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
Vvi18g990 . . . . . . . . . Cmo12g00398 Cma01g01931 Cma09g00137 Car01g01507 Car12g00423 . Cpe06g00096 Cpe07g00402 . . . . . . . Cla08g01466 Cam08g1954 Cec08g1529 Cco08g1667 Clacu08g1644 . Cre08g1429 . . . Cone20ag0124 Lsi04g01698 Csa03g04238 Chy04g00477 Cme03g01932 . Blo18g00805 . Bda01g01505 Bpe02g01703 . . . . Cmo01g01994 Cmo09g00133 Cma12g00448 . . Car09g00123 . Cpe02g00107 . . . . . . . Cla05g01913 Cam05g2051 Cec05g2062 Cco05g2115 Clacu05g2046 Cmu05g1922 Cre05g2045 Lsi08g01375 Csa02g02076 Chy03g01437 Cme04g00527
Vvi18g991 . . . . . . . . Cmo05g00266 Cmo12g00397 . . . Car12g00422 . . Cpe07g00401 Bhi04g00195 . . . Hepe10g0615 . . Cla08g01465 Cam08g1953 Cec08g1528 Cco08g1666 Clacu08g1643 . Cre08g1428 . . Cone17ag1357 . . . . Cme03g01931 . . . . . . . . . . . Cma12g00447 Cma05g00261 Car05g00219 . Cpe11g00216 . . . . . . . . . . . . . . . Lsi08g01374 Csa02g02077 Chy03g01436 .
Vvi18g992 . . . . . . . . . Cmo12g00396 . Cma09g00136 . Car12g00421 . Cpe06g00095 Cpe07g00400 Bhi04g00196 . . . Hepe10g0614 . . Cla08g01464 Cam08g1952 Cec08g1527 Cco08g1665 Clacu08g1642 . Cre08g1427 . . . Cone20ag0123 Lsi04g01699 Csa03g04240 Chy04g00476 Cme03g01930 . Blo18g00804 . Bda01g01509 . . Bma01g00751 . . . Cmo09g00132 Cma12g00446 . . Car09g00122 . . . . . . . . . Cla05g01912 Cam05g2049 Cec05g2060 Cco05g2114 Clacu05g2044 Cmu05g1921 Cre05g2044 Lsi08g01373 Csa02g02078 Chy03g01435 .
Vvi18g993 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g994 . . Bda01g00516 Bda03g00270 Bpe02g00373 Bpe04g00224 Bma04g00219 Bma01g02339 . . Cma01g01932 Cma09g00135 Car01g01508 . . Cpe06g00094 . . . . . . . . . . . . . . . . . Cone17ag1358 Cone20ag0122 Lsi04g01700 Csa03g04241 Chy04g00475 . . . . . . . . . . Cmo01g01995 Cmo09g00131 . . . Car09g00121 . Cpe02g00105 . . . . . . . Cla05g01911 Cam05g2048 Cec05g2059 Cco05g2113 Clacu05g2043 Cmu05g1920 Cre05g2043 . . . Cme04g00520
Vvi18g995 . . . . . . . . Cmo05g00267 Cmo12g00395 . . . . . . Cpe07g00399 Bhi04g00198 . . . . . . Cla08g01463 Cam08g1951 Cec08g1526 Cco08g1664 Clacu08g1641 . Cre08g1426 . . . . . . . Cme03g01929 . Blo18g00803 . Bda01g01510 Bpe02g01704 . Bma01g00750 . . . . Cma12g00445 Cma05g00263 . . Cpe11g00217 . . . . . . . . . . . . . . . Lsi08g01372 Csa02g02081 Chy03g01433 .
Vvi18g996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g997 . . . . . Bpe04g00225 Bma04g00220 . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g998 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1933 Cone7ag1845 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00392 Cam11g0437 Cec11g0432 Cco11g0426 Clacu11g0560 Cmu11g0417 Cre11g0902 . . . .
Vvi18g999 . . . . . . . . . . . . . . . . . Bhi04g00201 Tan02g2006 . . . . . . . . . . . . Cone4ag1934 Cone7ag1846 . . . . . Cme03g01927 . Blo18g00801 . Bda01g01511 Bpe02g01706 . Bma01g00748 . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01370 Csa02g02083 Chy03g01431 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32127138 32132534 + Bda002522.1 Bda01g00516 516
1 50903017 50909892 - Bda003762.1 Bda01g01505 1505
1 50933432 50934858 - Bda003766.1 Bda01g01509 1509
1 50947019 50949113 + Bda003767.1 Bda01g01510 1510
1 50957306 50959466 - Bda003768.3 Bda01g01511 1511
3 2380289 2384345 - Bda016226.1 Bda03g00270 270
4 4739677 4749397 - XM_039030386.1 Bhi04g00195 195
4 4773429 4778134 - XM_039029764.1 Bhi04g00196 196
4 4858824 4862874 + XM_039029296.1 Bhi04g00198 198
4 4894326 4897188 - XM_039030531.1 Bhi04g00201 201
18 23398234 23400583 + BLOR09289 Blo18g00801 801
18 23452152 23457423 - BLOR09291 Blo18g00803 803
18 23503624 23505059 + BLOR09292 Blo18g00804 804
18 23707222 23720248 + BLOR09293 Blo18g00805 805
1 6881751 6883812 + Bma000963.1 Bma01g00748 748
1 6890977 6893078 - Bma000965.1 Bma01g00750 750
1 6915264 6916690 + Bma000968.1 Bma01g00751 751
1 81005111 81009418 - Bma030297 Bma01g02339 2339
4 1877523 1881702 - Bma018670.1 Bma04g00219 219
4 1882898 1883470 - Bma018671.1 Bma04g00220 220
2 2454231 2458403 + Bpe008214.2 Bpe02g00373 373
2 19522611 19528369 - Bpe009537.2 Bpe02g01703 1703
2 19548284 19550382 + Bpe009538.1 Bpe02g01704 1704
2 19567873 19569878 - Bpe009539.2 Bpe02g01706 1706
4 1508418 1512487 - Bpe025585 Bpe04g00224 224
4 1513369 1513941 - Bpe014940.1 Bpe04g00225 225
5 29164478 29169663 + CaPI482276_05g020480.1 Cam05g2048 2048
5 29173947 29177509 + CaPI482276_05g020490.1 Cam05g2049 2049
5 29189059 29192209 + CaPI482276_05g020510.1 Cam05g2051 2051
8 25414855 25418309 - CaPI482276_08g019510.1 Cam08g1951 1951
8 25433774 25437396 + CaPI482276_08g019520.1 Cam08g1952 1952
8 25447772 25452578 + CaPI482276_08g019530.1 Cam08g1953 1953
8 25457606 25463329 + CaPI482276_08g019540.1 Cam08g1954 1954
11 5777494 5783229 - CaPI482276_11g004370.1 Cam11g0437 437
1 12764610 12767270 - Carg17162-RA Car01g01507 1507
1 12773826 12779524 - Carg17163-RA Car01g01508 1508
5 1128158 1133612 - Carg11782-RA Car05g00219 219
9 583179 588237 + Carg08705-RA Car09g00121 121
9 590225 591676 + Carg08706-RA Car09g00122 122
9 596765 599340 + Carg08707-RA Car09g00123 123
12 2700164 2702277 + Carg04029-RA Car12g00421 421
12 2708808 2717051 + Carg04030-RA Car12g00422 422
12 2718485 2722995 + Carg04031-RA Car12g00423 423
5 30101684 30106852 + CcPI632755_05g021130.1 Cco05g2113 2113
5 30110976 30114599 + CcPI632755_05g021140.1 Cco05g2114 2114
5 30128020 30131187 + CcPI632755_05g021150.1 Cco05g2115 2115
8 28095412 28098804 - CcPI632755_08g016640.1 Cco08g1664 1664
8 28114354 28117970 + CcPI632755_08g016650.1 Cco08g1665 1665
8 28128409 28134961 + CcPI632755_08g016660.1 Cco08g1666 1666
8 28138184 28143969 + CcPI632755_08g016670.1 Cco08g1667 1667
11 4390691 4393754 - CcPI632755_11g004260.1 Cco11g0426 426
5 32474754 32480015 + CePI673135_05g020590.1 Cec05g2059 2059
5 32484239 32487950 + CePI673135_05g020600.1 Cec05g2060 2060
5 32503238 32506393 + CePI673135_05g020620.1 Cec05g2062 2062
8 26958400 26961841 - CePI673135_08g015260.1 Cec08g1526 1526
8 26977595 26981199 + CePI673135_08g015270.1 Cec08g1527 1527
8 26991664 26998225 + CePI673135_08g015280.1 Cec08g1528 1528
8 27001543 27007263 + CePI673135_08g015290.1 Cec08g1529 1529
11 4513244 4516485 - CePI673135_11g004320.1 Cec11g0432 432
3 16989788 16992667 + Chy3G064110.1 Chy03g01431 1431
3 17007158 17009836 - Chy3G064130.1 Chy03g01433 1433
3 17017825 17020786 + Chy3G064150.1 Chy03g01435 1435
3 17025822 17030493 + Chy3G064160.1 Chy03g01436 1436
3 17034833 17036988 + Chy3G064170.1 Chy03g01437 1437
4 4466228 4473432 + Chy4G071930.1 Chy04g00475 475
4 4489597 4491070 + Chy4G071940.1 Chy04g00476 476
4 4510075 4513611 + Chy4G071950.1 Chy04g00477 477
5 29364304 29369492 + ClG42_05g0204300.10 Clacu05g2043 2043
5 29373737 29377264 + ClG42_05g0204400.10 Clacu05g2044 2044
5 29388641 29391576 + ClG42_05g0204600.10 Clacu05g2046 2046
8 26159707 26163212 - ClG42_08g0164100.10 Clacu08g1641 1641
8 26178531 26182111 + ClG42_08g0164200.10 Clacu08g1642 1642
8 26192407 26198903 + ClG42_08g0164300.10 Clacu08g1643 1643
8 26202219 26207937 + ClG42_08g0164400.10 Clacu08g1644 1644
11 5266876 5269980 - ClG42_11g0056000.10 Clacu11g0560 560
5 30962973 30969504 + ClCG05G018710.1 Cla05g01911 1911
5 30971888 30976055 + ClCG05G018720.2 Cla05g01912 1912
5 30987631 30991437 + ClCG05G018730.2 Cla05g01913 1913
8 27534927 27538762 - ClCG08G014770.2 Cla08g01463 1463
8 27556339 27559977 + ClCG08G014780.1 Cla08g01464 1464
8 27569075 27576688 + ClCG08G014790.1 Cla08g01465 1465
8 27580019 27585911 + ClCG08G014800.1 Cla08g01466 1466
11 4383513 4388111 - ClCG11G004160.1 Cla11g00392 392
1 12539255 12542309 - CmaCh01G019310.1 Cma01g01931 1931
1 12548399 12553988 - CmaCh01G019320.1 Cma01g01932 1932
5 1102526 1110061 - CmaCh05G002610.1 Cma05g00261 261
5 1112475 1116016 + CmaCh05G002630.1 Cma05g00263 263
9 585207 586791 + CmaCh09G001350.1 Cma09g00135 135
9 588782 590232 + CmaCh09G001360.1 Cma09g00136 136
9 595234 597466 + CmaCh09G001370.1 Cma09g00137 137
12 2332098 2336718 - CmaCh12G004450.1 Cma12g00445 445
12 2344959 2347653 + CmaCh12G004460.1 Cma12g00446 446
12 2353985 2361559 + CmaCh12G004470.1 Cma12g00447 447
12 2364423 2367848 + CmaCh12G004480.1 Cma12g00448 448
3 27332975 27336174 + MELO3C010968.2.1 Cme03g01927 1927
3 27348204 27352076 - MELO3C010966.2.1 Cme03g01929 1929
3 27360567 27363965 + MELO3C010965.2.1 Cme03g01930 1930
3 27367677 27375411 + MELO3C010964.2.1 Cme03g01931 1931
3 27376191 27380483 + MELO3C010963.2.1 Cme03g01932 1932
4 4345538 4353370 + MELO3C003795.2.1 Cme04g00520 520
4 4501055 4505049 + MELO3C003797.2.1 Cme04g00527 527
1 14073452 14076732 - CmoCh01G019940.1 Cmo01g01994 1994
1 14082655 14089422 - CmoCh01G019950.1 Cmo01g01995 1995
5 1141587 1146818 - CmoCh05G002660.1 Cmo05g00266 266
5 1150727 1155364 + CmoCh05G002670.1 Cmo05g00267 267
9 604317 609588 + CmoCh09G001310.1 Cmo09g00131 131
9 611454 613227 + CmoCh09G001320.1 Cmo09g00132 132
9 618117 620446 + CmoCh09G001330.1 Cmo09g00133 133
12 2454389 2457923 - CmoCh12G003950.1 Cmo12g00395 395
12 2468400 2470678 + CmoCh12G003960.1 Cmo12g00396 396
12 2477619 2484960 + CmoCh12G003970.1 Cmo12g00397 397
12 2487681 2491269 + CmoCh12G003980.1 Cmo12g00398 398
5 29090090 29095277 + CmPI595203_05g019200.1 Cmu05g1920 1920
5 29099511 29103048 + CmPI595203_05g019210.1 Cmu05g1921 1921
5 29114421 29117343 + CmPI595203_05g019220.1 Cmu05g1922 1922
11 4577716 4580819 - CmPI595203_11g004170.1 Cmu11g0417 417
4 13670426 13672068 - Conep04aG0199400.1 Cone4ag1932 1932
4 13672614 13675637 + Conep04aG0199500.1 Cone4ag1933 1933
4 13675789 13677533 - Conep04aG0199600.1 Cone4ag1934 1934
7 11973578 11975552 + Conep07aG0190000.1 Cone7ag1845 1845
7 11974022 11977715 - Conep07aG0190100.1 Cone7ag1846 1846
17 9493846 9496665 - Conep17aG0139000.1 Cone17ag1357 1357
17 9503291 9508018 - Conep17aG0139100.1 Cone17ag1358 1358
20 538728 542888 + Conep20aG0012900.1 Cone20ag0122 122
20 544406 546034 + Conep20aG0013000.1 Cone20ag0123 123
20 552676 555517 + Conep20aG0013100.1 Cone20ag0124 124
2 527833 532056 + Cp4.1LG02g07820.1 Cpe02g00105 105
2 540145 543051 + Cp4.1LG02g07550.1 Cpe02g00107 107
6 459303 466976 + Cp4.1LG06g00850.1 Cpe06g00094 94
6 468330 469780 + Cp4.1LG06g00790.1 Cpe06g00095 95
6 474349 476939 + Cp4.1LG06g00780.1 Cpe06g00096 96
7 2586999 2590886 - Cp4.1LG07g04020.1 Cpe07g00399 399
7 2600662 2603382 + Cp4.1LG07g03920.1 Cpe07g00400 400
7 2610575 2618677 + Cp4.1LG07g03930.1 Cpe07g00401 401
7 2619821 2624740 + Cp4.1LG07g03970.1 Cpe07g00402 402
11 1159128 1165862 - Cp4.1LG11g02170.1 Cpe11g00216 216
11 1168178 1172095 + Cp4.1LG11g02030.1 Cpe11g00217 217
5 32418339 32425313 + CrPI670011_05g020430.1 Cre05g2043 2043
5 32427852 32431463 + CrPI670011_05g020440.1 Cre05g2044 2044
5 32442787 32445970 + CrPI670011_05g020450.1 Cre05g2045 2045
8 27224856 27228372 - CrPI670011_08g014260.1 Cre08g1426 1426
8 27244134 27247729 + CrPI670011_08g014270.1 Cre08g1427 1427
8 27258572 27265152 + CrPI670011_08g014280.1 Cre08g1428 1428
8 27268475 27274316 + CrPI670011_08g014290.1 Cre08g1429 1429
11 6204886 6207997 - CrPI670011_11g009020.1 Cre11g0902 902
2 18953613 18956324 - CsaV3_2G028950.1 Csa02g02076 2076
2 18958082 18966358 - CsaV3_2G028960.1 Csa02g02077 2077
2 18969245 18972623 - CsaV3_2G028970.1 Csa02g02078 2078
2 18981944 18989908 + CsaV3_2G029000.1 Csa02g02081 2081
2 18994609 18998089 - CsaV3_2G029020.1 Csa02g02083 2083
3 37108680 37112535 - CsaV3_3G045440.1 Csa03g04238 4238
3 37124978 37126810 - CsaV3_3G045460.1 Csa03g04240 4240
3 37131306 37139349 - CsaV3_3G045470.1 Csa03g04241 4241
10 7609381 7613776 + Hsped.10g06140.1 Hepe10g0614 614
10 7650923 7663216 + Hsped.10g06150.1 Hepe10g0615 615
4 24360908 24364014 - Lsi04G016980.1 Lsi04g01698 1698
4 24372809 24375913 - Lsi04G016990.1 Lsi04g01699 1699
4 24379138 24382163 - Lsi04G017000.1 Lsi04g01700 1700
8 21982441 21986126 + Lsi08G013700.1 Lsi08g01370 1370
8 22013371 22017288 - Lsi08G013720.1 Lsi08g01372 1372
8 22029349 22033304 + Lsi08G013730.1 Lsi08g01373 1373
8 22042555 22048213 + Lsi08G013740.1 Lsi08g01374 1374
8 22053426 22058504 + Lsi08G013750.1 Lsi08g01375 1375
2 89244116 89247228 - Tan0008175.4 Tan02g2006 2006
18 11056810 11061172 - Vvi18g990 Vvi18g990 990
18 11070660 11090733 - Vvi18g991 Vvi18g991 991
18 11099583 11102318 - Vvi18g992 Vvi18g992 992
18 11105894 11106764 - Vvi18g993 Vvi18g993 993
18 11106836 11117007 - Vvi18g994 Vvi18g994 994
18 11125764 11129338 + Vvi18g995 Vvi18g995 995
18 11137542 11137828 - Vvi18g996 Vvi18g996 996
18 11143664 11148117 - Vvi18g997 Vvi18g997 997
18 11153816 11161309 + Vvi18g998 Vvi18g998 998
18 11161704 11165472 - Vvi18g999 Vvi18g999 999
       

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