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
Vvi18g880 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g881 . . . . . . Bma04g00196 . . . . . Car01g01470 . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00538 . . . . . . . . . . Cmo01g01949 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g882 . Blo12g00914 Bda01g00548 . . . Bma04g00197 Bma01g02301 Cmo05g00225 Cmo12g00442 Cma01g01887 Cma09g00176 Car01g01471 Car12g00466 Sed11g1001 Cpe06g00125 Cpe07g00444 Bhi04g00283 Tan02g1922 Cmetu03g0503 . Hepe10g0678 . . Cla08g01519 Cam08g2010 Cec08g1586 Cco08g1721 Clacu08g1699 . Cre08g1482 . . Cone17ag1318 Cone20ag0157 Lsi04g01637 Csa03g04181 Chy04g00537 Cme03g01985 Blo17g00817 . Bda08g01301 . . Bpe05g00076 . . . Cmo01g01950 Cmo09g00172 Cma12g00497 Cma05g00219 Car05g00179 Car09g00157 Cpe11g00181 Cpe02g00145 . . . . . . . Cla05g01964 Cam05g2115 Cec05g2126 Cco05g2178 Clacu05g2103 Cmu05g1979 Cre05g2098 Lsi08g01422 Csa02g02020 Chy03g01491 Cme04g00624
Vvi18g883 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g884 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g885 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g886 . . Bda01g00547 . Bpe02g00406 . Bma04g00198 Bma01g02302 Cmo05g00227 . . . . . Sed11g1002 . . Bhi04g00282 Tan02g1923 Cmetu03g0100 . Hepe10g0677 . Lcy13g2012 Cla08g01518 Cam08g2009 Cec08g1585 Cco08g1720 Clacu08g1698 . Cre08g1481 Cone4ag1888 Cone7ag1799 Cone17ag1319 Cone20ag0156 . . . Cme03g01984 . . . . . . . . . . . . Cma05g00220 Car05g00180 . Cpe11g00182 . . . . . . . . . . . . . . . Lsi08g01421 Csa02g02021 Chy03g01490 .
Vvi18g887 . . . . . . . . . . . . . . . . . Bhi04g00281 Tan02g1924 Cmetu03g2074 . Hepe10g0676 . Lcy13g2011 Cla08g01517 Cam08g2008 Cec08g1584 Cco08g1719 Clacu08g1697 . Cre08g1480 . . . . . . . Cme03g01983 . . . . . . . . . . . . Cma05g00221 Car05g00181 . . . . . . . . . . . . . . . . . . Csa02g02022 Chy03g01489 .
Vvi18g888 . . . . . . . . . Cmo12g00441 . . . Car12g00465 . . Cpe07g00443 Bhi04g00280 Tan02g0839 . . Hepe02g0536 . Lcy13g2010 Cla08g01516 Cam08g2007 Cec08g1583 Cco08g1718 Clacu08g1696 . Cre08g1479 Cone4ag1889 Cone7ag1800 . . . . . Cme03g01982 . Blo18g00826 . Bda01g01486 Bpe02g01681 . . . . . . Cma12g00496 . Car05g00182 . . . . . . . . . . . . . . . . . Lsi08g01420 Csa02g02023 Chy03g01488 .
Vvi18g889 . . . . . . . . Cmo05g00228 . . . . . . . . Bhi04g00279 . . . Hepe10g0162 . . . . . . . . . . . . . . . . Cme03g01981 Blo17g00815 Blo18g00825 Bda08g01300 . . Bpe05g00077 Bma01g00772 Bma05g00106 . . . . Cma05g00222 Car05g00183 . Cpe11g00183 . . . . . . . . . . . . . . . Lsi08g01419 Csa02g02024 Chy03g01487 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32387548 32388246 + Bda002559.1 Bda01g00547 547
1 32390048 32391163 + Bda002560.1 Bda01g00548 548
1 50754835 50767505 + Bda003741.1 Bda01g01486 1486
8 52670663 52671043 - Bda030333.1 Bda08g01300 1300
8 52691898 52692938 + Bda030335.1 Bda08g01301 1301
4 6654517 6656609 - XM_039030260.1 Bhi04g00279 279
4 6656654 6659008 - XM_039030259.1 Bhi04g00280 280
4 6663798 6665012 - XM_039030424.1 Bhi04g00281 281
4 6667926 6669424 + XM_039028095.1 Bhi04g00282 282
4 6679708 6681195 + XM_039029765.1 Bhi04g00283 283
12 27332658 27333722 + BLOR04933 Blo12g00914 914
17 26326885 26331771 - BLOR08361 Blo17g00815 815
17 26422176 26423216 + BLOR08363 Blo17g00817 817
18 24351434 24352376 - BLOR09313 Blo18g00825 825
18 24352925 24354270 - BLOR09314 Blo18g00826 826
1 7105640 7108441 - Bma000993.2 Bma01g00772 772
1 80595155 80596267 - Bma003163.1 Bma01g02301 2301
1 80598059 80598769 - Bma003164.1 Bma01g02302 2302
4 1744152 1745030 + Bma018645.1 Bma04g00196 196
4 1748430 1749500 - Bma018646.1 Bma04g00197 197
4 1756226 1756735 - Bma018647.1 Bma04g00198 198
5 3341307 3341984 + Bma020802.1 Bma05g00106 106
2 2636777 2640393 + Bpe008247.1 Bpe02g00406 406
2 19414126 19416894 + Bpe009517.1 Bpe02g01681 1681
5 1353467 1354498 - Bpe017465.1 Bpe05g00076 76
5 1361508 1362188 + Bpe017466.1 Bpe05g00077 77
5 29632738 29633769 + CaPI482276_05g021150.1 Cam05g2115 2115
8 25817381 25819074 - CaPI482276_08g020070.1 Cam08g2007 2007
8 25823530 25824375 - CaPI482276_08g020080.1 Cam08g2008 2008
8 25826885 25827577 + CaPI482276_08g020090.1 Cam08g2009 2009
8 25832379 25833425 + CaPI482276_08g020100.1 Cam08g2010 2010
1 12577470 12580250 - Carg17125-RA Car01g01470 1470
1 12580917 12581948 - Carg17126-RA Car01g01471 1471
5 954364 955425 - Carg11824-RA Car05g00179 179
5 958231 958923 - Carg11823-RA Car05g00180 180
5 960108 960953 + Carg11822-RA Car05g00181 181
5 962503 963983 + Carg11821-RA Car05g00182 182
5 965515 966469 + Carg11820-RA Car05g00183 183
9 747771 748805 + Carg08741-RA Car09g00157 157
12 2937246 2938619 - Carg04073-RA Car12g00465 465
12 2941124 2944812 + Carg04074-RA Car12g00466 466
5 30598936 30599970 + CcPI632755_05g021780.1 Cco05g2178 2178
8 28505641 28507349 - CcPI632755_08g017180.1 Cco08g1718 1718
8 28512265 28513110 - CcPI632755_08g017190.1 Cco08g1719 1719
8 28515573 28516265 + CcPI632755_08g017200.1 Cco08g1720 1720
8 28521116 28524134 + CcPI632755_08g017210.1 Cco08g1721 1721
5 32970648 32971682 + CePI673135_05g021260.1 Cec05g2126 2126
8 27374563 27376251 - CePI673135_08g015830.1 Cec08g1583 1583
8 27383126 27383971 - CePI673135_08g015840.1 Cec08g1584 1584
8 27386484 27387112 + CePI673135_08g015850.1 Cec08g1585 1585
8 27391952 27394861 + CePI673135_08g015860.1 Cec08g1586 1586
3 17304239 17305128 - Chy3G064670.1 Chy03g01487 1487
3 17306293 17310732 - Chy3G064680.1 Chy03g01488 1488
3 17310791 17311636 - Chy3G064690.1 Chy03g01489 1489
3 17316482 17317334 + Chy3G064700.1 Chy03g01490 1490
3 17320343 17321386 + Chy3G064710.1 Chy03g01491 1491
4 5406041 5407003 + Chy4G072550.1 Chy04g00537 537
4 5422414 5425080 + Chy4G072560.1 Chy04g00538 538
5 29842878 29843909 + ClG42_05g0210300.10 Clacu05g2103 2103
8 26562449 26564142 - ClG42_08g0169600.10 Clacu08g1696 1696
8 26570264 26571109 - ClG42_08g0169700.10 Clacu08g1697 1697
8 26573550 26574242 + ClG42_08g0169800.10 Clacu08g1698 1698
8 26578981 26580027 + ClG42_08g0169900.10 Clacu08g1699 1699
5 31463091 31464122 + ClCG05G019210.1 Cla05g01964 1964
8 27948716 27953482 - ClCG08G015360.2 Cla08g01516 1516
8 27959005 27959850 - ClCG08G015380.1 Cla08g01517 1517
8 27962138 27963255 + ClCG08G015390.1 Cla08g01518 1518
8 27967576 27968769 + ClCG08G015400.2 Cla08g01519 1519
1 12360780 12368052 - CmaCh01G018870.1 Cma01g01887 1887
5 926435 927493 - CmaCh05G002190.1 Cma05g00219 219
5 929144 931380 - CmaCh05G002200.1 Cma05g00220 220
5 932413 933258 + CmaCh05G002210.1 Cma05g00221 221
5 933871 938751 + CmaCh05G002220.1 Cma05g00222 222
9 749396 750436 + CmaCh09G001760.1 Cma09g00176 176
12 2573593 2575503 - CmaCh12G004960.1 Cma12g00496 496
12 2578149 2581414 + CmaCh12G004970.1 Cma12g00497 497
3 27651381 27652454 - MELO3C010919.2.1 Cme03g01981 1981
3 27653567 27655847 - MELO3C010918.2.1 Cme03g01982 1982
3 27657678 27658523 - MELO3C010917.2.1 Cme03g01983 1983
3 27660739 27662175 + MELO3C010916.2.1 Cme03g01984 1984
3 27665189 27666556 + MELO3C010915.2.1 Cme03g01985 1985
4 6043886 6045218 + MELO3C003886.2.1 Cme04g00624 624
3 1673874 1676659 - PI0003385.1 Cmetu03g0100 100
3 1669780 1671134 - PI0021175.1 Cmetu03g0503 503
3 1679152 1679982 + PI0016501.1 Cmetu03g2074 2074
1 13875971 13878751 - CmoCh01G019490.1 Cmo01g01949 1949
1 13881139 13882170 - CmoCh01G019500.1 Cmo01g01950 1950
5 964752 965810 - CmoCh05G002250.1 Cmo05g00225 225
5 968231 969700 - CmoCh05G002270.1 Cmo05g00227 227
5 972374 977090 + CmoCh05G002280.1 Cmo05g00228 228
9 775314 776348 + CmoCh09G001720.1 Cmo09g00172 172
12 2709265 2711447 - CmoCh12G004410.1 Cmo12g00441 441
12 2713840 2717090 + CmoCh12G004420.1 Cmo12g00442 442
5 29570069 29571100 + CmPI595203_05g019790.1 Cmu05g1979 1979
4 13476940 13478653 - Conep04aG0194900.1 Cone4ag1888 1888
4 13479018 13481163 + Conep04aG0195000.1 Cone4ag1889 1889
7 11780316 11781968 - Conep07aG0185300.1 Cone7ag1799 1799
7 11782763 11783908 + Conep07aG0185400.1 Cone7ag1800 1800
17 9335796 9337413 - Conep17aG0135000.1 Cone17ag1318 1318
17 9339349 9341033 - Conep17aG0135100.1 Cone17ag1319 1319
20 683521 684776 + Conep20aG0016400.1 Cone20ag0156 156
20 686361 687760 + Conep20aG0016500.1 Cone20ag0157 157
2 724870 725901 + Cp4.1LG02g07280.1 Cpe02g00145 145
6 627456 628490 + Cp4.1LG06g01210.1 Cpe06g00125 125
7 2849569 2851750 - Cp4.1LG07g04520.1 Cpe07g00443 443
7 2853315 2857068 + Cp4.1LG07g04500.1 Cpe07g00444 444
11 982405 983460 - Cp4.1LG11g01680.1 Cpe11g00181 181
11 984557 987421 - Cp4.1LG11g01720.1 Cpe11g00182 182
11 989874 995677 + Cp4.1LG11g01840.1 Cpe11g00183 183
5 32883234 32884265 + CrPI670011_05g020980.1 Cre05g2098 2098
8 27631153 27632846 - CrPI670011_08g014790.1 Cre08g1479 1479
8 27637901 27638746 - CrPI670011_08g014800.1 Cre08g1480 1480
8 27641267 27641959 + CrPI670011_08g014810.1 Cre08g1481 1481
8 27646886 27655126 + CrPI670011_08g014820.1 Cre08g1482 1482
2 18691225 18692820 - CsaV3_2G028390.1 Csa02g02020 2020
2 18695130 18696653 - CsaV3_2G028400.1 Csa02g02021 2021
2 18699746 18701025 + CsaV3_2G028410.1 Csa02g02022 2022
2 18702931 18705459 + CsaV3_2G028420.1 Csa02g02023 2023
2 18705493 18708124 + CsaV3_2G028430.1 Csa02g02024 2024
3 36682010 36683660 - CsaV3_3G044870.1 Csa03g04181 4181
2 5370839 5374405 - Hsped.02g05360.1 Hepe02g0536 536
10 1660582 1662815 + Hsped.10g01620.1 Hepe10g0162 162
10 8958288 8959142 - Hsped.10g06760.1 Hepe10g0676 676
10 8965466 8966158 + Hsped.10g06770.1 Hepe10g0677 677
10 8976376 8977403 + Hsped.10g06780.1 Hepe10g0678 678
13 39084367 39088371 - Maker00033720 Lcy13g2010 2010
13 39093530 39094384 - Maker00033687 Lcy13g2011 2011
13 39097005 39102318 + Maker00033707 Lcy13g2012 2012
4 23847682 23848710 - Lsi04G016370.1 Lsi04g01637 1637
8 22439427 22440466 - Lsi08G014190.1 Lsi08g01419 1419
8 22441517 22443996 - Lsi08G014200.1 Lsi08g01420 1420
8 22453337 22454029 + Lsi08G014210.1 Lsi08g01421 1421
8 22463031 22464074 + Lsi08G014220.1 Lsi08g01422 1422
11 25131633 25133110 - Sed0024757.1 Sed11g1001 1001
11 25145519 25146905 - Sed0010082.1 Sed11g1002 1002
2 8966396 8970140 - Tan0000427.1 Tan02g0839 839
2 87760897 87762407 - Tan0014891.1 Tan02g1922 1922
2 87800081 87802612 - Tan0014707.1 Tan02g1923 1923
2 87823609 87824448 + Tan0004098.1 Tan02g1924 1924
18 10097949 10099041 + Vvi18g880 Vvi18g880 880
18 10099743 10112854 + Vvi18g881 Vvi18g881 881
18 10118697 10119983 - Vvi18g882 Vvi18g882 882
18 10119989 10120448 + Vvi18g883 Vvi18g883 883
18 10127882 10134515 - Vvi18g884 Vvi18g884 884
18 10145284 10145615 + Vvi18g885 Vvi18g885 885
18 10145976 10147817 - Vvi18g886 Vvi18g886 886
18 10148252 10149416 + Vvi18g887 Vvi18g887 887
18 10155355 10159457 + Vvi18g888 Vvi18g888 888
18 10174162 10175673 + Vvi18g889 Vvi18g889 889
       

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