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
Vvi4g582 . Blo12g01049 . Bda03g00102 Bpe02g01263 . Bma04g00095 . . . Cma01g01670 . Car09g00355 . . . Cpe06g00291 . . . . . . . Cla05g01674 Cam05g1789 Cec05g1795 Cco05g1854 Clacu05g1777 Cmu05g1662 Cre05g1791 Cone4ag1743 Cone7ag1663 Cone17ag0979 Cone20ag0320 Lsi04g01341 . . . . . Bda01g01014 . . Bpe04g00086 Bma01g01262 . Sed05g1748 Cmo01g01719 Cmo09g00410 Cma09g00405 . Car01g01285 . . Cpe02g00321 Bhi09g03015 Tan01g3554 Cmetu07g1233 . . . . . . . . . . . . . . Cme07g00127
Vvi4g583 . . . . . . . . . . Cma01g01672 . . . . . . . . . . . . . Cla05g01673 Cam05g1788 Cec05g1794 Cco05g1853 Clacu05g1776 Cmu05g1661 Cre05g1790 . . . . Lsi04g01342 . . . . . . . . . . . Sed08g0580 Cmo01g01720 . . . Car01g01286 . . Cpe02g00320 Bhi09g03016 Tan01g3552 Cmetu07g1461 . Hepe01g1959 Mch11g0497 . . . . . . . . . . . Cme07g00129
Vvi4g584 . . . . Bpe02g01264 . . . Cmo05g00351 Cmo12g00319 . Cma05g00347 . Car12g00349 Sed11g1139 Cpe07g00325 . Bhi04g00052 Tan02g2764 Cmetu03g2012 . Hepe10g0215 . Lcy13g1834 . . . . . . . . . Cone17ag0978 Cone20ag0319 Lsi04g02065 . . . . . Bda01g01015 . . . . . . . . . Cma12g00366 . Car05g00293 . . . . . . . . . Cla08g01369 Cam08g1838 Cec08g1417 Cco08g1549 Clacu08g1533 . Cre08g1316 Lsi08g01251 . Chy03g01081 .
Vvi4g585 . Blo12g01048 . Bda03g00103 . . . . . . Cma01g01673 . Car09g00354 . . . Cpe06g00290 . . . . . . . Cla05g01672 Cam05g1787 Cec05g1793 Cco05g1852 Clacu05g1775 Cmu05g1660 Cre05g1789 . . Cone17ag0977 . Lsi04g01343 . . . . . . . . Bpe04g00087 . . Sed05g1752 Cmo01g01721 Cmo09g00407 Cma09g00403 . Car01g01288 . . Cpe02g00318 Bhi09g03017 Tan01g3551 Cmetu07g0231 . Hepe01g1957 Mch11g0495 . . . . . . . . . . . .
Vvi4g586 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g587 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g588 . Blo12g01046 . Bda03g00105 Bpe02g01265 . Bma04g00097 . . . Cma01g01674 . . . . . . . . . . . . . . . . . . . . Cone4ag1741 Cone7ag1661 . . Lsi04g01346 . . . . Blo18g00040 Bda01g01016 Bda13g01275 . Bpe04g00089 . . Sed13g1956 Cmo01g01722 . . . Car01g01289 . . Cpe02g00317 Bhi09g03020 Tan01g3547 Cmetu07g2290 . . . . . . . . . . . . . . Cme07g00041
Vvi4g589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g590 . Blo12g01045 Bda01g00660 Bda03g00106 . Bpe02g00533 Bma04g00098 . . . Cma01g01675 . Car09g00352 . . . Cpe06g00288 . . . . . . . Cla05g01671 Cam05g1786 Cec05g1792 Cco05g1851 Clacu05g1774 Cmu05g1659 . . . Cone17ag0976 Cone20ag0318 Lsi04g01347 . . . . . . . . Bpe04g00090 . . . Cmo01g01725 Cmo09g00404 Cma09g00401 . Car01g01290 . . Cpe02g00316 Bhi09g03026 Tan01g3539 . . . . . . . . . . . . . . . Cme07g00133
Vvi4g591 . Blo12g01044 . Bda03g00107 . . Bma04g00099 . . . Cma01g01676 . Car09g00351 . . . Cpe06g00287 . . . . . . . Cla05g01668 Cam05g1783 Cec05g1789 Cco05g1848 Clacu05g1771 Cmu05g1656 Cre05g1785 Cone4ag1740 Cone7ag1660 . . Lsi04g01348 . . . . . . . . Bpe04g00091 . . Sed05g1755 Cmo01g01726 Cmo09g00403 Cma09g00400 . Car01g01291 . . Cpe02g00315 Bhi09g03027 Tan01g3538 Cmetu07g1848 . Hepe01g1953 Mch11g0490 . . . . . . . . . . . Cme07g00134
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33611765 33618557 + Bda002688.1 Bda01g00660 660
1 43704810 43705973 + Bda003171.1 Bda01g01014 1014
1 43707226 43707855 + Bda003172.1 Bda01g01015 1015
1 43708717 43712477 - Bda003173.1 Bda01g01016 1016
3 936202 939294 - Bda016041.1 Bda03g00102 102
3 940947 942257 - Bda016042.2 Bda03g00103 103
3 950950 954549 - Bda016044.1 Bda03g00105 105
3 956482 961161 - Bda016045.1 Bda03g00106 106
3 966859 968337 + Bda016046.1 Bda03g00107 107
13 35110645 35112850 - Bda000080.1 Bda13g01275 1275
4 1539349 1540214 + XM_039028287.1 Bhi04g00052 52
9 78194968 78198432 + XM_039041579.1 Bhi09g03015 3015
9 78198151 78200042 - XM_039041581.1 Bhi09g03016 3016
9 78200187 78202597 - XM_039041580.1 Bhi09g03017 3017
9 78210122 78218956 - XM_039043776.1 Bhi09g03020 3020
9 78241012 78246576 - XM_039041741.1 Bhi09g03026 3026
9 78449759 78453158 + XM_039041777.1 Bhi09g03027 3027
12 28284416 28286159 - BLOR05063 Blo12g01044 1044
12 28287825 28292852 + BLOR05064 Blo12g01045 1045
12 28294284 28298448 + BLOR05065 Blo12g01046 1046
12 28305538 28306837 + BLOR05067 Blo12g01048 1048
12 28308037 28311149 + BLOR05068 Blo12g01049 1049
18 265747 267900 - BLOR08528 Blo18g00040 40
1 17077039 17080409 - Bma001577.3 Bma01g01262 1262
4 774096 775777 - Bma018544.1 Bma04g00095 95
4 786381 790723 - Bma031082 Bma04g00097 97
4 792116 797192 - Bma031083 Bma04g00098 98
4 797781 799733 + Bma018546.1 Bma04g00099 99
2 3446328 3451211 + Bpe008372.1 Bpe02g00533 533
2 16081242 16084605 + Bpe009119.1 Bpe02g01263 1263
2 16085611 16086268 + Bpe009120.1 Bpe02g01264 1264
2 16086942 16090674 - Bpe009121.1 Bpe02g01265 1265
4 643624 646716 - Bpe014809.1 Bpe04g00086 86
4 648243 649528 - Bpe025574 Bpe04g00087 87
4 656553 660937 - Bpe014811.1 Bpe04g00089 89
4 662151 667270 - Bpe014812.1 Bpe04g00090 90
4 668122 669654 + Bpe014813.1 Bpe04g00091 91
5 26621419 26624671 - CaPI482276_05g017830.1 Cam05g1783 1783
5 26670931 26677716 - CaPI482276_05g017860.1 Cam05g1786 1786
5 26678030 26679660 + CaPI482276_05g017870.1 Cam05g1787 1787
5 26681174 26681476 + CaPI482276_05g017880.1 Cam05g1788 1788
5 26682191 26685352 - CaPI482276_05g017890.1 Cam05g1789 1789
8 24491265 24491874 + CaPI482276_08g018380.1 Cam08g1838 1838
1 11618113 11620576 + Carg10752-RA Car01g01285 1285
1 11620677 11620979 - Carg10751-RA Car01g01286 1286
1 11623097 11624292 - Carg10749-RA Car01g01288 1288
1 11625862 11633888 - Carg10748-RA Car01g01289 1289
1 11635799 11641150 - Carg10747-RA Car01g01290 1290
1 11642947 11645893 + Carg10746-RA Car01g01291 1291
5 1619451 1620376 - Carg09366-RA Car05g00293 293
9 1920061 1923298 - Carg02831-RA Car09g00351 351
9 1924537 1929539 + Carg02832-RA Car09g00352 352
9 1935454 1937373 + Carg02834-RA Car09g00354 354
9 1937356 1941568 - Carg02835-RA Car09g00355 355
12 2220059 2225156 + Carg03956-RA Car12g00349 349
5 27415769 27419009 - CcPI632755_05g018480.1 Cco05g1848 1848
5 27451518 27456672 - CcPI632755_05g018510.1 Cco05g1851 1851
5 27458705 27460906 + CcPI632755_05g018520.1 Cco05g1852 1852
5 27461999 27462301 + CcPI632755_05g018530.1 Cco05g1853 1853
5 27463011 27466145 - CcPI632755_05g018540.1 Cco05g1854 1854
8 27154321 27154930 + CcPI632755_08g015490.1 Cco08g1549 1549
5 29763805 29766771 - CePI673135_05g017890.1 Cec05g1789 1789
5 29808294 29813434 - CePI673135_05g017920.1 Cec05g1792 1792
5 29816207 29817824 + CePI673135_05g017930.1 Cec05g1793 1793
5 29819319 29819621 + CePI673135_05g017940.1 Cec05g1794 1794
5 29820333 29823496 - CePI673135_05g017950.1 Cec05g1795 1795
8 26008340 26008949 + CePI673135_08g014170.1 Cec08g1417 1417
3 14196009 14196634 - Chy3G060610.1 Chy03g01081 1081
5 26825013 26828200 - ClG42_05g0177100.10 Clacu05g1771 1771
5 26878398 26883535 - ClG42_05g0177400.10 Clacu05g1774 1774
5 26885456 26887094 + ClG42_05g0177500.10 Clacu05g1775 1775
5 26888587 26888889 + ClG42_05g0177600.10 Clacu05g1776 1776
5 26889563 26892728 - ClG42_05g0177700.10 Clacu05g1777 1777
8 25231883 25232493 + ClG42_08g0153300.10 Clacu08g1533 1533
5 28332654 28336247 - ClCG05G016180.1 Cla05g01668 1668
5 28393446 28399022 - ClCG05G016210.2 Cla05g01671 1671
5 28400628 28402666 + ClCG05G016220.2 Cla05g01672 1672
5 28404037 28404848 + ClCG05G016230.1 Cla05g01673 1673
5 28404702 28408316 - ClCG05G016240.2 Cla05g01674 1674
8 26575174 26575950 + ClCG08G013730.1 Cla08g01369 1369
1 11415131 11418440 + CmaCh01G016700.1 Cma01g01670 1670
1 11418891 11419193 - CmaCh01G016720.1 Cma01g01672 1672
1 11419501 11422048 - CmaCh01G016730.1 Cma01g01673 1673
1 11423158 11431584 - CmaCh01G016740.1 Cma01g01674 1674
1 11433259 11439254 - CmaCh01G016750.1 Cma01g01675 1675
1 11441095 11443850 + CmaCh01G016760.1 Cma01g01676 1676
5 1531886 1534103 - CmaCh05G003470.1 Cma05g00347 347
9 1696017 1699367 - CmaCh09G004000.1 Cma09g00400 400
9 1700705 1706150 + CmaCh09G004010.1 Cma09g00401 401
9 1711527 1712734 + CmaCh09G004030.1 Cma09g00403 403
9 1714011 1717837 - CmaCh09G004050.1 Cma09g00405 405
12 1874711 1876151 + CmaCh12G003660.1 Cma12g00366 366
7 257040 261095 + MELO3C017042.2.1 Cme07g00041 41
7 845304 848917 + MELO3C016956.2.1 Cme07g00127 127
7 849316 849632 - MELO3C016955.2.1 Cme07g00129 129
7 870114 875548 - MELO3C016952.2.1 Cme07g00133 133
7 878626 882238 + MELO3C016951.2.1 Cme07g00134 134
3 4655778 4655963 + PI0024647.1 Cmetu03g2012 2012
7 23905766 23908197 + PI0024016.1 Cmetu07g0231 231
7 23920252 23923120 + PI0006647.1 Cmetu07g1233 1233
7 23909870 23910172 + PI0002461.1 Cmetu07g1461 1461
7 23878289 23881501 - PI0008190.1 Cmetu07g1848 1848
7 23892294 23904385 + PI0016156.2 Cmetu07g2290 2290
1 12890120 12893701 + CmoCh01G017190.1 Cmo01g01719 1719
1 12893876 12894178 - CmoCh01G017200.1 Cmo01g01720 1720
1 12895114 12897635 - CmoCh01G017210.1 Cmo01g01721 1721
1 12898714 12902069 - CmoCh01G017220.1 Cmo01g01722 1722
1 12910386 12916457 - CmoCh01G017250.1 Cmo01g01725 1725
1 12918033 12921300 + CmoCh01G017260.1 Cmo01g01726 1726
5 1574445 1575787 - CmoCh05G003510.1 Cmo05g00351 351
9 1771258 1775168 - CmoCh09G004030.1 Cmo09g00403 403
9 1776429 1781418 + CmoCh09G004040.1 Cmo09g00404 404
9 1787192 1788412 + CmoCh09G004070.1 Cmo09g00407 407
9 1789958 1793361 - CmoCh09G004100.1 Cmo09g00410 410
12 1988556 1990055 + CmoCh12G003190.1 Cmo12g00319 319
5 26543918 26547105 - CmPI595203_05g016560.1 Cmu05g1656 1656
5 26597370 26602507 - CmPI595203_05g016590.1 Cmu05g1659 1659
5 26604429 26606072 + CmPI595203_05g016600.1 Cmu05g1660 1660
5 26607570 26607872 + CmPI595203_05g016610.1 Cmu05g1661 1661
5 26608546 26611711 - CmPI595203_05g016620.1 Cmu05g1662 1662
4 12827825 12829683 - Conep04aG0179500.1 Cone4ag1740 1740
4 12829972 12833727 - Conep04aG0179600.1 Cone4ag1741 1741
4 12839235 12843566 - Conep04aG0179800.1 Cone4ag1743 1743
7 11156141 11157893 - Conep07aG0170900.1 Cone7ag1660 1660
7 11158108 11161766 - Conep07aG0171000.1 Cone7ag1661 1661
7 11166828 11170543 - Conep07aG0171200.1 Cone7ag1663 1663
17 7547006 7551246 + Conep17aG0100300.1 Cone17ag0976 976
17 7551636 7553149 + Conep17aG0100400.1 Cone17ag0977 977
17 7553243 7553909 - Conep17aG0100500.1 Cone17ag0978 978
17 7555238 7558211 - Conep17aG0100600.1 Cone17ag0979 979
20 1410362 1414655 + Conep20aG0033100.1 Cone20ag0318 318
20 1416036 1416572 - Conep20aG0033200.1 Cone20ag0319 319
20 1418271 1421274 - Conep20aG0033300.1 Cone20ag0320 320
2 1665192 1668246 - Cp4.1LG02g05510.1 Cpe02g00315 315
2 1669715 1675560 + Cp4.1LG02g05590.1 Cpe02g00316 316
2 1677448 1685907 + Cp4.1LG02g05640.1 Cpe02g00317 317
2 1686687 1689268 + Cp4.1LG02g05560.1 Cpe02g00318 318
2 1690242 1690544 + Cp4.1LG02g05540.1 Cpe02g00320 320
2 1695416 1699700 + Cp4.1LG02g05610.1 Cpe02g00321 321
6 1573904 1578058 - Cp4.1LG06g02890.1 Cpe06g00287 287
6 1578984 1584725 + Cp4.1LG06g02750.1 Cpe06g00288 288
6 1590043 1591988 + Cp4.1LG06g02900.1 Cpe06g00290 290
6 1592619 1596466 - Cp4.1LG06g03000.1 Cpe06g00291 291
7 2102734 2104271 + Cp4.1LG07g03160.1 Cpe07g00325 325
5 29793379 29796550 - CrPI670011_05g017850.1 Cre05g1785 1785
5 29839177 29840834 + CrPI670011_05g017890.1 Cre05g1789 1789
5 29842340 29842642 + CrPI670011_05g017900.1 Cre05g1790 1790
5 29843371 29846532 - CrPI670011_05g017910.1 Cre05g1791 1791
8 26292352 26292961 + CrPI670011_08g013160.1 Cre08g1316 1316
1 84355553 84359445 - Hsped.01g19530.1 Hepe01g1953 1953
1 84389450 84392041 + Hsped.01g19570.1 Hepe01g1957 1957
1 84392923 84393225 + Hsped.01g19590.1 Hepe01g1959 1959
10 2168595 2169377 - Hsped.10g02150.1 Hepe10g0215 215
13 37323574 37325721 + Maker00033964 Lcy13g1834 1834
4 21198669 21202396 + Lsi04G013410.1 Lsi04g01341 1341
4 21202150 21203059 - Lsi04G013420.1 Lsi04g01342 1342
4 21205292 21206698 - Lsi04G013430.1 Lsi04g01343 1343
4 21213825 21222396 - Lsi04G013460.1 Lsi04g01346 1346
4 21227360 21233949 - Lsi04G013470.1 Lsi04g01347 1347
4 21240467 21246379 + Lsi04G013480.1 Lsi04g01348 1348
4 27778890 27781458 + Lsi04G020650.1 Lsi04g02065 2065
8 20976998 20979817 + Lsi08G012510.1 Lsi08g01251 1251
11 3115333 3119175 - MC11g0395 Mch11g0490 490
11 3141809 3144097 + MC11g0399 Mch11g0495 495
11 3145309 3145623 + MC11g0401 Mch11g0497 497
5 31320574 31324930 - Sed0014655.1 Sed05g1748 1748
5 31337731 31341572 - Sed0015580.3 Sed05g1752 1752
5 31356568 31360683 + Sed0020114.1 Sed05g1755 1755
8 3957233 3957675 + Sed0002480.1 Sed08g0580 580
11 27170074 27171021 - Sed0000952.1 Sed11g1139 1139
13 24458326 24467021 + Sed0021743.2 Sed13g1956 1956
1 100539945 100543530 - Tan0007222.1 Tan01g3538 3538
1 100545887 100551599 + Tan0018994.1 Tan01g3539 3539
1 100557282 100567291 + Tan0004998.7 Tan01g3547 3547
1 100573937 100575519 + Tan0019162.2 Tan01g3551 3551
1 100576959 100577545 + Tan0005300.1 Tan01g3552 3552
1 100590122 100593881 + Tan0010685.1 Tan01g3554 3554
2 96006214 96011477 + Tan0019092.1 Tan02g2764 2764
4 6637505 6644647 + Vvi4g582 Vvi4g582 582
4 6654257 6654769 - Vvi4g583 Vvi4g583 583
4 6657069 6658020 + Vvi4g584 Vvi4g584 584
4 6665973 6668116 - Vvi4g585 Vvi4g585 585
4 6678207 6682125 + Vvi4g586 Vvi4g586 586
4 6686871 6688595 + Vvi4g587 Vvi4g587 587
4 6710109 6726284 - Vvi4g588 Vvi4g588 588
4 6751662 6752535 - Vvi4g589 Vvi4g589 589
4 6768476 6777086 - Vvi4g590 Vvi4g590 590
4 6786213 6792883 + Vvi4g591 Vvi4g591 591
       

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