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
Vvi18g230 Blo01g01510 . . . Bpe02g00023 . . . Cmo04g02500 Cmo15g00668 . . . . . . . . . . . . . . Cla08g00616 Cam08g1030 Cec08g0619 Cco08g0731 Clacu08g0740 . Cre08g0548 . . Cone17ag0870 . . . . . . Blo18g00177 . Bda13g01473 Bpe02g01650 Bpe14g00391 Bma01g00805 Bma02g00210 . . . . . . Car15g00608 Cpe01g02068 . . . . . . . . . . . . . . . Lsi08g00456 . Chy03g00762 .
Vvi18g231 . Blo12g01123 . Bda03g00016 . Bpe04g00011 Bma04g00016 Bma01g02668 . . Cma01g01369 . . . . . . . . . . . . . . . . . . . . Cone4ag1422 Cone7ag1515 . . . Csa04g01779 . . . . . . . . . . . Cmo01g01421 . . . . . . . . . . . . . . . . . . . . . . . . Cme07g00817
Vvi18g232 . . . . Bpe02g00634 . . . . . . . . . Sed01g3098 . . Bhi04g01880 Tan11g1251 Cmetu03g2206 . Hepe02g2229 . Lcy10g1244 . . . . . . . . . . Cone20ag0432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g00765 .
Vvi18g233 . . . . . . . . Cmo04g02499 . . . . . . . . . . . . . . . Cla08g00615 Cam08g1029 Cec08g0618 Cco08g0730 Clacu08g0739 . Cre08g0547 . . . . . . . . . . . . . . . . . . . . . . . Cpe01g02067 . . . . . . . . . . . . . . . Lsi08g00455 . . .
Vvi18g234 Blo01g01303 . . . . . . Bma01g02078 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme03g00518 . . . . . . . . . . . . . Car04g02304 . . . . . . . . . . . . . . . . . . . . .
Vvi18g235 . Blo12g01124 . Bda03g00015 . Bpe04g00010 Bma04g00014 . . . Cma01g01377 Cma09g00777 . . . Cpe06g00612 . . . . . . . . . . . . . . . . . . Cone20ag0433 Lsi04g02409 Csa04g01782 . . . . . . . . . . Sed06g0997 Cmo01g01428 Cmo09g00769 . . . Car09g00686 . Cpe02g00561 Bhi09g02703 Tan01g4053 Cmetu07g1927 . Hepe01g1595 Mch11g0847 . Cla11g01548 Cam11g1612 Cec11g1641 Cco11g1642 Clacu11g1770 Cmu11g1587 Cre11g2004 . . Chy07g00621 Cme07g00826
Vvi18g236 . . . . . . . . . Cmo15g00669 . . . . Sed01g3102 . . Bhi04g01882 Tan11g1252 Cmetu03g0437 . Hepe02g2230 . Lcy10g1243 Cla08g00614 Cam08g1028 Cec08g0617 Cco08g0729 Clacu08g0738 . Cre08g0546 . . . . . . . Cme03g00519 . Blo18g00178 . Bda01g01453 Bpe02g01649 . Bma01g00806 . . . . . . . Car15g00609 . . . . . . . . . . . . . . . . Lsi08g00454 . Chy03g00766 .
Vvi18g237 . . . . Bpe02g00635 . . . Cmo04g02498 . Cma01g01934 . . . . . . Bhi04g01883 . . . . . . Cla08g00613 Cam08g1027 Cec08g0616 . . . . . . . . . . Chy04g00471 . . . . Bda13g01474 . Bpe14g00390 . Bma02g00211 . . Cmo09g00128 . . . . Cpe01g02065 . . . . . . . . . . . . . . . Lsi08g00453 . . .
Vvi18g238 Blo01g01301 . . . . . . . . Cmo15g00671 . Cma09g00131 Car01g01511 . Sed01g3103 . . Bhi04g01884 Tan11g1253 Cmetu03g1102 . Hepe02g2231 . Lcy10g1241 . . . . . . . . . . . . . . Cme03g00520 . . . . . . . . . Cmo01g01997 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g239 . . . . Bpe02g00636 . . Bma01g02077 Cmo04g02490 Cmo15g00672 . . . . Sed11g1620 . . Bhi04g01885 Tan11g1888 Cmetu03g0875 . Hepe02g2232 . . Cla08g00612 Cam08g1026 Cec08g0615 Cco08g0727 Clacu08g0736 . Cre08g0544 . . . Cone20ag0434 . . . Cme03g00522 . . . . . . . . . . . . . . . Cpe01g02064 . . . . . . . . . . . . . . . Lsi08g00452 . Chy03g00768 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50447554 50449296 - Bda003699.1 Bda01g01453 1453
3 368445 374494 + Bda015948.1 Bda03g00015 15
3 377462 380909 - Bda033471 Bda03g00016 16
13 37627034 37636121 - Bda000316.2 Bda13g01473 1473
13 37637106 37642952 - Bda000317.1 Bda13g01474 1474
4 47372134 47384840 + XM_039030368.1 Bhi04g01880 1880
4 47385502 47388310 + XM_039029307.1 Bhi04g01882 1882
4 47388394 47395321 - XM_039029305.1 Bhi04g01883 1883
4 47388394 47393817 - XM_039029306.1 Bhi04g01884 1884
4 47473949 47479333 + XM_039030397.1 Bhi04g01885 1885
9 72487120 72493757 + XM_039041701.1 Bhi09g02703 2703
1 49842744 49847066 + BLOR01301 Blo01g01301 1301
1 49945022 49946719 - BLOR01303 Blo01g01303 1303
1 54659954 54663033 + BLOR01510 Blo01g01510 1510
12 28861147 28864507 + BLOR05142 Blo12g01123 1123
12 28868050 28874887 - BLOR05143 Blo12g01124 1124
18 1706331 1709443 - BLOR08665 Blo18g00177 177
18 1711753 1714220 + BLOR08666 Blo18g00178 178
1 7537800 7540887 - Bma001023.1 Bma01g00805 805
1 7543598 7545327 + Bma001024.1 Bma01g00806 806
1 76204513 76207455 - Bma002889.1 Bma01g02077 2077
1 76251511 76252248 - Bma002891.1 Bma01g02078 2078
1 84176956 84193154 + Bma030313 Bma01g02668 2668
2 2260698 2263482 - Bma014667.1 Bma02g00210 210
2 2266603 2272952 - Bma014668.1 Bma02g00211 211
4 208568 214644 + Bma018463.1 Bma04g00014 14
4 217900 221398 - Bma031077 Bma04g00016 16
2 208686 210531 + Bpe025044 Bpe02g00023 23
2 4141432 4144337 + Bpe008474.1 Bpe02g00634 634
2 4146716 4151262 - Bpe025091 Bpe02g00635 635
2 4159677 4162550 + Bpe008475.1 Bpe02g00636 636
2 19231732 19233481 - Bpe009492.1 Bpe02g01649 1649
2 19236533 19239611 + Bpe025163 Bpe02g01650 1650
4 104811 110818 + Bpe025561 Bpe04g00010 10
4 114133 117389 - Bpe025562 Bpe04g00011 11
14 3662783 3668914 + Bpe007043.2 Bpe14g00390 390
14 3671314 3676350 + Bpe007044.1 Bpe14g00391 391
8 16480452 16484651 - CaPI482276_08g010260.1 Cam08g1026 1026
8 16497840 16504787 + CaPI482276_08g010270.1 Cam08g1027 1027
8 16505381 16508026 - CaPI482276_08g010280.1 Cam08g1028 1028
8 16510114 16517059 - CaPI482276_08g010290.1 Cam08g1029 1029
8 16541368 16544432 + CaPI482276_08g010300.1 Cam08g1030 1030
11 28879858 28886139 + CaPI482276_11g016120.1 Cam11g1612 1612
1 12794727 12800277 + Carg17166-RA Car01g01511 1511
4 18560778 18564564 - Carg15738-RA Car04g02304 2304
9 4026463 4034343 - Carg20093-RA Car09g00686 686
15 3365078 3368123 - Carg01547-RA Car15g00608 608
15 3371958 3373392 + Carg01546-RA Car15g00609 609
8 18840412 18844662 - CcPI632755_08g007270.1 Cco08g0727 727
8 18863360 18866010 - CcPI632755_08g007290.1 Cco08g0729 729
8 18868106 18875208 - CcPI632755_08g007300.1 Cco08g0730 730
8 18900794 18903855 + CcPI632755_08g007310.1 Cco08g0731 731
11 29252665 29258815 + CcPI632755_11g016420.1 Cco11g1642 1642
8 17675587 17679822 - CePI673135_08g006150.1 Cec08g0615 615
8 17692022 17698518 + CePI673135_08g006160.1 Cec08g0616 616
8 17699111 17701744 - CePI673135_08g006170.1 Cec08g0617 617
8 17703809 17711220 - CePI673135_08g006180.1 Cec08g0618 618
8 17738459 17741548 + CePI673135_08g006190.1 Cec08g0619 619
11 30708673 30714964 + CePI673135_11g016410.1 Cec11g1641 1641
3 10263733 10266708 - Chy3G057420.1 Chy03g00762 762
3 10331082 10337965 + Chy3G057450.1 Chy03g00765 765
3 10340540 10342906 + Chy3G057460.1 Chy03g00766 766
3 10376412 10380547 + Chy3G057480.1 Chy03g00768 768
4 4388839 4393987 - Chy4G071890.1 Chy04g00471 471
7 5750717 5756600 - Chy7G134510.1 Chy07g00621 621
8 17216444 17220518 - ClG42_08g0073600.10 Clacu08g0736 736
8 17241013 17243880 - ClG42_08g0073800.10 Clacu08g0738 738
8 17245945 17253419 - ClG42_08g0073900.10 Clacu08g0739 739
8 17279867 17282922 + ClG42_08g0074000.10 Clacu08g0740 740
11 28901644 28907916 + ClG42_11g0177000.10 Clacu11g1770 1770
8 18046574 18051479 - ClCG08G005890.2 Cla08g00612 612
8 18064464 18071262 + ClCG08G005900.2 Cla08g00613 613
8 18068164 18074542 - ClCG08G005910.2 Cla08g00614 614
8 18076250 18084180 - ClCG08G005920.2 Cla08g00615 615
8 18110480 18116350 + ClCG08G005930.1 Cla08g00616 616
11 29191602 29199542 + ClCG11G015890.1 Cla11g01548 1548
1 9736991 9741622 - CmaCh01G013690.1 Cma01g01369 1369
1 9767066 9773971 - CmaCh01G013770.1 Cma01g01377 1377
1 12568834 12574799 + CmaCh01G019340.1 Cma01g01934 1934
9 563148 568452 - CmaCh09G001310.1 Cma09g00131 131
9 3750999 3758253 - CmaCh09G007770.1 Cma09g00777 777
3 7727087 7737305 + MELO3C010638.2.1 Cme03g00518 518
3 7764241 7768061 + MELO3C010637.2.1 Cme03g00519 519
3 7766418 7774314 - MELO3C010636.2.1 Cme03g00520 520
3 7834096 7839944 + MELO3C010635.2.1 Cme03g00522 522
7 7770374 7776011 - MELO3C010507.2.1 Cme07g00817 817
7 7965718 7971075 - MELO3C010503.2.1 Cme07g00826 826
3 12187063 12187533 + PI0019135.1 Cmetu03g0437 437
3 16795051 16799034 - PI0022561.1 Cmetu03g0875 875
3 12189837 12196644 - PI0027949.1 Cmetu03g1102 1102
3 12139020 12144600 + PI0005403.1 Cmetu03g2206 2206
7 19906004 19912581 + PI0026772.1 Cmetu07g1927 1927
1 11145632 11149982 - CmoCh01G014210.1 Cmo01g01421 1421
1 11173786 11181527 - CmoCh01G014280.1 Cmo01g01428 1428
1 14104998 14110775 + CmoCh01G019970.1 Cmo01g01997 1997
4 18339594 18343563 - CmoCh04G024900.1 Cmo04g02490 2490
4 18373896 18379714 + CmoCh04G024980.1 Cmo04g02498 2498
4 18379971 18383985 - CmoCh04G024990.1 Cmo04g02499 2499
4 18395584 18398522 + CmoCh04G025000.1 Cmo04g02500 2500
9 587447 592567 - CmoCh09G001280.1 Cmo09g00128 128
9 3895041 3903065 - CmoCh09G007690.1 Cmo09g00769 769
15 3266992 3270297 - CmoCh15G006680.1 Cmo15g00668 668
15 3273761 3277119 + CmoCh15G006690.1 Cmo15g00669 669
15 3275661 3281374 - CmoCh15G006710.1 Cmo15g00671 671
15 3284498 3287742 + CmoCh15G006720.1 Cmo15g00672 672
11 28155152 28161424 + CmPI595203_11g015870.1 Cmu11g1587 1587
4 11344487 11346796 - Conep04aG0147400.1 Cone4ag1422 1422
7 10545761 10546509 + Conep07aG0155800.1 Cone7ag1515 1515
17 6897358 6899174 - Conep17aG0089000.1 Cone17ag0870 870
20 2151827 2155843 + Conep20aG0044700.1 Cone20ag0432 432
20 2157113 2163195 - Conep20aG0044800.1 Cone20ag0433 433
20 2167755 2170554 + Conep20aG0044900.1 Cone20ag0434 434
1 17474083 17479707 - Cp4.1LG01g20640.1 Cpe01g02064 2064
1 17481680 17517566 + Cp4.1LG01g20690.1 Cpe01g02065 2065
1 17516796 17521129 - Cp4.1LG01g20720.1 Cpe01g02067 2067
1 17525206 17536624 + Cp4.1LG01g20680.1 Cpe01g02068 2068
2 3355557 3363381 + Cp4.1LG02g03080.1 Cpe02g00561 561
6 3776713 3784200 - Cp4.1LG06g06080.1 Cpe06g00612 612
8 18124022 18128300 - CrPI670011_08g005440.1 Cre08g0544 544
8 18147670 18150544 - CrPI670011_08g005460.1 Cre08g0546 546
8 18152741 18160435 - CrPI670011_08g005470.1 Cre08g0547 547
8 18186605 18189614 + CrPI670011_08g005480.1 Cre08g0548 548
11 31801349 31807642 + CrPI670011_11g020040.1 Cre11g2004 2004
4 17453127 17458839 - CsaV3_4G028050.1 Csa04g01779 1779
4 17485340 17491964 - CsaV3_4G028080.1 Csa04g01782 1782
1 81252381 81259096 - Hsped.01g15950.1 Hepe01g1595 1595
2 63236468 63242258 + Hsped.02g22290.1 Hepe02g2229 2229
2 63252268 63254398 + Hsped.02g22300.1 Hepe02g2230 2230
2 63254575 63261855 - Hsped.02g22310.1 Hepe02g2231 2231
2 63355430 63359463 + Hsped.02g22320.1 Hepe02g2232 2232
10 35087819 35092611 + Maker00008856 Lcy10g1241 1241
10 35094827 35097137 - Maker00008801 Lcy10g1243 1243
10 35098624 35106701 - Maker00008711 Lcy10g1244 1244
4 31223204 31231420 + Lsi04G024090.1 Lsi04g02409 2409
8 12153594 12156398 - Lsi08G004520.1 Lsi08g00452 452
8 12174193 12181511 + Lsi08G004530.1 Lsi08g00453 453
8 12180202 12184266 - Lsi08G004540.1 Lsi08g00454 454
8 12185700 12195406 - Lsi08G004550.1 Lsi08g00455 455
8 12228253 12232132 + Lsi08G004560.1 Lsi08g00456 456
11 5737145 5745151 + MC11g0713 Mch11g0847 847
1 42187146 42190748 + Sed0006355.1 Sed01g3098 3098
1 42323008 42325037 + Sed0022381.3 Sed01g3102 3102
1 42325225 42350845 - Sed0024306.1 Sed01g3103 3103
6 14390516 14401873 - Sed0006418.1 Sed06g0997 997
11 31586036 31590951 + Sed0006171.2 Sed11g1620 1620
1 105461089 105469105 + Tan0017247.2 Tan01g4053 4053
11 10668825 10676551 + Tan0006547.1 Tan11g1251 1251
11 10677925 10679847 + Tan0005606.1 Tan11g1252 1252
11 10680458 10687455 - Tan0016266.1 Tan11g1253 1253
11 24631944 24635951 - Tan0004920.1 Tan11g1888 1888
18 2485709 2489651 - Vvi18g230 Vvi18g230 230
18 2496617 2503398 + Vvi18g231 Vvi18g231 231
18 2513714 2517765 + Vvi18g232 Vvi18g232 232
18 2519474 2521072 + Vvi18g233 Vvi18g233 233
18 2521401 2542260 + Vvi18g234 Vvi18g234 234
18 2543732 2568290 - Vvi18g235 Vvi18g235 235
18 2573309 2584523 + Vvi18g236 Vvi18g236 236
18 2592420 2602002 - Vvi18g237 Vvi18g237 237
18 2604467 2613076 - Vvi18g238 Vvi18g238 238
18 2618398 2626185 + Vvi18g239 Vvi18g239 239
       

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