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
Vvi18g530 . Blo12g00736 . Bda03g00451 . Bpe04g00414 . . . . Cma01g01471 . . . . . . . . . . . . . . . . . . . . Cone4ag1289 . . . Lsi04g02285 Csa03g04501 Chy04g00200 . . . . . . . . . . Cmo01g01527 . . . . . . Cpe02g00481 Bhi09g02508 . . . Hepe01g2176 Mch11g0715 . Cla11g01433 Cam11g1487 Cec11g1521 Cco11g1517 Clacu11g1649 Cmu11g1467 Cre11g1885 . . . Cme04g00231
Vvi18g531 . . . Bda03g00450 Bpe02g00145 . . . Cmo05g00561 . . . . Car12g00188 . . . Bhi04g01395 Tan02g2468 . . Hepe10g0439 . . . . . . . . . . . . . . . . . . . Bda11g00806 . . . . Bma02g00116 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01015 Csa02g02198 . .
Vvi18g532 . Blo12g00738 . . Bpe02g00146 Bpe04g00413 Bma04g00427 Bma01g02579 Cmo05g00563 Cmo12g00161 . . . . Sed03g1396 . Cpe07g00176 Bhi04g01396 Tan02g2466 Cmetu03g0931 . . . . . . . . . . . . . . . . . . . . . Bda11g00807 . . . . . . . . Cma12g00207 . . . . . . . . . . . . . . . . . . . Lsi08g01017 Csa02g02199 . .
Vvi18g533 . . . . . . . . . . . . . Car12g00189 Sed04g0198 . Cpe07g00177 Bhi04g01397 Tan02g2458 Cmetu03g1114 . Hepe10g0440 . Lcy13g1490 . . . . . . . Cone4ag1288 . . . . . . . . . . . . . . Bma02g00117 . . . Cma12g00209 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g534 . . . . . . . . . . Cma01g01470 . . . . . . . . . . . . . . . . . . . . Cone4ag1287 Cone7ag0866 . . Lsi04g02286 Csa03g04502 . . . . . . . . . . Sed05g1553 Cmo01g01526 . . . . . . Cpe02g00482 Bhi09g02514 Tan01g3865 Cmetu04g2990 . Hepe01g2178 Mch11g0717 . Cla11g01435 Cam11g1489 . . Clacu11g1651 Cmu11g1468 Cre11g1886 . . . Cme04g00229
Vvi18g535 . . Bda01g00905 . . . . . . Cmo12g00163 . . . Car12g00190 Sed03g1389 . Cpe07g00178 Bhi04g01399 Tan02g2457 Cmetu03g1095 . Hepe10g0441 . Lcy13g1491 . . . . . . . . . . . . . . . . . . . Bpe02g01144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g536 . . . . . . . . . Cmo12g00164 . . . Car12g00191 Sed04g0192 . Cpe07g00179 Bhi04g01401 Tan02g2454 Cmetu03g0187 . Hepe10g0442 . Lcy13g1492 . . . . . . . . . . . . . . . . . . . . Bpe05g00436 . . . . . Cma12g00210 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g538 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g539 . . . . . . . . . . . Cma09g00335 . . . Cpe06g00238 . . . . . . . . . . . . . . . . . . . . Csa04g02535 . . . . . . . . . . . . Cmo09g00336 . . . . . Cpe02g00257 . . . . . . . Cla05g01828 . . . . . . . . Chy07g00239 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42045431 42049901 + Bda003046.1 Bda01g00905 905
3 3847408 3850897 - Bda016418.1 Bda03g00450 450
3 3852722 3908829 - Bda016419.2 Bda03g00451 451
11 7985592 7988797 + Bda005555.1 Bda11g00806 806
11 7991287 7995179 + Bda005556.1 Bda11g00807 807
4 35144633 35153723 + XM_039028902.1 Bhi04g01395 1395
4 35144811 35153723 + XM_039028900.1 Bhi04g01396 1396
4 35160882 35191931 - XM_039029102.1 Bhi04g01397 1397
4 35372086 35377710 - XM_039029384.1 Bhi04g01399 1399
4 35405283 35407969 - XM_039030445.1 Bhi04g01401 1401
9 67970413 68022894 + XM_039041602.1 Bhi09g02508 2508
9 68056869 68060431 + XM_039040962.1 Bhi09g02514 2514
12 25693567 25708533 + BLOR04755 Blo12g00736 736
12 25745729 25749121 + BLOR04757 Blo12g00738 738
1 83419158 83423341 - Bma003463.1 Bma01g02579 2579
2 1077281 1080895 + Bma014571.1 Bma02g00116 116
2 1081929 1108668 - Bma014572.1 Bma02g00117 117
4 3442149 3499801 - Bma018893.1 Bma04g00427 427
2 998149 1001178 + Bpe007995.1 Bpe02g00145 145
2 1002727 1006845 + Bpe007996.1 Bpe02g00146 146
2 15024397 15028926 + Bpe009004.1 Bpe02g01144 1144
4 2603195 2606913 - Bpe015098.1 Bpe04g00413 413
4 2608677 2670022 - Bpe015099.1 Bpe04g00414 414
5 18782741 18783138 - Bpe017855.1 Bpe05g00436 436
11 27653391 27692400 + CaPI482276_11g014870.1 Cam11g1487 1487
11 27707307 27708705 + CaPI482276_11g014890.1 Cam11g1489 1489
12 1159979 1172938 + Carg22506-RA Car12g00188 188
12 1173705 1193983 - Carg22505-RA Car12g00189 189
12 1195513 1200631 - Carg22504-RA Car12g00190 190
12 1201790 1203662 - Carg22503-RA Car12g00191 191
11 28038980 28039844 + CcPI632755_11g015170.1 Cco11g1517 1517
11 29448038 29477969 + CePI673135_11g015210.1 Cec11g1521 1521
4 1768336 1821395 - Chy4G069180.1 Chy04g00200 200
7 1908825 1917538 - Chy7G130690.1 Chy07g00239 239
11 27664131 27729856 + ClG42_11g0164900.10 Clacu11g1649 1649
11 27737135 27738491 + ClG42_11g0165100.10 Clacu11g1651 1651
5 30182438 30191099 - ClCG05G017830.2 Cla05g01828 1828
11 27922220 27966720 + ClCG11G014665.1 Cla11g01433 1433
11 27971286 27972788 + ClCG11G014680.1 Cla11g01435 1435
1 10346072 10351860 - CmaCh01G014700.1 Cma01g01470 1470
1 10351894 10375941 - CmaCh01G014710.1 Cma01g01471 1471
9 1377586 1385367 - CmaCh09G003350.1 Cma09g00335 335
12 975513 989072 + CmaCh12G002070.1 Cma12g00207 207
12 989726 1009739 - CmaCh12G002090.1 Cma12g00209 209
12 1009922 1036010 - CmaCh12G002100.1 Cma12g00210 210
4 1731194 1739882 - MELO3C003509.2.1 Cme04g00229 229
4 1740197 1798474 - MELO3C003512.2.1 Cme04g00231 231
3 2848868 2853801 + PI0013018.1 Cmetu03g0187 187
3 2895263 2902743 - PI0007293.2 Cmetu03g0931 931
3 2855499 2862266 + PI0001395.1 Cmetu03g1095 1095
3 2863371 2893403 + PI0009051.1 Cmetu03g1114 1114
4 31629568 31632610 + PI0001803.1 Cmetu04g2990 2990
1 11764484 11771508 - CmoCh01G015260.1 Cmo01g01526 1526
1 11771542 11794466 - CmoCh01G015270.1 Cmo01g01527 1527
5 2750666 2759563 - CmoCh05G005610.1 Cmo05g00561 561
5 2759604 2767115 - CmoCh05G005630.1 Cmo05g00563 563
9 1444748 1452831 - CmoCh09G003360.1 Cmo09g00336 336
12 1036433 1049295 + CmoCh12G001610.1 Cmo12g00161 161
12 1050191 1077537 - CmoCh12G001630.1 Cmo12g00163 163
12 1078005 1080265 - CmoCh12G001640.1 Cmo12g00164 164
11 26933920 26984053 + CmPI595203_11g014670.1 Cmu11g1467 1467
11 26988793 26990148 + CmPI595203_11g014680.1 Cmu11g1468 1468
4 10598980 10600866 - Conep04aG0133300.1 Cone4ag1287 1287
4 10601436 10612537 + Conep04aG0133400.1 Cone4ag1288 1288
4 10618710 10656927 - Conep04aG0133500.1 Cone4ag1289 1289
7 6637757 6639995 + Conep07aG0089500.1 Cone7ag0866 866
2 1330695 1337874 - Cp4.1LG02g06190.1 Cpe02g00257 257
2 2751505 2763482 + Cp4.1LG02g03890.1 Cpe02g00481 481
2 2764543 2767899 + Cp4.1LG02g03930.1 Cpe02g00482 482
6 1261090 1271084 - Cp4.1LG06g02390.1 Cpe06g00238 238
7 1051500 1064423 + Cp4.1LG07g01700.1 Cpe07g00176 176
7 1065087 1083951 - Cp4.1LG07g01760.1 Cpe07g00177 177
7 1086605 1091602 - Cp4.1LG07g01770.1 Cpe07g00178 178
7 1093173 1095330 - Cp4.1LG07g01790.1 Cpe07g00179 179
11 30558518 30609788 + CrPI670011_11g018850.1 Cre11g1885 1885
11 30614076 30620922 + CrPI670011_11g018860.1 Cre11g1886 1886
2 19791788 19799588 - CsaV3_2G030170.1 Csa02g02198 2198
2 19800418 19806745 - CsaV3_2G030180.1 Csa02g02199 2199
3 39217197 39261355 + CsaV3_3G048070.1 Csa03g04501 4501
3 39263710 39271279 + CsaV3_3G048080.1 Csa03g04502 4502
4 25059511 25068121 - CsaV3_4G035610.1 Csa04g02535 2535
1 86413679 86454587 + Hsped.01g21760.1 Hepe01g2176 2176
1 86461283 86465595 + Hsped.01g21780.1 Hepe01g2178 2178
10 4953485 4960627 + Hsped.10g04390.1 Hepe10g0439 439
10 4962124 4984764 - Hsped.10g04400.1 Hepe10g0440 440
10 4987259 4994649 - Hsped.10g04410.1 Hepe10g0441 441
10 5002501 5004974 - Hsped.10g04420.1 Hepe10g0442 442
13 33525010 33558116 - Maker00034177 Lcy13g1490 1490
13 33559455 33567008 - Maker00033779 Lcy13g1491 1491
13 33571554 33573233 - Maker00034041 Lcy13g1492 1492
4 29951982 29999718 + Lsi04G022850.1 Lsi04g02285 2285
4 30002172 30005621 + Lsi04G022860.1 Lsi04g02286 2286
8 18728509 18731941 - Lsi08G010150.1 Lsi08g01015 1015
8 18737338 18743935 - Lsi08G010170.1 Lsi08g01017 1017
11 4742475 4781452 + MC11g0604 Mch11g0715 715
11 4785402 4788453 + MC11g0606 Mch11g0717 717
3 8838781 8844617 + Sed0013990.1 Sed03g1389 1389
3 8892742 8900282 - Sed0027362.4 Sed03g1396 1396
4 1369209 1371699 + Sed0004611.1 Sed04g0192 192
4 1414955 1441960 + Sed0001865.1 Sed04g0198 198
5 29238130 29242826 - Sed0005434.1 Sed05g1553 1553
1 103522513 103526955 + Tan0012202.4 Tan01g3865 3865
2 93181704 93183827 + Tan0012995.1 Tan02g2454 2454
2 93188743 93196530 + Tan0015491.3 Tan02g2457 2457
2 93199839 93225388 + Tan0012711.1 Tan02g2458 2458
2 93249038 93257826 - Tan0020695.4 Tan02g2466 2466
2 93249720 93257826 - Tan0020695.1 Tan02g2468 2468
18 5963490 6027423 + Vvi18g530 Vvi18g530 530
18 6040225 6058566 + Vvi18g531 Vvi18g531 531
18 6060380 6094675 + Vvi18g532 Vvi18g532 532
18 6095227 6184479 - Vvi18g533 Vvi18g533 533
18 6198614 6201341 + Vvi18g534 Vvi18g534 534
18 6203360 6209638 - Vvi18g535 Vvi18g535 535
18 6210894 6213254 - Vvi18g536 Vvi18g536 536
18 6214128 6218479 + Vvi18g537 Vvi18g537 537
18 6219118 6225014 - Vvi18g538 Vvi18g538 538
18 6227652 6234972 + Vvi18g539 Vvi18g539 539
       

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