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
Vvi4g1112 Blo04g00885 Blo16g00079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g00961 . . . . Cma16g01237 . . . . . . . . . . . . . . . . . . . Lsi07g01105 . . .
Vvi4g1113 . Blo16g00080 . Bda10g00183 . Bpe13g00415 . Bma15g00946 . . Cma03g00686 Cma07g00428 Car03g00632 Car07g00375 . Cpe19g00859 Cpe10g00663 Bhi03g00867 . . . . . . Cla01g01979 Cam01g2073 Cec04g1732 Cco04g1797 Clacu01g2094 Cmu01g1970 Cre04g1645 . . . . Lsi01g00602 . Chy07g01192 Cme08g00926 . . Bda11g01836 . Bpe10g00155 . . Bma06g00096 . Cmo03g00711 Cmo07g00425 . . . . . . . . . . . . . . . . . . . . . Csa06g03324 Chy02g00574 .
Vvi4g1114 Blo04g00884 . . . . . . . . . Cma03g00685 Cma07g00427 Car03g00631 Car07g00374 Sed14g1197 Cpe19g00860 Cpe10g00664 Bhi03g00866 Tan03g2084 Cmetu04g0958 . Hepe04g1592 . . Cla01g01980 Cam01g2074 Cec04g1733 Cco04g1798 Clacu01g2095 Cmu01g1971 Cre04g1646 Cone8ag0851 Cone12ag0715 . . Lsi01g00601 . . Cme08g00928 . . . . . . Bma03g00960 . Sed01g0221 Cmo03g00709 Cmo07g00424 . . . . . . Bhi10g01891 Tan05g1191 Cmetu11g1417 . Hepe08g0945 . . . . . . . . . . Csa06g03326 Chy02g00573 .
Vvi4g1115 . . . Bda10g00185 . . . . . . . Cma07g00426 . Car07g00373 Sed10g0999 . . Bhi03g00865 Tan03g2085 Cmetu04g0755 . Hepe04g1593 . . . . . . . . . . . Cone6ag1683 . Lsi01g00600 . . . . Blo06g00300 . . . . . . . . Cmo07g00423 . . . . . . . . . . . . . . . . . . . . . . Chy02g00572 .
Vvi4g1116 . . . . . . . Bma15g00943 . . . . . . . Cpe19g00861 . . . . . . . . Cla01g01981 Cam01g2075 Cec04g1734 Cco04g1799 Clacu01g2096 Cmu01g1972 Cre04g1647 . . . . . . . Cme08g00929 . . . . Bpe10g00156 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03327 . .
Vvi4g1117 . . . . . . . Bma15g00941 . . Cma03g00681 Cma07g00424 Car03g00628 Car07g00371 Sed14g1200 Cpe19g00863 Cpe10g00667 Bhi03g00862 Tan03g2088 Cmetu04g1901 . Hepe04g1596 . . Cla01g01984 Cam01g2077 Cec04g1736 Cco04g1802 Clacu01g2099 Cmu01g1974 Cre04g1650 . . Cone6ag1684 Cone9ag1606 Lsi01g00597 . . Cme08g00933 Blo05g00710 Blo06g00299 . . Bpe10g00158 Bpe06g00129 . . Sed01g0209 Cmo03g00706 Cmo07g00421 . . . . . . Bhi10g01872 Tan05g1164 Cmetu11g2261 . Hepe08g0276 . . . . . . . . . . Csa06g03331 Chy02g00569 .
Vvi4g1118 . Blo16g00081 . . . Bpe13g00414 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1685 Cone9ag1607 . . . . . . Bda11g01835 . . . . Bma06g00095 . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01103 . . .
Vvi4g1119 Blo04g00883 . . . Bpe15g00473 Bpe13g00413 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0853 Cone12ag0714 Cone6ag1686 . . . . . . . Bda11g01834 . . . Bma03g00959 Bma06g00094 . . . Cma16g01239 . . . . . . . . . . . . . . . . . . . Lsi07g01102 . . .
Vvi4g1120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1121 Blo04g00882 Blo16g00082 . . . . . . . . Cma03g00680 Cma07g00423 . . . . Cpe10g00668 Bhi03g00861 Tan03g2089 Cmetu04g0243 . . . . . . . . . . . . . . Cone9ag1608 Lsi01g00595 . . Cme08g00937 Blo05g00709 . . . . . Bma03g00958 Bma06g00093 Sed05g3598 Cmo03g00705 Cmo07g00420 Cma16g01240 Cma20g00764 . . . . Bhi10g01870 Tan05g1162 Cmetu11g0544 . . . . . . . . . . . Lsi07g01100 Csa06g03333 Chy02g00567 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 5990363 5992734 + Bda006680.1 Bda10g00183 183
10 6107878 6112782 - Bda006685.2 Bda10g00185 185
11 53574057 53574818 - Bda008771.1 Bda11g01834 1834
11 53575309 53577312 - Bda008772.1 Bda11g01835 1835
11 53578563 53582092 - Bda008773.1 Bda11g01836 1836
3 15782764 15785076 - XM_039027167.1 Bhi03g00861 861
3 15819344 15821897 - XM_039026727.1 Bhi03g00862 862
3 15872412 15880760 - XM_039025365.1 Bhi03g00865 865
3 15881477 15884988 + XM_039025366.1 Bhi03g00866 866
3 15888403 15893585 - XM_039026615.1 Bhi03g00867 867
10 46621274 46623585 - XM_039046774.1 Bhi10g01870 1870
10 46709921 46712234 - XM_039045005.1 Bhi10g01872 1872
10 47505098 47508860 + XM_039046607.1 Bhi10g01891 1891
4 10098299 10099418 - BLOR13794 Blo04g00882 882
4 10115411 10138603 - BLOR13795 Blo04g00883 883
4 10141757 10143310 + BLOR13796 Blo04g00884 884
4 10143794 10144458 - BLOR13797 Blo04g00885 885
5 24415784 24417766 - BLOR15671 Blo05g00709 709
5 24511028 24512944 + BLOR15672 Blo05g00710 710
6 16686477 16688423 - BLOR16882 Blo06g00299 299
6 17092980 17100728 + BLOR16883 Blo06g00300 300
16 2182628 2184209 + BLOR07327 Blo16g00079 79
16 2200235 2203590 + BLOR07328 Blo16g00080 80
16 2206795 2208739 + BLOR07329 Blo16g00081 81
16 2209602 2215792 + BLOR07330 Blo16g00082 82
3 10178704 10189786 - Bma017297.1 Bma03g00958 958
3 10191490 10192260 - Bma017298.1 Bma03g00959 959
3 10194011 10195046 + Bma017299.1 Bma03g00960 960
3 10204288 10205555 - Bma017300.1 Bma03g00961 961
6 1413130 1414337 - Bma022711.1 Bma06g00093 93
6 1428808 1429581 - Bma022713.1 Bma06g00094 94
6 1430049 1432135 - Bma031263 Bma06g00095 95
6 1433623 1437085 - Bma022714.1 Bma06g00096 96
15 34535918 34537870 - Bma014183.1 Bma15g00941 941
15 34733530 35076573 - Bma030836 Bma15g00943 943
15 35102709 35105052 - Bma014201.1 Bma15g00946 946
6 2215824 2217746 + Bpe019580.1 Bpe06g00129 129
10 3692761 3696495 + Bpe002464.2 Bpe10g00155 155
10 3723008 3729303 + Bpe002466.1 Bpe10g00156 156
10 3818988 3820934 + Bpe002469.1 Bpe10g00158 158
13 11820036 11820791 - Bpe006538.2 Bpe13g00413 413
13 11821289 11823281 - Bpe006539.1 Bpe13g00414 414
13 11823934 11827472 - Bpe006540.1 Bpe13g00415 415
15 16077605 16078390 + Bpe001407.1 Bpe15g00473 473
1 33796468 33800897 + CaPI482276_01g020730.1 Cam01g2073 2073
1 33802738 33805497 - CaPI482276_01g020740.1 Cam01g2074 2074
1 33806411 33812144 + CaPI482276_01g020750.1 Cam01g2075 2075
1 33840661 33842631 + CaPI482276_01g020770.1 Cam01g2077 2077
3 5725110 5727080 - Carg00588-RA Car03g00628 628
3 5736414 5739455 + Carg00591-RA Car03g00631 631
3 5740646 5745320 - Carg00592-RA Car03g00632 632
7 1853404 1855374 - Carg07951-RA Car07g00371 371
7 1862515 1867859 - Carg07953-RA Car07g00373 373
7 1868212 1872290 + Carg07954-RA Car07g00374 374
7 1872268 1876838 - Carg07955-RA Car07g00375 375
4 32869657 32874074 + CcPI632755_04g017970.1 Cco04g1797 1797
4 32875983 32878737 - CcPI632755_04g017980.1 Cco04g1798 1798
4 32879712 32885323 + CcPI632755_04g017990.1 Cco04g1799 1799
4 32911484 32913454 + CcPI632755_04g018020.1 Cco04g1802 1802
4 36361177 36365584 + CePI673135_04g017320.1 Cec04g1732 1732
4 36367063 36370249 - CePI673135_04g017330.1 Cec04g1733 1733
4 36371429 36377020 + CePI673135_04g017340.1 Cec04g1734 1734
4 36403182 36405152 + CePI673135_04g017360.1 Cec04g1736 1736
2 3412351 3413733 - Chy2G028340.1 Chy02g00567 567
2 3421212 3423185 - Chy2G028360.1 Chy02g00569 569
2 3442561 3448108 - Chy2G028390.1 Chy02g00572 572
2 3449042 3451636 + Chy2G028400.1 Chy02g00573 573
2 3453503 3457799 - Chy2G028410.1 Chy02g00574 574
7 16775357 16779522 + Chy7G140220.1 Chy07g01192 1192
1 32652493 32658582 + ClG42_01g0209400.10 Clacu01g2094 2094
1 32658842 32661602 - ClG42_01g0209500.10 Clacu01g2095 2095
1 32661776 32668253 + ClG42_01g0209600.10 Clacu01g2096 2096
1 32695506 32697476 + ClG42_01g0209900.10 Clacu01g2099 2099
1 34444185 34449559 + ClCG01G020310.2 Cla01g01979 1979
1 34450499 34453773 - ClCG01G020320.1 Cla01g01980 1980
1 34454589 34461909 + ClCG01G020330.1 Cla01g01981 1981
1 34487724 34489694 + ClCG01G020350.1 Cla01g01984 1984
3 5628886 5630563 - CmaCh03G006800.1 Cma03g00680 680
3 5634137 5636107 - CmaCh03G006810.1 Cma03g00681 681
3 5646124 5649405 + CmaCh03G006850.1 Cma03g00685 685
3 5649956 5654985 - CmaCh03G006860.1 Cma03g00686 686
7 1816089 1817784 - CmaCh07G004230.1 Cma07g00423 423
7 1819468 1821438 - CmaCh07G004240.1 Cma07g00424 424
7 1828317 1834524 - CmaCh07G004260.1 Cma07g00426 426
7 1835142 1838621 + CmaCh07G004270.1 Cma07g00427 427
7 1838714 1844093 - CmaCh07G004280.1 Cma07g00428 428
16 9362199 9365013 + CmaCh16G012370.1 Cma16g01237 1237
16 9367876 9370147 + CmaCh16G012390.1 Cma16g01239 1239
16 9373372 9376657 + CmaCh16G012400.1 Cma16g01240 1240
20 3604467 3606270 - CmaCh20G007640.1 Cma20g00764 764
8 6117065 6121899 + MELO3C007904.2.1 Cme08g00926 926
8 6123063 6126600 - MELO3C007905.2.1 Cme08g00928 928
8 6126800 6133187 + MELO3C007906.2.1 Cme08g00929 929
8 6154064 6156504 + MELO3C007909.2.1 Cme08g00933 933
8 6165372 6166939 + MELO3C007912.2.1 Cme08g00937 937
4 3678023 3679567 - PI0010675.1 Cmetu04g0243 243
4 3712903 3718398 - PI0017975.1 Cmetu04g0755 755
4 3719570 3722963 + PI0028146.2 Cmetu04g0958 958
4 3688517 3690486 - PI0022986.1 Cmetu04g1901 1901
11 28436243 28439751 + PI0012558.2 Cmetu11g0544 544
11 28240320 28242916 - PI0004209.1 Cmetu11g1417 1417
11 28412065 28414237 + PI0004525.1 Cmetu11g2261 2261
3 6122594 6124318 - CmoCh03G007050.1 Cmo03g00705 705
3 6127439 6129409 - CmoCh03G007060.1 Cmo03g00706 706
3 6141152 6144495 + CmoCh03G007090.1 Cmo03g00709 709
3 6145380 6150102 - CmoCh03G007110.1 Cmo03g00711 711
7 1903420 1904713 - CmoCh07G004200.1 Cmo07g00420 420
7 1906404 1908374 - CmoCh07G004210.1 Cmo07g00421 421
7 1915641 1921729 - CmoCh07G004230.1 Cmo07g00423 423
7 1922093 1926789 + CmoCh07G004240.1 Cmo07g00424 424
7 1926823 1934331 - CmoCh07G004250.1 Cmo07g00425 425
1 32989900 32995990 + CmPI595203_01g019700.1 Cmu01g1970 1970
1 32996250 32999010 - CmPI595203_01g019710.1 Cmu01g1971 1971
1 32999183 33005660 + CmPI595203_01g019720.1 Cmu01g1972 1972
1 33033026 33034996 + CmPI595203_01g019740.1 Cmu01g1974 1974
6 12768990 12772563 + Conep06aG0174800.1 Cone6ag1683 1683
6 12774870 12777303 + Conep06aG0174900.1 Cone6ag1684 1684
6 12779373 12781533 + Conep06aG0175000.1 Cone6ag1685 1685
6 12782102 12783239 + Conep06aG0175100.1 Cone6ag1686 1686
8 8463240 8466431 - Conep08aG0087700.1 Cone8ag0851 851
8 8472957 8474322 + Conep08aG0087900.1 Cone8ag0853 853
9 11495450 11497828 + Conep09aG0165600.1 Cone9ag1606 1606
9 11498760 11501994 + Conep09aG0165700.1 Cone9ag1607 1607
9 11503598 11505277 + Conep09aG0165800.1 Cone9ag1608 1608
12 6597626 6598895 - Conep12aG0073700.1 Cone12ag0714 714
12 6609367 6612928 + Conep12aG0073800.1 Cone12ag0715 715
10 3829441 3834261 + Cp4.1LG10g00280.1 Cpe10g00663 663
10 3835404 3838820 - Cp4.1LG10g00190.1 Cpe10g00664 664
10 3848663 3850633 + Cp4.1LG10g00290.1 Cpe10g00667 667
10 3853700 3855532 + Cp4.1LG10g00250.1 Cpe10g00668 668
19 6350188 6356825 + Cp4.1LG19g08920.1 Cpe19g00859 859
19 6354924 6359374 - Cp4.1LG19g08860.1 Cpe19g00860 860
19 6359837 6365839 + Cp4.1LG19g08950.1 Cpe19g00861 861
19 6372160 6374130 + Cp4.1LG19g08700.1 Cpe19g00863 863
4 34838414 34842842 + CrPI670011_04g016450.1 Cre04g1645 1645
4 34844307 34847561 - CrPI670011_04g016460.1 Cre04g1646 1646
4 34848536 34854142 + CrPI670011_04g016470.1 Cre04g1647 1647
4 34882055 34884025 + CrPI670011_04g016500.1 Cre04g1650 1650
6 27808576 27814638 + CsaV3_6G047100.1 Csa06g03324 3324
6 27815147 27818761 - CsaV3_6G047120.1 Csa06g03326 3326
6 27819289 27824769 + CsaV3_6G047130.1 Csa06g03327 3327
6 27843274 27846390 + CsaV3_6G047170.1 Csa06g03331 3331
6 27851431 27853127 + CsaV3_6G047190.1 Csa06g03333 3333
4 71405335 71408671 - Hsped.04g15920.1 Hepe04g1592 1592
4 71409745 71414801 + Hsped.04g15930.1 Hepe04g1593 1593
4 71444173 71446512 + Hsped.04g15960.1 Hepe04g1596 1596
8 2496954 2498897 + Hsped.08g02760.1 Hepe08g0276 276
8 8751741 8755540 + Hsped.08g09450.1 Hepe08g0945 945
1 4750179 4751881 - Lsi01G005950.1 Lsi01g00595 595
1 4765863 4767833 - Lsi01G005970.1 Lsi01g00597 597
1 4795937 4801495 - Lsi01G006000.1 Lsi01g00600 600
1 4802303 4805715 + Lsi01G006010.1 Lsi01g00601 601
1 4806747 4812257 - Lsi01G006020.1 Lsi01g00602 602
7 16405759 16410026 - Lsi07G011000.1 Lsi07g01100 1100
7 16416031 16416840 - Lsi07G011020.1 Lsi07g01102 1102
7 16422076 16426919 - Lsi07G011030.1 Lsi07g01103 1103
7 16437375 16446406 - Lsi07G011050.1 Lsi07g01105 1105
1 1678412 1680597 - Sed0004005.1 Sed01g0209 209
1 1761469 1766515 + Sed0015022.2 Sed01g0221 221
5 44399214 44402040 + Sed0003388.2 Sed05g3598 3598
10 8609202 8615512 + Sed0019779.1 Sed10g0999 999
14 21229329 21233245 - Sed0015691.4 Sed14g1197 1197
14 21273493 21275974 + Sed0008611.1 Sed14g1200 1200
3 75709675 75713232 - Tan0006972.2 Tan03g2084 2084
3 75717290 75722396 + Tan0019407.1 Tan03g2085 2085
3 75768031 75770576 + Tan0004311.1 Tan03g2088 2088
3 75777090 75778995 + Tan0021889.1 Tan03g2089 2089
5 10679264 10681698 - Tan0007240.2 Tan05g1162 1162
5 10917445 10919655 - Tan0012668.1 Tan05g1164 1164
5 11789296 11797171 - Tan0014788.1 Tan05g1191 1191
4 19932425 19981450 + Vvi4g1112 Vvi4g1112 1112
4 20005135 20011413 + Vvi4g1113 Vvi4g1113 1113
4 20011687 20015380 - Vvi4g1114 Vvi4g1114 1114
4 20015676 20020532 + Vvi4g1115 Vvi4g1115 1115
4 20020598 20021567 + Vvi4g1116 Vvi4g1116 1116
4 20052329 20057465 + Vvi4g1117 Vvi4g1117 1117
4 20077076 20079876 + Vvi4g1118 Vvi4g1118 1118
4 20080785 20081788 + Vvi4g1119 Vvi4g1119 1119
4 20084813 20085182 - Vvi4g1120 Vvi4g1120 1120
4 20085217 20086815 + Vvi4g1121 Vvi4g1121 1121
       

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