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
Vvi18g580 Blo01g01784 . . . Bpe02g00157 . . Bma01g02568 . . . Cma09g00613 . . . Cpe06g00474 . . . . . . . . . . . . . . . Cone4ag1264 Cone7ag0879 . . Lsi04g02311 Csa03g04530 Chy04g00173 . . . Bda11g00816 . . . . . Sed05g1523 Cmo01g01505 Cmo09g00601 . . . Car09g00545 . Cpe02g00498 Bhi09g02548 Tan01g3895 Cmetu04g0312 . Hepe01g2200 . . Cla11g01461 Cam11g1513 Cec11g1551 Cco11g1546 . Cmu11g1494 Cre11g1915 . . . Cme04g00201
Vvi18g581 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1262 Cone7ag0880 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g582 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g583 . . . . . . . . Cmo05g00598 Cmo12g00187 . . . Car12g00213 Sed01g1243 . Cpe07g00196 Bhi04g00887 Tan02g2526 Cmetu03g1186 . . . . Cla08g01196 Cam08g1658 Cec08g1235 Cco08g1354 Clacu08g1355 . Cre08g1142 . . Cone17ag1147 Cone20ag0580 . . . Cme03g01769 Blo17g00078 . . Bda13g01339 . Bpe14g00508 . Bma02g00094 . . . Cma12g00232 Cma05g00573 Car05g00519 . Cpe11g00502 . . . . . . . . . . . . . . . Lsi08g01058 Csa02g02240 Chy03g01276 .
Vvi18g584 Blo01g01782 . . Bda03g00441 Bpe02g00159 Bpe04g00407 Bma04g00418 Bma01g02567 . . Cma01g01450 Cma09g00617 . . . Cpe06g00476 . . . . . . . . . . . . . . . Cone4ag1261 Cone7ag0882 Cone17ag1146 Cone20ag0581 Lsi04g02313 Csa03g04531 Chy04g00172 . . . Bda11g00817 . . . . . Sed12g1374 Cmo01g01503 Cmo09g00602 . . . Car09g00547 . Cpe02g00499 Bhi09g02549 Tan01g3897 Cmetu04g0381 . Hepe01g2202 Mch11g0751 . Cla11g01463 Cam11g1515 Cec11g1554 Cco11g1549 Clacu11g1679 Cmu11g1496 Cre11g1917 . . . Cme04g00199
Vvi18g585 . . . . . . . Bma01g02566 . . Cma01g01449 . . . . . . . . . . . . . . . . . . . . Cone4ag1260 Cone7ag0883 . . Lsi04g02314 Csa03g04532 Chy04g00171 . . . Bda11g00818 . . . . . Sed12g1375 Cmo01g01502 . . . . . . Cpe02g00500 Bhi09g02550 Tan01g3898 Cmetu04g0667 . . Mch11g0752 . Cla11g01464 Cam11g1516 Cec11g1555 Cco11g1550 Clacu11g1680 Cmu11g1497 Cre11g1918 . . . Cme04g00198
Vvi18g586 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g587 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0186 . . . . . Blo17g00077 Blo18g00089 . Bda13g01338 Bpe02g01175 Bpe14g00509 Bma01g01355 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g588 Blo01g01781 . Bda01g00855 . Bpe02g00160 . . Bma01g02565 . . Cma01g01447 Cma09g00619 . . . Cpe06g00478 . . . . . . . . . . . . . . . Cone4ag1259 . . . Lsi04g02315 Csa03g04533 Chy04g00170 . . . Bda11g00819 . Bpe02g01094 . . . . Cmo01g01501 Cmo09g00604 . . . Car09g00549 . Cpe02g00501 Bhi09g02551 . . . . . . Cla11g01465 Cam11g1518 Cec11g1556 Cco11g1551 Clacu11g1682 Cmu11g1499 . . . . Cme04g00196
Vvi18g589 Blo01g01478 . Bda01g00606 . Bpe02g00474 . . . . . . Cma09g00324 Car01g01368 . . Cpe06g00229 . . . . . . . . . . . . . . . Cone4ag1643 Cone7ag1307 . . Lsi04g01444 Csa04g02514 . . . . . . . . . . Sed11g1863 Cmo01g01816 Cmo09g00322 . . . Car09g00272 . Cpe02g00245 Bhi09g03181 Tan01g4651 Cmetu07g1847 . . Mch11g0395 . Cla05g01811 Cam05g1933 Cec05g1946 Cco05g2008 Clacu05g1925 Cmu05g1807 Cre05g1933 . . Chy07g00222 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33063585 33067447 - Bda002629.1 Bda01g00606 606
1 41112820 41115098 - Bda002982.1 Bda01g00855 855
3 3795831 3797607 - Bda016409.1 Bda03g00441 441
11 8093191 8097297 - Bda005567.1 Bda11g00816 816
11 8105093 8106315 + Bda005568.1 Bda11g00817 817
11 8108928 8110377 + Bda005569.1 Bda11g00818 818
11 8111873 8113687 - Bda005570.1 Bda11g00819 819
13 35667620 35667937 + Bda000149.1 Bda13g01338 1338
13 35671383 35674875 - Bda000150.1 Bda13g01339 1339
4 22332637 22337696 - XM_039030177.1 Bhi04g00887 887
9 69353328 69358542 - XM_039040821.1 Bhi09g02548 2548
9 69380663 69383349 + XM_039043519.1 Bhi09g02549 2549
9 69390961 69394069 + XM_039041356.1 Bhi09g02550 2550
9 69394865 69399699 - XM_039041352.1 Bhi09g02551 2551
9 81428147 81433980 + XM_039042413.1 Bhi09g03181 3181
1 54086207 54090768 + BLOR01478 Blo01g01478 1478
1 57544189 57549294 + BLOR01781 Blo01g01781 1781
1 57553366 57559264 - BLOR01782 Blo01g01782 1782
1 57567627 57572125 + BLOR01784 Blo01g01784 1784
17 580617 581136 + BLOR15898 Blo17g00077 77
17 583345 586794 - BLOR15899 Blo17g00078 78
18 730578 736074 + BLOR08577 Blo18g00089 89
1 20307451 20307768 + Bma001687.1 Bma01g01355 1355
1 83282170 83284605 + Bma003447.1 Bma01g02565 2565
1 83285452 83286456 - Bma003448.2 Bma01g02566 2566
1 83288093 83289912 - Bma003449.1 Bma01g02567 2567
1 83296114 83300195 + Bma003450.1 Bma01g02568 2568
2 819965 822808 - Bma014549.1 Bma02g00094 94
4 3389038 3390815 - Bma018883.1 Bma04g00418 418
2 1095776 1099885 - Bpe008008.2 Bpe02g00157 157
2 1107624 1109381 + Bpe008010.1 Bpe02g00159 159
2 1113106 1115499 - Bpe008011.1 Bpe02g00160 160
2 3079873 3083239 - Bpe008315.1 Bpe02g00474 474
2 14463365 14465644 - Bpe008951.2 Bpe02g01094 1094
2 15431874 15432104 - Bpe009036.1 Bpe02g01175 1175
4 2556409 2558184 - Bpe025621 Bpe04g00407 407
14 4496846 4500292 + Bpe007158.3 Bpe14g00508 508
14 4502361 4502672 - Bpe007159.1 Bpe14g00509 509
5 28271791 28275707 - CaPI482276_05g019330.1 Cam05g1933 1933
8 22841391 22847473 + CaPI482276_08g016580.1 Cam08g1658 1658
11 28005464 28010541 - CaPI482276_11g015130.1 Cam11g1513 1513
11 28018225 28020092 + CaPI482276_11g015150.1 Cam11g1515 1515
11 28026015 28028742 + CaPI482276_11g015160.1 Cam11g1516 1516
11 28030349 28037605 - CaPI482276_11g015180.1 Cam11g1518 1518
1 12027667 12031620 + Carg10669-RA Car01g01368 1368
5 3018247 3020451 + Carg08262-RA Car05g00519 519
9 1486765 1491081 - Carg21749-RA Car09g00272 272
9 3096309 3101772 - Carg03027-RA Car09g00545 545
9 3104781 3106687 + Carg03029-RA Car09g00547 547
9 3109881 3114453 - Carg03031-RA Car09g00549 549
12 1353128 1357748 + Carg22481-RA Car12g00213 213
5 29191377 29196025 - CcPI632755_05g020080.1 Cco05g2008 2008
8 25480597 25484967 + CcPI632755_08g013540.1 Cco08g1354 1354
11 28370826 28375258 - CcPI632755_11g015460.1 Cco11g1546 1546
11 28383572 28385439 + CcPI632755_11g015490.1 Cco11g1549 1549
11 28391452 28394104 + CcPI632755_11g015500.1 Cco11g1550 1550
11 28395729 28399102 - CcPI632755_11g015510.1 Cco11g1551 1551
5 31534490 31538422 - CePI673135_05g019460.1 Cec05g1946 1946
8 24323050 24329156 + CePI673135_08g012350.1 Cec08g1235 1235
11 29814740 29819199 - CePI673135_11g015510.1 Cec11g1551 1551
11 29827120 29829391 + CePI673135_11g015540.1 Cec11g1554 1554
11 29834907 29838809 + CePI673135_11g015550.1 Cec11g1555 1555
11 29839224 29842595 - CePI673135_11g015560.1 Cec11g1556 1556
3 15776375 15780466 - Chy3G062560.1 Chy03g01276 1276
4 1489242 1493046 + Chy4G068880.1 Chy04g00170 170
4 1493177 1496766 - Chy4G068890.1 Chy04g00171 171
4 1498810 1500491 - Chy4G068900.1 Chy04g00172 172
4 1504917 1511087 + Chy4G068910.1 Chy04g00173 173
7 1814951 1818847 - Chy7G130520.1 Chy07g00222 222
5 28473666 28477589 - ClG42_05g0192500.10 Clacu05g1925 1925
8 23616681 23621061 + ClG42_08g0135500.10 Clacu08g1355 1355
11 28048495 28050362 + ClG42_11g0167900.10 Clacu11g1679 1679
11 28056276 28058939 + ClG42_11g0168000.10 Clacu11g1680 1680
11 28060548 28064124 - ClG42_11g0168200.10 Clacu11g1682 1682
5 30042832 30048122 - ClCG05G017670.2 Cla05g01811 1811
8 24895517 24900767 + ClCG08G012000.2 Cla08g01196 1196
11 28281865 28286300 - ClCG11G014940.2 Cla11g01461 1461
11 28294673 28296540 + ClCG11G014960.1 Cla11g01463 1463
11 28302454 28306381 + ClCG11G014970.2 Cla11g01464 1464
11 28305841 28309722 - ClCG11G014980.2 Cla11g01465 1465
1 10191260 10195732 + CmaCh01G014470.1 Cma01g01447 1447
1 10197177 10199549 - CmaCh01G014490.1 Cma01g01449 1449
1 10201118 10203874 - CmaCh01G014500.1 Cma01g01450 1450
5 2836690 2840805 + CmaCh05G005730.1 Cma05g00573 573
9 1334367 1338299 - CmaCh09G003240.1 Cma09g00324 324
9 2904444 2909630 - CmaCh09G006130.1 Cma09g00613 613
9 2913082 2915252 + CmaCh09G006170.1 Cma09g00617 617
9 2918772 2922320 - CmaCh09G006190.1 Cma09g00619 619
12 1152659 1157479 + CmaCh12G002320.1 Cma12g00232 232
3 26169297 26174116 - MELO3C011119.2.1 Cme03g01769 1769
4 1456966 1461302 + MELO3C003480.2.1 Cme04g00196 196
4 1461738 1464637 - MELO3C003481.2.1 Cme04g00198 198
4 1465909 1468297 - MELO3C003482.2.1 Cme04g00199 199
4 1473597 1479330 + MELO3C003484.2.1 Cme04g00201 201
3 3255072 3260070 + PI0014453.1 Cmetu03g1186 1186
4 31927022 31932282 - PI0007103.2 Cmetu04g0312 312
4 31936379 31938766 + PI0024175.1 Cmetu04g0381 381
4 31940369 31944315 + PI0010671.1 Cmetu04g0667 667
7 23203275 23210276 - PI0019901.3 Cmetu07g1847 1847
1 11604592 11608971 + CmoCh01G015010.1 Cmo01g01501 1501
1 11610153 11612577 - CmoCh01G015020.1 Cmo01g01502 1502
1 11614019 11616322 - CmoCh01G015030.1 Cmo01g01503 1503
1 11620244 11627444 + CmoCh01G015050.1 Cmo01g01505 1505
1 13312093 13316401 + CmoCh01G018160.1 Cmo01g01816 1816
5 2982571 2986643 + CmoCh05G005980.1 Cmo05g00598 598
9 1400176 1404112 - CmoCh09G003220.1 Cmo09g00322 322
9 2991375 2998174 - CmoCh09G006010.1 Cmo09g00601 601
9 2999286 3001905 + CmoCh09G006020.1 Cmo09g00602 602
9 3005472 3009441 - CmoCh09G006040.1 Cmo09g00604 604
12 1223779 1228302 + CmoCh12G001870.1 Cmo12g00187 187
5 28191970 28195893 - CmPI595203_05g018070.1 Cmu05g1807 1807
11 27288111 27292319 - CmPI595203_11g014940.1 Cmu11g1494 1494
11 27300262 27302555 + CmPI595203_11g014960.1 Cmu11g1496 1496
11 27308445 27311113 + CmPI595203_11g014970.1 Cmu11g1497 1497
11 27312722 27316295 - CmPI595203_11g014990.1 Cmu11g1499 1499
4 10389803 10393196 + Conep04aG0130500.1 Cone4ag1259 1259
4 10396117 10397850 - Conep04aG0130600.1 Cone4ag1260 1260
4 10398619 10400289 - Conep04aG0130700.1 Cone4ag1261 1261
4 10401666 10404433 - Conep04aG0130800.1 Cone4ag1262 1262
4 10405265 10411488 + Conep04aG0131000.1 Cone4ag1264 1264
4 12402304 12406533 - Conep04aG0169600.1 Cone4ag1643 1643
7 6840483 6845330 - Conep07aG0090800.1 Cone7ag0879 879
7 6845762 6848833 + Conep07aG0090900.1 Cone7ag0880 880
7 6857898 6860007 + Conep07aG0091100.1 Cone7ag0882 882
7 6870810 6873391 + Conep07aG0091200.1 Cone7ag0883 883
7 9602345 9603031 + Conep07aG0134600.1 Cone7ag1307 1307
8 971754 972328 + Conep08aG0018900.1 Cone8ag0186 186
17 8439796 8441761 - Conep17aG0117500.1 Cone17ag1146 1146
17 8443658 8448140 - Conep17aG0117600.1 Cone17ag1147 1147
20 3336086 3340926 + Conep20aG0059700.1 Cone20ag0580 580
20 3341565 3343553 + Conep20aG0059800.1 Cone20ag0581 581
2 1271997 1276151 - Cp4.1LG02g06160.1 Cpe02g00245 245
2 2908051 2917668 - Cp4.1LG02g03740.1 Cpe02g00498 498
2 2922583 2925362 + Cp4.1LG02g03760.1 Cpe02g00499 499
2 2927085 2930076 + Cp4.1LG02g03780.1 Cpe02g00500 500
2 2931525 2933933 - Cp4.1LG02g03750.1 Cpe02g00501 501
6 1216999 1223700 - Cp4.1LG06g02320.1 Cpe06g00229 229
6 2804232 2809662 - Cp4.1LG06g03900.1 Cpe06g00474 474
6 2812143 2815020 + Cp4.1LG06g03810.1 Cpe06g00476 476
6 2817561 2822273 - Cp4.1LG06g03750.1 Cpe06g00478 478
7 1248591 1253168 + Cp4.1LG07g02620.1 Cpe07g00196 196
11 2933420 2937581 + Cp4.1LG11g04990.1 Cpe11g00502 502
5 31515127 31519049 - CrPI670011_05g019330.1 Cre05g1933 1933
8 24648678 24654975 + CrPI670011_08g011420.1 Cre08g1142 1142
11 30922465 30927631 - CrPI670011_11g019150.1 Cre11g1915 1915
11 30935048 30937341 + CrPI670011_11g019170.1 Cre11g1917 1917
11 30943452 30946153 + CrPI670011_11g019180.1 Cre11g1918 1918
2 20135197 20140152 + CsaV3_2G030590.1 Csa02g02240 2240
3 39503513 39509334 - CsaV3_3G048360.1 Csa03g04530 4530
3 39514005 39516228 + CsaV3_3G048370.1 Csa03g04531 4531
3 39517737 39521972 + CsaV3_3G048380.1 Csa03g04532 4532
3 39521151 39525828 - CsaV3_3G048390.1 Csa03g04533 4533
4 24975815 24982935 - CsaV3_4G035400.1 Csa04g02514 2514
1 86726327 86730501 - Hsped.01g22000.1 Hepe01g2200 2200
1 86740543 86743186 + Hsped.01g22020.1 Hepe01g2202 2202
4 22177011 22182264 + Lsi04G014440.1 Lsi04g01444 1444
4 30332948 30337615 - Lsi04G023110.1 Lsi04g02311 2311
4 30350024 30353036 + Lsi04G023130.1 Lsi04g02313 2313
4 30355329 30358068 + Lsi04G023140.1 Lsi04g02314 2314
4 30358034 30362756 - Lsi04G023160.1 Lsi04g02315 2315
8 19202776 19207865 + Lsi08G010580.1 Lsi08g01058 1058
11 2500016 2504873 - MC11g0316 Mch11g0395 395
11 5062449 5066153 + MC11g0630 Mch11g0751 751
11 5067561 5069807 + MC11g0631 Mch11g0752 752
1 9249993 9255208 + Sed0011909.3 Sed01g1243 1243
5 28873568 28880624 + Sed0014189.1 Sed05g1523 1523
11 33253226 33259350 + Sed0014249.9 Sed11g1863 1863
12 11024400 11027009 + Sed0022698.1 Sed12g1374 1374
12 11037931 11040551 + Sed0011969.1 Sed12g1375 1375
1 103970750 103974803 - Tan0009296.1 Tan01g3895 3895
1 103986981 103990044 + Tan0010455.1 Tan01g3897 3897
1 103992595 103996339 + Tan0015879.1 Tan01g3898 3898
1 112380060 112385974 + Tan0009571.1 Tan01g4651 4651
2 93871690 93876979 + Tan0004725.4 Tan02g2526 2526
18 6775054 6788180 - Vvi18g580 Vvi18g580 580
18 6793813 6796181 + Vvi18g581 Vvi18g581 581
18 6802504 6803965 - Vvi18g582 Vvi18g582 582
18 6810137 6817991 + Vvi18g583 Vvi18g583 583
18 6826939 6830995 + Vvi18g584 Vvi18g584 584
18 6831203 6834669 + Vvi18g585 Vvi18g585 585
18 6835809 6836625 - Vvi18g586 Vvi18g586 586
18 6840930 6841164 - Vvi18g587 Vvi18g587 587
18 6843127 6848829 - Vvi18g588 Vvi18g588 588
18 6852091 6857755 + Vvi18g589 Vvi18g589 589
       

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