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
Vvi18g490 . Blo12g00727 . . Bpe02g00136 . Bma04g00435 Bma01g02589 . . Cma01g01639 Cma09g00589 . . . Cpe06g00450 . . . . . . . . . . . . . . . . Cone9ag1452 . . Lsi04g02273 Csa03g04484 Chy04g00216 . . . Bda11g00795 . . . . . Sed01g0609 Cmo01g01687 Cmo09g00575 . . . Car09g00520 . . Bhi09g02488 Tan01g3841 Cmetu04g2748 . Hepe01g2163 Mch11g0702 . Cla11g01416 Cam11g1473 Cec11g1503 Cco11g1498 Clacu11g1634 Cmu11g1452 Cre11g1870 . . . Cme04g00244
Vvi18g491 . . . . . . . . . Cmo12g00146 . . . Car12g00171 . . Cpe07g00159 . . . . . . . . . . . . . . Cone4ag1304 . . . . . . . . . . . . . . Bma02g00107 . . . Cma12g00189 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g492 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g493 . . . . . . . . . Cmo12g00147 . . . Car12g00172 . . Cpe07g00160 . . . . . . . . . . . . . . Cone4ag1303 . . . . . . . . . . . Bpe02g01158 . . . . . . Cma12g00190 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g494 . . Bda01g00915 . . . . . . . . . . Car12g00174 . . Cpe07g00162 . . . . . . . . . . . . . . Cone6ag1536 Cone9ag1451 . . . . . . . . . . Bpe02g01157 . . . . . . Cma12g00193 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g495 . Blo12g00728 . Bda03g00460 Bpe02g00137 Bpe04g00421 . Bma01g02588 . . . . . . . Cpe06g00451 . . . . . . . . . . . . . . . . . . . Lsi04g02275 Csa03g04487 Chy04g00213 . . . Bda11g00796 . . . . . . Cmo01g01690 Cmo09g00576 . . . . . . . . . . . . . Cla11g01419 Cam11g1475 Cec11g1505 Cco11g1501 Clacu11g1636 Cmu11g1454 Cre11g1872 . . . Cme04g00243
Vvi18g496 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g01156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g497 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g498 . . Bda01g00914 . . . . . . Cmo12g00148 . . . Car12g00175 . . Cpe07g00163 . . . . . . . . . . . . . . . Cone7ag0852 . . . . . . . . . . Bpe02g01155 . . Bma02g00108 . . . Cma12g00194 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g499 . Blo12g00729 . Bda03g00459 . Bpe04g00420 Bma04g00434 . . Cmo12g00149 Cma01g01643 Cma09g00591 . Car12g00176 . Cpe06g00452 Cpe07g00164 . . . . . . . . . . . . . . Cone4ag1301 Cone7ag0854 . . Lsi04g02276 Csa03g04488 Chy04g00212 . . . . . . . . Bma02g00109 Sed05g1565 Cmo01g01692 Cmo09g00577 Cma12g00195 . . Car09g00522 . . Bhi09g02494 Tan01g3848 Cmetu04g0414 . Hepe01g2166 Mch11g0705 . Cla11g01420 Cam11g1476 Cec11g1506 Cco11g1502 Clacu11g1637 Cmu11g1455 Cre11g1873 . . . Cme04g00241
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42245613 42246740 + Bda003059.1 Bda01g00914 914
1 42297018 42298004 + Bda003060.1 Bda01g00915 915
3 3963791 3969259 - Bda016427.2 Bda03g00459 459
3 3970363 3971545 - Bda016428.1 Bda03g00460 460
11 7919775 7928840 + Bda005545.1 Bda11g00795 795
11 7930181 7931473 + Bda005546.1 Bda11g00796 796
9 67400923 67411022 + XM_039043088.1 Bhi09g02488 2488
9 67467393 67474040 + XM_039041965.1 Bhi09g02494 2494
12 25595767 25616948 + BLOR04746 Blo12g00727 727
12 25618439 25619731 + BLOR04747 Blo12g00728 728
12 25623742 25629219 + BLOR04748 Blo12g00729 729
1 83513972 83514895 - Bma003474.1 Bma01g02588 2588
1 83516631 83526059 - Bma003475.3 Bma01g02589 2589
2 973335 976176 - Bma014561.1 Bma02g00107 107
2 989031 990682 - Bma014563.2 Bma02g00108 108
2 992800 997899 + Bma014564.1 Bma02g00109 109
4 3556484 3561970 - Bma018902.1 Bma04g00434 434
4 3566382 3581409 - Bma018903.1 Bma04g00435 435
2 936069 946855 + Bpe007986.1 Bpe02g00136 136
2 948289 949575 + Bpe007987.1 Bpe02g00137 137
2 15153620 15154239 + Bpe009016.1 Bpe02g01155 1155
2 15166775 15167911 + Bpe009018.1 Bpe02g01156 1156
2 15196541 15197527 + Bpe009019.1 Bpe02g01157 1157
2 15198037 15215734 - Bpe009020.1 Bpe02g01158 1158
4 2709267 2714765 - Bpe015105.1 Bpe04g00420 420
4 2715897 2717081 - Bpe015106.1 Bpe04g00421 421
11 27463091 27472263 + CaPI482276_11g014730.1 Cam11g1473 1473
11 27480393 27481337 + CaPI482276_11g014750.1 Cam11g1475 1475
11 27495112 27501645 + CaPI482276_11g014760.1 Cam11g1476 1476
9 2911873 2920650 + Carg03002-RA Car09g00520 520
9 2929452 2935788 + Carg03004-RA Car09g00522 522
12 1049677 1053785 - Carg22523-RA Car12g00171 171
12 1055716 1073031 + Carg22522-RA Car12g00172 172
12 1077675 1079204 + Carg22520-RA Car12g00174 174
12 1080652 1085023 - Carg22519-RA Car12g00175 175
12 1086759 1092953 + Carg22518-RA Car12g00176 176
11 27806825 27815898 + CcPI632755_11g014980.1 Cco11g1498 1498
11 27824157 27825101 + CcPI632755_11g015010.1 Cco11g1501 1501
11 27838018 27844600 + CcPI632755_11g015020.1 Cco11g1502 1502
11 29231624 29241276 + CePI673135_11g015030.1 Cec11g1503 1503
11 29249483 29250427 + CePI673135_11g015050.1 Cec11g1505 1505
11 29269949 29276739 + CePI673135_11g015060.1 Cec11g1506 1506
4 1938930 1944463 - Chy4G069300.1 Chy04g00212 212
4 1952846 1953781 - Chy4G069310.1 Chy04g00213 213
4 1962356 1971898 - Chy4G069340.1 Chy04g00216 216
11 27493056 27502195 + ClG42_11g0163400.10 Clacu11g1634 1634
11 27510249 27511193 + ClG42_11g0163600.10 Clacu11g1636 1636
11 27524733 27531368 + ClG42_11g0163700.10 Clacu11g1637 1637
11 27723350 27733172 + ClCG11G014490.2 Cla11g01416 1416
11 27740908 27741852 + ClCG11G014520.1 Cla11g01419 1419
11 27755640 27762321 + ClCG11G014530.1 Cla11g01420 1420
1 11233899 11241460 + CmaCh01G016390.1 Cma01g01639 1639
1 11252104 11258738 + CmaCh01G016430.1 Cma01g01643 1643
9 2718635 2729664 + CmaCh09G005890.1 Cma09g00589 589
9 2731642 2737797 + CmaCh09G005910.1 Cma09g00591 591
12 867483 871608 - CmaCh12G001890.1 Cma12g00189 189
12 872913 890612 + CmaCh12G001900.1 Cma12g00190 190
12 894932 895897 + CmaCh12G001930.1 Cma12g00193 193
12 897180 901069 - CmaCh12G001940.1 Cma12g00194 194
12 902804 908961 + CmaCh12G001950.1 Cma12g00195 195
4 1900973 1907221 - MELO3C003528.2.1 Cme04g00241 241
4 1915346 1916272 - MELO3C003530.2.1 Cme04g00243 243
4 1923134 1933254 - MELO3C003532.2.1 Cme04g00244 244
4 31449726 31455470 + PI0011820.1 Cmetu04g0414 414
4 31422295 31432761 + PI0028953.1 Cmetu04g2748 2748
1 12707183 12714725 + CmoCh01G016870.1 Cmo01g01687 1687
1 12720247 12721203 + CmoCh01G016900.1 Cmo01g01690 1690
1 12727037 12733656 + CmoCh01G016920.1 Cmo01g01692 1692
9 2801253 2810080 + CmoCh09G005750.1 Cmo09g00575 575
9 2811581 2816811 + CmoCh09G005760.1 Cmo09g00576 576
9 2819129 2825650 + CmoCh09G005770.1 Cmo09g00577 577
12 927636 931713 - CmoCh12G001460.1 Cmo12g00146 146
12 933431 951518 + CmoCh12G001470.1 Cmo12g00147 147
12 957708 961841 - CmoCh12G001480.1 Cmo12g00148 148
12 961855 969684 + CmoCh12G001490.1 Cmo12g00149 149
11 26744848 26753987 + CmPI595203_11g014520.1 Cmu11g1452 1452
11 26762043 26762987 + CmPI595203_11g014540.1 Cmu11g1454 1454
11 26776533 26783168 + CmPI595203_11g014550.1 Cmu11g1455 1455
4 10728505 10734602 - Conep04aG0134700.1 Cone4ag1301 1301
4 10738741 10745688 - Conep04aG0134900.1 Cone4ag1303 1303
4 10746877 10748507 - Conep04aG0135000.1 Cone4ag1304 1304
6 12081786 12083292 + Conep06aG0159600.1 Cone6ag1536 1536
7 6489845 6491041 - Conep07aG0088100.1 Cone7ag0852 852
7 6502750 6512661 + Conep07aG0088300.1 Cone7ag0854 854
9 10774072 10775612 + Conep09aG0149400.1 Cone9ag1451 1451
9 10776250 10781598 - Conep09aG0149500.1 Cone9ag1452 1452
6 2614176 2622864 + Cp4.1LG06g04220.1 Cpe06g00450 450
6 2624432 2625978 + Cp4.1LG06g04090.1 Cpe06g00451 451
6 2631538 2638145 + Cp4.1LG06g04080.1 Cpe06g00452 452
7 935415 939420 - Cp4.1LG07g01610.1 Cpe07g00159 159
7 940623 961005 + Cp4.1LG07g01570.1 Cpe07g00160 160
7 963681 964646 + Cp4.1LG07g01530.1 Cpe07g00162 162
7 966914 970938 - Cp4.1LG07g01620.1 Cpe07g00163 163
7 972471 978497 + Cp4.1LG07g01550.1 Cpe07g00164 164
11 30360499 30369608 + CrPI670011_11g018700.1 Cre11g1870 1870
11 30377790 30378737 + CrPI670011_11g018720.1 Cre11g1872 1872
11 30394612 30401229 + CrPI670011_11g018730.1 Cre11g1873 1873
3 39073730 39083789 + CsaV3_3G047900.1 Csa03g04484 4484
3 39091112 39092018 + CsaV3_3G047930.1 Csa03g04487 4487
3 39098697 39105331 + CsaV3_3G047940.1 Csa03g04488 4488
1 86281081 86291389 + Hsped.01g21630.1 Hepe01g2163 2163
1 86306524 86314179 + Hsped.01g21660.1 Hepe01g2166 2166
4 29751907 29762256 + Lsi04G022730.1 Lsi04g02273 2273
4 29771173 29772378 + Lsi04G022750.1 Lsi04g02275 2275
4 29785323 29791808 + Lsi04G022760.1 Lsi04g02276 2276
11 4621207 4629839 + MC11g0591 Mch11g0702 702
11 4642592 4649636 + MC11g0594 Mch11g0705 705
1 4352597 4363882 - Sed0014702.1 Sed01g0609 609
5 29411206 29419212 - Sed0005755.1 Sed05g1565 1565
1 103200402 103211371 + Tan0018452.1 Tan01g3841 3841
1 103229341 103237828 + Tan0022155.2 Tan01g3848 3848
18 5517923 5535125 + Vvi18g490 Vvi18g490 490
18 5539752 5544866 - Vvi18g491 Vvi18g491 491
18 5554567 5565201 + Vvi18g492 Vvi18g492 492
18 5565991 5604360 + Vvi18g493 Vvi18g493 493
18 5605381 5606712 - Vvi18g494 Vvi18g494 494
18 5615060 5616841 + Vvi18g495 Vvi18g495 495
18 5617212 5618770 - Vvi18g496 Vvi18g496 496
18 5621303 5622359 - Vvi18g497 Vvi18g497 497
18 5622528 5628323 - Vvi18g498 Vvi18g498 498
18 5634169 5644314 + Vvi18g499 Vvi18g499 499
       

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