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
Vvi18g540 . Blo12g01013 . . . . . . . Cmo12g00165 . . . Car12g00192 Sed04g0191 . Cpe07g00180 Bhi04g01402 Tan02g2453 Cmetu03g0486 . . . . Cla08g01683 Cam08g2186 Cec08g1775 Cco08g1894 Clacu08g1874 . . Cone4ag1286 Cone7ag0867 . . . . . Cme03g02136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01561 . Chy03g01627 .
Vvi18g541 . . . . . . . . . . . . . . . . . Bhi04g01403 . . . Hepe10g0443 . Lcy13g1495 . . . . . . . . . . . . . . . . . . . . . . Bma02g00118 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g543 . . Bda01g00904 . Bpe02g00487 . . . . . Cma01g01469 Cma09g00597 . . . Cpe06g00458 . . . . . . . . . . . . . . . Cone4ag1285 Cone7ag0868 . . Lsi04g02288 . . . . . . . Bpe02g01142 . . Bma02g00119 Sed05g1552 Cmo01g01525 Cmo09g00584 . . . Car09g00529 . Cpe02g00483 Bhi09g02516 Tan01g3866 Cmetu03g1161 . Hepe01g2179 Mch11g0718 . Cla11g01436 . . . . . . . . . .
Vvi18g544 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g545 . Blo12g00739 . Bda03g00448 . Bpe04g00412 Bma04g00426 . . Cmo12g00167 . . . Car12g00194 Sed04g0189 Cpe06g00459 Cpe07g00181 Bhi04g01405 Tan02g2451 Cmetu03g0272 . . . . . . . . . . . Cone4ag1284 Cone7ag0869 . . Lsi04g02289 Csa03g04505 Chy04g00196 . . . . . Bpe02g01140 . . . Sed05g1551 Cmo01g01524 Cmo09g00585 Cma12g00212 . . Car09g00530 . Cpe02g00484 Bhi09g02518 Tan01g3867 Cmetu04g0993 . Hepe01g2180 Mch11g0720 . Cla11g01437 Cam11g1493 Cec11g1528 Cco11g1522 Clacu11g1655 Cmu11g1472 Cre11g1890 . . . Cme04g00225
Vvi18g546 . . . . Bpe02g00147 . . . . . Cma01g01467 Cma09g00598 . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00195 . . . Bda11g00808 . . . . . . Cmo01g01523 . . . . . . . Bhi09g02524 Tan01g3870 . . Hepe01g2183 Mch11g0723 . . . . . . . . . . . Cme04g00223
Vvi18g547 . . . . . Bpe04g00411 Bma04g00425 Bma01g02578 . . . . . . . Cpe06g00460 . . . . . . . . . . . . . . . Cone4ag1661 Cone7ag0870 . . Lsi04g02290 Csa03g04507 . . . . . . . . . . Sed05g1547 . Cmo09g00586 . . . Car09g00531 . Cpe02g00485 Bhi09g02525 Tan01g3871 Cmetu04g0727 . . . . Cla11g01438 Cam11g1494 Cec11g1530 Cco11g1525 Clacu11g1656 Cmu11g1473 Cre11g1891 . . . .
Vvi18g548 . . . . Bpe02g00148 . . . . . Cma01g01466 Cma09g00600 . . . Cpe06g00463 . . . . . . . . . . . . . . . Cone4ag1281 . . Cone20ag0564 Lsi04g02291 Csa03g04509 Chy04g00194 . . . . . Bpe02g01163 Bpe14g00493 . Bma02g00105 . Cmo01g01520 Cmo09g00589 . . . Car09g00532 . Cpe02g00486 Bhi09g02527 . . . . . . Cla05g02127 Cam05g2281 Cec05g2304 Cco05g2345 Clacu05g2278 Cmu05g2141 Cre05g2263 . . . .
Vvi18g549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42028552 42030650 + Bda003045.1 Bda01g00904 904
3 3841403 3843007 + Bda016416.1 Bda03g00448 448
11 7995852 7997972 - Bda005557.1 Bda11g00808 808
4 35426290 35442784 - XM_039028360.1 Bhi04g01402 1402
4 35426290 35442784 - XM_039028361.1 Bhi04g01403 1403
4 35586119 35594417 - XM_039030284.1 Bhi04g01405 1405
9 68161440 68163377 - XM_039041115.1 Bhi09g02516 2516
9 68190288 68199342 - XM_039043468.1 Bhi09g02518 2518
9 68222446 68226314 - XM_039041995.1 Bhi09g02524 2524
9 68222446 68226314 - XM_039041996.1 Bhi09g02525 2525
9 68307216 68326611 + XM_039043043.1 Bhi09g02527 2527
12 25750097 25758081 - BLOR04758 Blo12g00739 739
12 28074927 28081473 - BLOR05032 Blo12g01013 1013
1 83416149 83418365 + Bma003462.1 Bma01g02578 2578
2 951013 968218 - Bma014559.1 Bma02g00105 105
2 1109452 1124546 - Bma014573.1 Bma02g00118 118
2 1127218 1133536 - Bma014574.1 Bma02g00119 119
4 3433940 3435345 + Bma018891.1 Bma04g00425 425
4 3436560 3440809 + Bma018892.1 Bma04g00426 426
2 1007450 1010279 - Bpe007997.2 Bpe02g00147 147
2 1012227 1019007 + Bpe007998.2 Bpe02g00148 148
2 3147429 3155760 - Bpe008326.1 Bpe02g00487 487
2 14996907 15001614 + Bpe008999.1 Bpe02g01140 1140
2 15003523 15005651 + Bpe009001.1 Bpe02g01142 1142
2 15251324 15267655 + Bpe009025.1 Bpe02g01163 1163
4 2594109 2596622 + Bpe015096.1 Bpe04g00411 411
4 2597790 2602048 + Bpe015097.1 Bpe04g00412 412
14 4388416 4401521 + Bpe007143.1 Bpe14g00493 493
5 30935572 30943065 - CaPI482276_05g022810.1 Cam05g2281 2281
8 27238490 27240818 + CaPI482276_08g021860.1 Cam08g2186 2186
11 27738624 27746159 - CaPI482276_11g014930.1 Cam11g1493 1493
11 27746375 27750802 - CaPI482276_11g014940.1 Cam11g1494 1494
9 2981286 2983097 - Carg03011-RA Car09g00529 529
9 2983546 2988866 - Carg03012-RA Car09g00530 530
9 2990197 2993359 - Carg03013-RA Car09g00531 531
9 2996348 3006409 + Carg03014-RA Car09g00532 532
12 1205072 1220841 - Carg22502-RA Car12g00192 192
12 1225621 1230610 - Carg22500-RA Car12g00194 194
5 31967542 31975329 - CcPI632755_05g023450.1 Cco05g2345 2345
8 29958466 29958932 + CcPI632755_08g018940.1 Cco08g1894 1894
11 28070757 28076498 - CcPI632755_11g015220.1 Cco11g1522 1522
11 28100553 28104932 - CcPI632755_11g015250.1 Cco11g1525 1525
5 34320812 34328695 - CePI673135_05g023040.1 Cec05g2304 2304
8 28854779 28856137 + CePI673135_08g017750.1 Cec08g1775 1775
11 29520212 29535956 - CePI673135_11g015280.1 Cec11g1528 1528
11 29549798 29554141 - CePI673135_11g015300.1 Cec11g1530 1530
3 18190544 18199765 + Chy3G066070.1 Chy03g01627 1627
4 1706043 1725241 - Chy4G069120.1 Chy04g00194 194
4 1736506 1739038 + Chy4G069130.1 Chy04g00195 195
4 1740653 1747176 + Chy4G069140.1 Chy04g00196 196
5 31139710 31147713 - ClG42_05g0227800.10 Clacu05g2278 2278
8 27996973 27998063 + ClG42_08g0187400.10 Clacu08g1874 1874
11 27769025 27775827 - ClG42_11g0165500.10 Clacu11g1655 1655
11 27776043 27780467 - ClG42_11g0165600.10 Clacu11g1656 1656
5 32860705 32869397 - ClCG05G020850.1 Cla05g02127 2127
8 29452933 29454707 + ClCG08G017170.2 Cla08g01683 1683
11 27974236 27978793 - ClCG11G014690.2 Cla11g01436 1436
11 27980311 28011104 - ClCG11G014710.1 Cla11g01437 1437
11 28012266 28015378 - ClCG11G014720.2 Cla11g01438 1438
1 10310670 10321893 - CmaCh01G014660.1 Cma01g01466 1466
1 10326381 10334537 + CmaCh01G014670.1 Cma01g01467 1467
1 10336662 10346026 + CmaCh01G014690.1 Cma01g01469 1469
9 2782929 2798084 - CmaCh09G005970.1 Cma09g00597 597
9 2799326 2802428 - CmaCh09G005980.1 Cma09g00598 598
9 2804731 2816447 + CmaCh09G006000.1 Cma09g00600 600
12 1038153 1043169 - CmaCh12G002120.1 Cma12g00212 212
3 28572606 28574070 + MELO3C010773.2.1 Cme03g02136 2136
4 1698444 1701758 + MELO3C003503.2.1 Cme04g00223 223
4 1705493 1711780 + MELO3C003505.2.1 Cme04g00225 225
3 2823001 2831275 + PI0013022.1 Cmetu03g0272 272
3 2833121 2849315 + PI0027348.1 Cmetu03g0486 486
3 26022049 26027691 + PI0011294.1 Cmetu03g1161 1161
4 31662991 31666446 - PI0021969.1 Cmetu04g0727 727
4 31636348 31643109 - PI0016288.1 Cmetu04g0993 993
1 11729875 11731449 - CmoCh01G015200.1 Cmo01g01520 1520
1 11746787 11749734 + CmoCh01G015230.1 Cmo01g01523 1523
1 11750520 11755089 + CmoCh01G015240.1 Cmo01g01524 1524
1 11756585 11765771 + CmoCh01G015250.1 Cmo01g01525 1525
9 2871408 2872759 - CmoCh09G005840.1 Cmo09g00584 584
9 2873512 2880308 - CmoCh09G005850.1 Cmo09g00585 585
9 2881669 2884776 - CmoCh09G005860.1 Cmo09g00586 586
9 2898282 2901053 + CmoCh09G005890.1 Cmo09g00589 589
12 1081063 1097501 - CmoCh12G001650.1 Cmo12g00165 165
12 1101111 1106511 - CmoCh12G001670.1 Cmo12g00167 167
5 30877080 30884595 - CmPI595203_05g021410.1 Cmu05g2141 2141
11 27020344 27027862 - CmPI595203_11g014720.1 Cmu11g1472 1472
11 27028078 27032488 - CmPI595203_11g014730.1 Cmu11g1473 1473
4 10526697 10540216 - Conep04aG0132700.1 Cone4ag1281 1281
4 10555096 10558325 + Conep04aG0133000.1 Cone4ag1284 1284
4 10567067 10570291 + Conep04aG0133100.1 Cone4ag1285 1285
4 10571443 10587072 + Conep04aG0133200.1 Cone4ag1286 1286
4 12479695 12485816 - Conep04aG0171400.1 Cone4ag1661 1661
7 6645030 6660715 - Conep07aG0089600.1 Cone7ag0867 867
7 6668579 6672059 - Conep07aG0089700.1 Cone7ag0868 868
7 6678678 6682437 - Conep07aG0089800.1 Cone7ag0869 869
7 6688826 6691152 - Conep07aG0089900.1 Cone7ag0870 870
20 3151511 3165734 + Conep20aG0058000.1 Cone20ag0564 564
2 2768373 2770091 - Cp4.1LG02g03840.1 Cpe02g00483 483
2 2771306 2783485 - Cp4.1LG02g03870.1 Cpe02g00484 484
2 2784718 2788042 - Cp4.1LG02g03850.1 Cpe02g00485 485
2 2793523 2806151 + Cp4.1LG02g03920.1 Cpe02g00486 486
6 2683953 2688936 - Cp4.1LG06g04050.1 Cpe06g00458 458
6 2689080 2692870 - Cp4.1LG06g04070.1 Cpe06g00459 459
6 2696521 2699510 - Cp4.1LG06g04010.1 Cpe06g00460 460
6 2711981 2714210 + Cp4.1LG06g04100.1 Cpe06g00463 463
7 1096880 1113580 - Cp4.1LG07g01740.1 Cpe07g00180 180
7 1116332 1124604 - Cp4.1LG07g01810.1 Cpe07g00181 181
5 34197596 34205162 - CrPI670011_05g022630.1 Cre05g2263 2263
11 30650641 30657533 - CrPI670011_11g018900.1 Cre11g1890 1890
11 30659092 30662186 - CrPI670011_11g018910.1 Cre11g1891 1891
3 39279931 39287293 - CsaV3_3G048110.1 Csa03g04505 4505
3 39297531 39300938 - CsaV3_3G048130.1 Csa03g04507 4507
3 39311564 39327673 + CsaV3_3G048150.1 Csa03g04509 4509
1 86465690 86467906 - Hsped.01g21790.1 Hepe01g2179 2179
1 86473331 86480111 - Hsped.01g21800.1 Hepe01g2180 2180
1 86504152 86507365 - Hsped.01g21830.1 Hepe01g2183 2183
10 5006622 5023741 - Hsped.10g04430.1 Hepe10g0443 443
13 33590914 33608666 - Maker00033942 Lcy13g1495 1495
4 30011702 30012568 - Lsi04G022880.1 Lsi04g02288 2288
4 30016075 30029418 - Lsi04G022890.1 Lsi04g02289 2289
4 30035350 30047044 - Lsi04G022900.1 Lsi04g02290 2290
4 30056403 30076240 + Lsi04G022910.1 Lsi04g02291 2291
8 23686383 23695898 + Lsi08G015610.1 Lsi08g01561 1561
11 4788329 4791351 - MC11g0607 Mch11g0718 718
11 4797070 4802328 - MC11g0609 Mch11g0720 720
11 4819189 4822473 - MC11g0610 Mch11g0723 723
4 1340280 1347915 + Sed0006316.1 Sed04g0189 189
4 1352219 1367873 + Sed0006720.1 Sed04g0191 191
5 29195867 29200267 + Sed0023619.3 Sed05g1547 1547
5 29220105 29230077 + Sed0004180.2 Sed05g1551 1551
5 29235763 29237878 + Sed0016266.1 Sed05g1552 1552
1 103527213 103529108 - Tan0006777.1 Tan01g3866 3866
1 103533285 103540075 - Tan0018060.1 Tan01g3867 3867
1 103567117 103570890 - Tan0006920.1 Tan01g3870 3870
1 103567117 103570890 - Tan0006920.2 Tan01g3871 3871
2 93136837 93143149 + Tan0006768.1 Tan02g2451 2451
2 93152054 93169019 + Tan0002785.1 Tan02g2453 2453
18 6235026 6247312 - Vvi18g540 Vvi18g540 540
18 6249097 6255464 - Vvi18g541 Vvi18g541 541
18 6273221 6275070 + Vvi18g542 Vvi18g542 542
18 6278099 6282770 - Vvi18g543 Vvi18g543 543
18 6286067 6286564 + Vvi18g544 Vvi18g544 544
18 6286735 6292127 - Vvi18g545 Vvi18g545 545
18 6313165 6319284 + Vvi18g546 Vvi18g546 546
18 6335983 6343462 - Vvi18g547 Vvi18g547 547
18 6350900 6376307 + Vvi18g548 Vvi18g548 548
18 6387733 6394700 + Vvi18g549 Vvi18g549 549
       

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