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
Vvi4g332 . . . . . . . . Cmo05g00727 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g333 . Blo12g00798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0612 . . Chy04g00266 . . . . . . Bpe04g00340 . . Sed13g2120 . . . . . . . . Bhi09g02416 Tan01g3776 Cmetu04g2828 . Hepe01g2116 Mch11g0654 . . . . . . . . . . . Cme04g00297
Vvi4g334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda01g00949 . . . Bma01g01334 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g335 . . . . . . . . . . . . Car09g00482 . . . Cpe06g00417 . . . . . . . . . . . . . . . . . . Lsi04g02221 Csa03g04433 . . . . . . . . . . Sed13g2118 . Cmo09g00540 Cma09g00550 . . . . . Bhi09g02414 Tan01g3775 Cmetu04g1652 . Hepe01g2115 Mch11g0653 . . . . . . . . . . . Cme04g00298
Vvi4g336 Blo01g01708 . . . . Bpe02g00235 . Bma01g02485 . . Cma01g01595 . . . . . . . . . . . . . . . . . . . . Cone4ag1537 Cone7ag1415 . . Lsi04g02220 Csa03g04432 Chy04g00267 . . . . . . . . . Sed05g1613 Cmo01g01643 . . . Car01g01214 . . Cpe02g00382 Bhi09g02413 Tan01g3774 Cmetu04g2386 . Hepe01g2114 Mch11g0652 . . . . . . . . . . . Cme04g00299
Vvi4g337 Blo01g01709 . . . . Bpe02g00234 . Bma01g02486 . . Cma01g01594 . Car09g00481 . . . Cpe06g00416 . . . . . . . . . . . . . . . . . . Lsi04g02219 Csa03g04429 Chy04g00272 . . . . . . . . . Sed01g1228 Cmo01g01642 Cmo09g00539 Cma09g00549 . Car01g01213 . . Cpe02g00383 Bhi09g02412 Tan01g3773 Cmetu11g1083 . Hepe01g2113 Mch11g0651 . . . . . . . . . . . Cme04g00302
Vvi4g338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g339 . . . Bda03g00026 Bpe02g01196 . Bma04g00024 . Cmo05g00631 Cmo12g00219 . Cma05g00605 . Car12g00249 Sed01g1287 Cpe07g00228 . Bhi04g00822 Tan02g2580 Cmetu03g1256 . Hepe10g0344 . Lcy13g1389 . . . . . . . Cone4ag1539 Cone7ag1413 Cone17ag1107 Cone20ag0614 . . . Cme03g01726 Blo17g00055 Blo18g00069 . . Bpe14g00534 . Bma01g01332 Bma02g00070 . . . . Cma12g00265 . Car05g00547 Cpe11g00528 . . . . . . . . Cla08g01237 Cam08g1694 Cec08g1273 Cco08g1394 Clacu08g1391 . Cre08g1176 Lsi08g01100 . Chy03g01231 .
Vvi4g340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g1616 . . . . . . . . Bhi09g02410 Tan01g3770 Cmetu04g1481 . Hepe01g2112 Mch11g0650 . . . . . . . . . . . .
Vvi4g341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42931718 42934054 - Bda003103.1 Bda01g00949 949
3 447265 448543 + Bda015959.1 Bda03g00026 26
4 20693588 20724013 + XM_039029903.1 Bhi04g00822 822
9 65589592 65592771 - XM_039042481.1 Bhi09g02410 2410
9 65610144 65614144 - XM_039044089.1 Bhi09g02412 2412
9 65616873 65624068 + XM_039042694.1 Bhi09g02413 2413
9 65625594 65627825 + XM_039041102.1 Bhi09g02414 2414
9 65767907 65772510 - XM_039042539.1 Bhi09g02416 2416
1 56840254 56846667 - BLOR01708 Blo01g01708 1708
1 56847941 56850170 + BLOR01709 Blo01g01709 1709
12 26377966 26382730 + BLOR04817 Blo12g00798 798
17 394136 396448 + BLOR15876 Blo17g00055 55
18 526060 528223 + BLOR08557 Blo18g00069 69
1 18514297 18516357 + Bma030248 Bma01g01332 1332
1 18597513 18599830 + Bma001655.1 Bma01g01334 1334
1 82618752 82625925 - Bma003363.1 Bma01g02485 2485
1 82626843 82629045 + Bma003364.1 Bma01g02486 2486
2 613889 616135 + Bma014525.1 Bma02g00070 70
4 306459 307752 + Bma018475.1 Bma04g00024 24
2 1602544 1604763 - Bpe008078.1 Bpe02g00234 234
2 1606343 1612083 + Bpe008079.1 Bpe02g00235 235
2 15650513 15652570 - Bpe009057.1 Bpe02g01196 1196
4 2151465 2154098 - Bpe015035.1 Bpe04g00340 340
14 4654913 4657146 - Bpe007184.1 Bpe14g00534 534
8 23240989 23244170 - CaPI482276_08g016940.1 Cam08g1694 1694
1 11172106 11175884 - Carg21194-RA Car01g01213 1213
1 11176396 11181829 + Carg21195-RA Car01g01214 1214
5 3204074 3206440 - Carg08290-RA Car05g00547 547
9 2680177 2683152 - Carg02963-RA Car09g00481 481
9 2683482 2685733 + Carg02964-RA Car09g00482 482
12 1672991 1675418 - Carg03856-RA Car12g00249 249
8 25874076 25877268 - CcPI632755_08g013940.1 Cco08g1394 1394
8 24723047 24726246 - CePI673135_08g012730.1 Cec08g1273 1273
3 15403049 15405661 + Chy3G062110.1 Chy03g01231 1231
4 2360097 2367659 - Chy4G069840.1 Chy04g00266 266
4 2369619 2376597 - Chy4G069850.1 Chy04g00267 267
4 2390653 2394447 + Chy4G069900.1 Chy04g00272 272
8 23993264 23996389 - ClG42_08g0139100.10 Clacu08g1391 1391
8 25283922 25288693 - ClCG08G012390.2 Cla08g01237 1237
1 11010643 11015389 - CmaCh01G015940.1 Cma01g01594 1594
1 11016782 11023527 + CmaCh01G015950.1 Cma01g01595 1595
5 3024674 3027138 - CmaCh05G006050.1 Cma05g00605 605
9 2488376 2491396 - CmaCh09G005490.1 Cma09g00549 549
9 2491611 2494248 + CmaCh09G005500.1 Cma09g00550 550
12 1361349 1364140 - CmaCh12G002650.1 Cma12g00265 265
3 25847150 25850980 + MELO3C011158.2.1 Cme03g01726 1726
4 2335654 2340243 - MELO3C003585.2.1 Cme04g00297 297
4 2341726 2343988 - MELO3C003586.2.1 Cme04g00298 298
4 2345153 2352589 - MELO3C003587.2.1 Cme04g00299 299
4 2360079 2364199 + MELO3C003590.2.1 Cme04g00302 302
3 3584818 3588398 - PI0008970.1 Cmetu03g1256 1256
4 30970734 30973238 - PI0001951.1 Cmetu04g1481 1481
4 30997548 30999898 + PI0028261.1 Cmetu04g1652 1652
4 30989767 30996414 + PI0001423.1 Cmetu04g2386 2386
4 31001563 31006246 + PI0020535.2 Cmetu04g2828 2828
11 28818560 28821513 + PI0019382.1 Cmetu11g1083 1083
1 12463948 12467829 - CmoCh01G016420.1 Cmo01g01642 1642
1 12468563 12475272 + CmoCh01G016430.1 Cmo01g01643 1643
5 3174132 3176660 - CmoCh05G006310.1 Cmo05g00631 631
5 3775187 3786182 - CmoCh05G007270.1 Cmo05g00727 727
9 2562010 2564902 - CmoCh09G005390.1 Cmo09g00539 539
9 2565176 2567869 + CmoCh09G005400.1 Cmo09g00540 540
12 1439894 1443097 - CmoCh12G002190.1 Cmo12g00219 219
4 11873556 11874151 - Conep04aG0158900.1 Cone4ag1537 1537
4 11880067 11882733 - Conep04aG0159100.1 Cone4ag1539 1539
7 10091266 10093615 + Conep07aG0145500.1 Cone7ag1413 1413
7 10099562 10101052 + Conep07aG0145700.1 Cone7ag1415 1415
17 8217826 8220545 + Conep17aG0113500.1 Cone17ag1107 1107
20 3608765 3612437 + Conep20aG0062900.1 Cone20ag0612 612
20 3626390 3629659 - Conep20aG0063100.1 Cone20ag0614 614
2 2104418 2111160 - Cp4.1LG02g04910.1 Cpe02g00382 382
2 2111957 2116052 + Cp4.1LG02g04970.1 Cpe02g00383 383
6 2374685 2377274 - Cp4.1LG06g04440.1 Cpe06g00416 416
6 2377508 2380273 + Cp4.1LG06g04550.1 Cpe06g00417 417
7 1480648 1483611 - Cp4.1LG07g02100.1 Cpe07g00228 228
11 3128660 3131139 - Cp4.1LG11g05300.1 Cpe11g00528 528
8 25033784 25036992 - CrPI670011_08g011760.1 Cre08g1176 1176
3 38671972 38677135 - CsaV3_3G047350.1 Csa03g04429 4429
3 38686969 38694871 + CsaV3_3G047380.1 Csa03g04432 4432
3 38695638 38698202 + CsaV3_3G047390.1 Csa03g04433 4433
1 85760033 85762579 - Hsped.01g21120.1 Hepe01g2112 2112
1 85768690 85773706 - Hsped.01g21130.1 Hepe01g2113 2113
1 85775124 85781927 + Hsped.01g21140.1 Hepe01g2114 2114
1 85782805 85785220 + Hsped.01g21150.1 Hepe01g2115 2115
1 85786770 85792142 + Hsped.01g21160.1 Hepe01g2116 2116
10 3728259 3732279 + Hsped.10g03440.1 Hepe10g0344 344
13 32110727 32114754 + Maker00025532 Lcy13g1389 1389
4 29246182 29251551 - Lsi04G022190.1 Lsi04g02219 2219
4 29252759 29259464 + Lsi04G022200.1 Lsi04g02220 2220
4 29259847 29262206 + Lsi04G022210.1 Lsi04g02221 2221
8 19629326 19633126 - Lsi08G011000.1 Lsi08g01100 1100
11 4238290 4240433 - MC11g0542 Mch11g0650 650
11 4242932 4247390 - MC11g0543 Mch11g0651 651
11 4248918 4255854 + MC11g0544 Mch11g0652 652
11 4256040 4258534 + MC11g_new0109 Mch11g0653 653
11 4260599 4264191 + MC11g0545 Mch11g0654 654
1 9123744 9127659 - Sed0005219.2 Sed01g1228 1228
1 9591270 9595424 - Sed0013098.1 Sed01g1287 1287
5 30050571 30060014 - Sed0018896.1 Sed05g1613 1613
5 30068127 30070846 + Sed0010077.1 Sed05g1616 1616
13 25863785 25864795 + Sed0021692.1 Sed13g2118 2118
13 25866784 25871378 + Sed0002455.2 Sed13g2120 2120
1 102545312 102547576 - Tan0010777.1 Tan01g3770 3770
1 102574102 102578449 - Tan0000886.3 Tan01g3773 3773
1 102580749 102587495 + Tan0019506.1 Tan01g3774 3774
1 102588455 102589853 + Tan0007705.1 Tan01g3775 3775
1 102592723 102596581 + Tan0021665.1 Tan01g3776 3776
2 94397276 94401128 - Tan0016291.1 Tan02g2580 2580
4 3182894 3185794 + Vvi4g332 Vvi4g332 332
4 3185997 3191025 - Vvi4g333 Vvi4g333 333
4 3191978 3196494 + Vvi4g334 Vvi4g334 334
4 3197529 3199397 - Vvi4g335 Vvi4g335 335
4 3199792 3211964 - Vvi4g336 Vvi4g336 336
4 3216167 3228200 + Vvi4g337 Vvi4g337 337
4 3228994 3231532 - Vvi4g338 Vvi4g338 338
4 3246966 3250173 - Vvi4g339 Vvi4g339 339
4 3274430 3276202 + Vvi4g340 Vvi4g340 340
4 3276689 3281635 + Vvi4g341 Vvi4g341 341
       

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