625 Cec06g0628 Cco06g0633 Clacu06g0612 Cmu06g0605 Cre06g1373 Cone14ag0852 Cone15ag0831 . . . . . . Blo02g00540 . . Bda13g00125 . . Bma02g00849 . Sed04g1907 . . Cma08g01140 Cma17g00231 Car08g01024 Car17g00211 Cpe12g00194 Cpe17g00149 Bhi12g01705 Tan06g2519 Cmetu01g0765 Lac12g2276 Hepe03g0202 . Lcy13g0286 . . . . . . . Lsi09g01317 . . Cme01g01568
Vvi5g503 . . . . . . . . . . Cma06g01412 . Car06g01218 . . . . Bhi01g00816 . . . Hepe05g1549 . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo06g01414 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g504 . . . . . . . . . . . Cma14g01705 . Car14g01540 . . Cpe03g01433 . . . . . . . . . . . . . . . . Cone7ag0252 . Lsi05g01602 . . Cme06g00612 . Blo07g00219 Bda11g00577 . . Bpe13g00606 . Bma06g01556 . . Cmo14g01748 . . . . . . . . . . . . . Cla05g00546 Cam05g0596 Cec05g0606 Cco05g0603 Clacu05g0593 Cmu05g0563 Cre05g0632 . Csa03g01332 Chy06g00583 .
Vvi5g505 . . . . . Bpe14g01188 . . . . . Cma14g01706 Car06g01217 Car14g01541 . Cpe08g00258 Cpe03g01434 Bhi01g00814 . . . Hepe05g1550 . . . . . . . . . Cone14ag0854 . . . Lsi05g01603 . . . . . . . . . Bma02g00847 . . . Cmo14g01749 . . . . . . . . . . . . . Cla05g00544 Cam05g0595 Cec05g0605 Cco05g0602 Clacu05g0592 Cmu05g0562 Cre05g0631 . . . .
Vvi5g506 . . . . . . . . . . . Cma14g01708 . Car14g01543 Sed02g1321 . Cpe03g01436 Bhi01g00812 Tan10g0843 Cmetu06g2511 . Hepe05g1552 . Lcy11g1546 Cla06g00588 Cam06g0626 Cec06g0630 . Clacu06g0613 Cmu06g0606 Cre06g1374 Cone14ag0855 . . . Lsi05g01605 . . Cme06g00610 . . . Bda13g00121 . . Bma02g00846 . Sed09g1121 . Cmo14g01751 . . . . . . Bhi12g01704 Tan06g2518 Cmetu01g1315 Lac12g2275 Hepe03g0203 . . Cla05g00543 Cam05g0593 Cec05g0603 Cco05g0600 Clacu05g0590 Cmu05g0560 Cre05g0629 Lsi09g01315 Csa03g01329 Chy06g00580 .
Vvi5g507 . . . . . . . . Cmo08g01116 . . . Car06g01215 . Sed02g1319 Cpe08g00260 Cpe03g01437 Bhi01g00811 Tan10g0842 Cmetu06g1654 Lac12g2274 Hepe05g1553 . . Cla06g00589 Cam06g0628 Cec06g0631 Cco06g0634 Clacu06g0614 Cmu06g0607 Cre06g1375 . . Cone7ag0256 . Lsi05g01606 . . Cme06g00609 . Blo07g00220 Bda11g00578 Bda13g00120 . Bpe13g00605 . Bma06g01557 Sed06g0669 Cmo06g01411 . Cma08g01139 . Car08g01023 . . Cpe17g00150 Bhi12g01703 Tan06g0980 Cmetu01g1750 Lac12g2274 Hepe03g0204 . Lcy13g0287 Cla05g00542 . . . . . . Lsi09g01314 Csa03g01328 Chy06g00579 Cme01g01569
Vvi5g508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7630440 7631627 - Bda016875.1 Bda03g00884 884
8 2369898 2371154 + Bda024652.1 Bda08g00237 237
11 5924911 5934233 + Bda005316.1 Bda11g00576 576
11 5934656 5935111 - Bda005317.1 Bda11g00577 577
11 5943014 5943967 - Bda005318.1 Bda11g00578 578
13 1602908 1603820 + Bda000977.1 Bda13g00120 120
13 1606448 1607203 + Bda000978.1 Bda13g00121 121
13 1630631 1634613 - Bda000984.1 Bda13g00125 125
13 1652317 1653381 - Bda000986.1 Bda13g00127 127
1 15183090 15186230 + XM_039025446.1 Bhi01g00811 811
1 15192970 15193596 + XM_039029844.1 Bhi01g00812 812
1 15199076 15202665 - XM_039040659.1 Bhi01g00814 814
1 15200230 15202654 - XM_039040645.1 Bhi01g00816 816
12 54942202 54945238 + XM_039020370.1 Bhi12g01703 1703
12 54947747 54948324 + XM_039020388.1 Bhi12g01704 1704
12 55181757 55185010 - XM_039018339.1 Bhi12g01705 1705
12 55190849 55205524 - XM_039018640.1 Bhi12g01706 1706
2 9199784 9202223 - BLOR10270 Blo02g00540 540
7 2747731 2759699 + BLOR18150 Blo07g00218 218
7 2760079 2760534 - BLOR18151 Blo07g00219 219
7 2765618 2766597 - BLOR18152 Blo07g00220 220
2 45583507 45584283 + Bma015598.1 Bma02g00846 846
2 45603123 45603563 - Bma015599.1 Bma02g00847 847
2 45617718 45620207 - Bma015601.1 Bma02g00849 849
2 45633955 45635019 - Bma015602.1 Bma02g00850 850
4 8508013 8509357 - Bma019305.1 Bma04g00782 782
5 49838627 49839695 - Bma022281.1 Bma05g01108 1108
6 51864715 51874598 + Bma024673.1 Bma06g01555 1555
6 51875021 51875476 - Bma024674.1 Bma06g01556 1556
6 51879284 51880245 - Bma024675.1 Bma06g01557 1557
4 5447587 5448732 - Bpe015489.1 Bpe04g00829 829
5 22046822 22047915 - Bpe018312.1 Bpe05g00901 901
13 13096539 13097524 + Bpe010304.3 Bpe13g00605 605
13 13102283 13102735 + Bpe025232 Bpe13g00606 606
13 13103154 13113799 - Bpe010305.1 Bpe13g00607 607
14 8864206 8875797 + Bpe025537 Bpe14g01186 1186
14 8891472 8891915 + Bpe014558.1 Bpe14g01188 1188
5 5210106 5211189 + CaPI482276_05g005930.1 Cam05g0593 593
5 5215416 5217400 - CaPI482276_05g005950.1 Cam05g0595 595
5 5221258 5221701 + CaPI482276_05g005960.1 Cam05g0596 596
6 8473303 8481821 + CaPI482276_06g006240.1 Cam06g0624 624
6 8487242 8490090 + CaPI482276_06g006250.1 Cam06g0625 625
6 8505052 8505639 - CaPI482276_06g006260.1 Cam06g0626 626
6 8511954 8512187 - CaPI482276_06g006280.1 Cam06g0628 628
6 8825433 8826218 + Carg17420-RA Car06g01215 1215
6 8828329 8828775 - Carg17418-RA Car06g01217 1217
6 8829391 8830398 - Carg17417-RA Car06g01218 1218
8 6979532 6982196 + Carg15902-RA Car08g01023 1023
8 6983431 6985730 - Carg15903-RA Car08g01024 1024
8 6989537 6997002 - Carg15904-RA Car08g01025 1025
14 12697522 12697965 - Carg23523-RA Car14g01540 1540
14 12699041 12702398 + Carg23522-RA Car14g01541 1541
14 12705179 12705793 - Carg23520-RA Car14g01543 1543
17 1276864 1279897 - Carg05415-RA Car17g00211 211
17 1284077 1292347 - Carg05416-RA Car17g00212 212
5 4884385 4885461 + CcPI632755_05g006000.1 Cco05g0600 600
5 4889578 4891562 - CcPI632755_05g006020.1 Cco05g0602 602
5 4895498 4895941 + CcPI632755_05g006030.1 Cco05g0603 603
6 6984134 6993411 + CcPI632755_06g006320.1 Cco06g0632 632
6 6997925 7000762 + CcPI632755_06g006330.1 Cco06g0633 633
6 7008303 7022424 - CcPI632755_06g006340.1 Cco06g0634 634
5 4912590 4913219 + CePI673135_05g006030.1 Cec05g0603 603
5 4917873 4919857 - CePI673135_05g006050.1 Cec05g0605 605
5 4923764 4924207 + CePI673135_05g006060.1 Cec05g0606 606
6 7027961 7036419 + CePI673135_06g006270.1 Cec06g0627 627
6 7041799 7044647 + CePI673135_06g006280.1 Cec06g0628 628
6 7059267 7059854 - CePI673135_06g006300.1 Cec06g0630 630
6 7065907 7068044 - CePI673135_06g006310.1 Cec06g0631 631
6 3933109 3935117 + Chy6G111070.1 Chy06g00579 579
6 3937386 3942490 + Chy6G111080.1 Chy06g00580 580
6 3944539 3944973 + Chy6G111110.1 Chy06g00583 583
5 4925590 4926669 + ClG42_05g0059000.10 Clacu05g0590 590
5 4930809 4932791 - ClG42_05g0059200.10 Clacu05g0592 592
5 4936628 4937071 + ClG42_05g0059300.10 Clacu05g0593 593
6 7034272 7043474 + ClG42_06g0061100.10 Clacu06g0611 611
6 7048136 7050975 + ClG42_06g0061200.10 Clacu06g0612 612
6 7065804 7066391 - ClG42_06g0061300.10 Clacu06g0613 613
6 7070964 7072895 - ClG42_06g0061400.10 Clacu06g0614 614
5 4961124 4967487 + ClCG05G005140.2 Cla05g00542 542
5 4972750 4973376 + ClCG05G005155.1 Cla05g00543 543
5 4977855 4980852 - ClCG05G005160.1 Cla05g00544 544
5 4984693 4985136 + ClCG05G005167.1 Cla05g00546 546
6 7140286 7149565 + ClCG06G006230.1 Cla06g00586 586
6 7154037 7157418 + ClCG06G006240.1 Cla06g00587 587
6 7171814 7172401 - ClCG06G006250.1 Cla06g00588 588
6 7176973 7178904 - ClCG06G006260.2 Cla06g00589 589
6 9087675 9091473 - CmaCh06G014120.1 Cma06g01412 1412
8 7030104 7032484 + CmaCh08G011390.1 Cma08g01139 1139
8 7033356 7036155 - CmaCh08G011400.1 Cma08g01140 1140
8 7037118 7047190 - CmaCh08G011410.1 Cma08g01141 1141
14 12624196 12624639 - CmaCh14G017050.1 Cma14g01705 1705
14 12626758 12628494 + CmaCh14G017060.1 Cma14g01706 1706
14 12632214 12632837 - CmaCh14G017080.1 Cma14g01708 1708
17 1173252 1176926 - CmaCh17G002310.1 Cma17g00231 231
17 1184220 1189342 - CmaCh17G002330.1 Cma17g00233 233
1 20793856 20804041 + MELO3C012650.2.1 Cme01g01567 1567
1 20808696 20813416 + MELO3C012651.2.1 Cme01g01568 1568
1 20824810 20826858 - MELO3C012653.2.1 Cme01g01569 1569
6 3887988 3891062 + MELO3C006530.2.1 Cme06g00609 609
6 3893045 3893916 + MELO3C006531.2.1 Cme06g00610 610
6 3900194 3900934 + MELO3C006533.2.1 Cme06g00612 612
1 7771551 7776130 + PI0025779.1 Cmetu01g0765 765
1 23799995 23801064 + PI0024415.1 Cmetu01g1315 1315
1 23790846 23792370 + PI0028483.1 Cmetu01g1750 1750
1 7756688 7768124 + PI0005892.1 Cmetu01g2519 2519
6 4127617 4130454 + PI0013955.1 Cmetu06g1654 1654
6 4133245 4135306 + PI0026211.1 Cmetu06g2511 2511
6 10287585 10290992 + CmoCh06G014110.1 Cmo06g01411 1411
6 10294064 10296315 - CmoCh06G014140.1 Cmo06g01414 1414
8 7117421 7119959 + CmoCh08G011160.1 Cmo08g01116 1116
8 7121066 7123447 - CmoCh08G011170.1 Cmo08g01117 1117
8 7133088 7134308 - CmoCh08G011190.1 Cmo08g01119 1119
14 13595027 13595470 - CmoCh14G017480.1 Cmo14g01748 1748
14 13595687 13599229 + CmoCh14G017490.1 Cmo14g01749 1749
14 13602681 13603292 - CmoCh14G017510.1 Cmo14g01751 1751
17 1285574 1290818 - CmoCh17G002190.1 Cmo17g00219 219
17 1292783 1303540 - CmoCh17G002200.1 Cmo17g00220 220
5 4769233 4770312 + CmPI595203_05g005600.1 Cmu05g0560 560
5 4774444 4776426 - CmPI595203_05g005620.1 Cmu05g0562 562
5 4780262 4780705 + CmPI595203_05g005630.1 Cmu05g0563 563
6 6840613 6849598 + CmPI595203_06g006040.1 Cmu06g0604 604
6 6854463 6857302 + CmPI595203_06g006050.1 Cmu06g0605 605
6 6872132 6872719 - CmPI595203_06g006060.1 Cmu06g0606 606
6 6877262 6879187 - CmPI595203_06g006070.1 Cmu06g0607 607
4 1099587 1105005 + Conep04aG0025400.1 Cone4ag0245 245
7 1051553 1058952 + Conep07aG0025600.1 Cone7ag0251 251
7 1059820 1060269 - Conep07aG0025700.1 Cone7ag0252 252
7 1069080 1070012 - Conep07aG0026100.1 Cone7ag0256 256
14 5438959 5443099 + Conep14aG0086900.1 Cone14ag0852 852
14 5451448 5453994 + Conep14aG0087100.1 Cone14ag0854 854
14 5457467 5458180 - Conep14aG0087200.1 Cone14ag0855 855
15 6026307 6030496 - Conep15aG0084700.1 Cone15ag0831 831
3 11507386 11507829 - Cp4.1LG03g10600.1 Cpe03g01433 1433
3 11508818 11514003 + Cp4.1LG03g10740.1 Cpe03g01434 1434
3 11516292 11516915 - Cp4.1LG03g10610.1 Cpe03g01436 1436
3 11518205 11521904 - Cp4.1LG03g10660.1 Cpe03g01437 1437
8 1697950 1703131 + Cp4.1LG08g04180.1 Cpe08g00258 258
8 1704855 1706774 - Cp4.1LG08g04030.1 Cpe08g00260 260
12 1242780 1246220 - Cp4.1LG12g01920.1 Cpe12g00194 194
12 1256969 1258253 - Cp4.1LG12g02000.1 Cpe12g00196 196
17 948194 955504 + Cp4.1LG17g01510.1 Cpe17g00148 148
17 959252 962185 + Cp4.1LG17g01440.1 Cpe17g00149 149
17 962866 967059 - Cp4.1LG17g01550.1 Cpe17g00150 150
5 5558211 5559711 + CrPI670011_05g006290.1 Cre05g0629 629
5 5563674 5565659 - CrPI670011_05g006310.1 Cre05g0631 631
5 5569554 5569997 + CrPI670011_05g006320.1 Cre05g0632 632
6 7909168 7917749 + CrPI670011_06g013720.1 Cre06g1372 1372
6 7923261 7926108 + CrPI670011_06g013730.1 Cre06g1373 1373
6 7941797 7942375 - CrPI670011_06g013740.1 Cre06g1374 1374
6 7946403 7949069 - CrPI670011_06g013750.1 Cre06g1375 1375
3 10072053 10074049 + CsaV3_3G013280.1 Csa03g01328 1328
3 10076362 10081382 + CsaV3_3G013290.1 Csa03g01329 1329
3 10083378 10083812 + CsaV3_3G013320.1 Csa03g01332 1332
3 2564791 2572689 + Hsped.03g02010.1 Hepe03g0201 201
3 2578452 2582543 + Hsped.03g02020.1 Hepe03g0202 202
3 2613421 2614070 - Hsped.03g02030.1 Hepe03g0203 203
3 2619648 2621420 - Hsped.03g02040.1 Hepe03g0204 204
5 65118755 65119768 + Hsped.05g15490.1 Hepe05g1549 1549
5 65120161 65120610 + Hsped.05g15500.1 Hepe05g1550 1550
5 65127328 65128185 - Hsped.05g15520.1 Hepe05g1552 1552
5 65137993 65141135 - Hsped.05g15530.1 Hepe05g1553 1553
12 39866251 39867699 + Lag0016646.1 Lac12g2274 2274
12 39870881 39871489 + Lag0016647.1 Lac12g2275 2275
12 39879944 39882905 - Lag0016648.1 Lac12g2276 2276
12 39888333 39902519 - Lag0016649.1 Lac12g2277 2277
11 39327825 39328439 - Maker00031889 Lcy11g1546 1546
13 3103645 3107133 + Maker00023544 Lcy13g0285 285
13 3112427 3115396 + Maker00023532 Lcy13g0286 286
13 3128111 3130277 - Maker00023223 Lcy13g0287 287
5 23755584 23756027 - Lsi05G016020.1 Lsi05g01602 1602
5 23758485 23760796 + Lsi05G016030.1 Lsi05g01603 1603
5 23765127 23765741 - Lsi05G016050.1 Lsi05g01605 1605
5 23769606 23772254 - Lsi05G016060.1 Lsi05g01606 1606
9 21013147 21015902 + Lsi09G013140.1 Lsi09g01314 1314
9 21019958 21026266 + Lsi09G013150.1 Lsi09g01315 1315
9 21027061 21030342 - Lsi09G013170.1 Lsi09g01317 1317
9 21033557 21042298 - Lsi09G013180.1 Lsi09g01318 1318
2 49642127 49644182 + Sed0003127.8 Sed02g1319 1319
2 49646700 49648020 + Sed0003149.1 Sed02g1321 1321
4 33794665 33805950 + Sed0017994.1 Sed04g1906 1906
4 33810830 33814864 + Sed0018003.1 Sed04g1907 1907
6 6305734 6308192 + Sed0002124.1 Sed06g0669 669
9 35306676 35307446 + Sed0023818.1 Sed09g1121 1121
6 8631407 8632855 - Tan0005151.1 Tan06g0980 980
6 77801874 77802437 + Tan0012772.1 Tan06g2518 2518
6 77811877 77815626 - Tan0022451.1 Tan06g2519 2519
6 77819996 77830170 - Tan0016679.1 Tan06g2520 2520
10 6964819 6967108 + Tan0014501.1 Tan10g0842 842
10 6988477 6989548 + Tan0006872.1 Tan10g0843 843
5 5212913 5215828 + Vvi5g499 Vvi5g499 499
5 5228980 5252763 + Vvi5g500 Vvi5g500 500
5 5255045 5255439 - Vvi5g501 Vvi5g501 501
5 5255465 5259119 + Vvi5g502 Vvi5g502 502
5 5261958 5263005 + Vvi5g503 Vvi5g503 503
5 5264178 5264916 - Vvi5g504 Vvi5g504 504
5 5265546 5277125 + Vvi5g505 Vvi5g505 505
5 5284996 5285856 - Vvi5g506 Vvi5g506 506
5 5290149 5291427 - Vvi5g507 Vvi5g507 507
5 5291970 5292289 - Vvi5g508 Vvi5g508 508
       

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