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
Vvi19g1004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1006 . . . . . . . Bma13g00893 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0276 . . . . . . . . . . Bda12g00774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1007 . . . . . . . . Cmo16g00527 Cmo04g00662 Cma01g01332 . . . . . . . . . . . . . Cla11g01639 Cam11g1705 Cec11g1731 Cco11g1727 Clacu11g1861 Cmu11g1673 Cre11g2088 . . . . Lsi04g01921 . . Cme07g00692 . . . . . . . . . Cmo01g01388 Cmo09g00703 Cma04g00616 Cma16g00486 . . . . . . . . . . . Cla07g01033 Cam07g1472 Cec07g1186 Cco07g1163 Clacu07g1088 Cmu07g1076 Cre07g1452 . . Chy07g01074 .
Vvi19g1008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1009 . . . . . . . . . . . . . . Sed05g1856 Cpe04g00854 . Bhi05g02031 Tan02g0066 Cmetu01g2586 Lac12g0881 Hepe02g0032 . . Cla02g01808 Cam02g1911 Cec02g1931 Cco02g1975 Clacu02g1893 Cmu02g1838 Cre02g2155 . . . . . Csa07g01181 . Cme11g01580 Blo15g00602 . . . . . . Bma12g00622 Sed01g0743 . . . . . . . . Bhi10g00978 Tan05g0620 Cmetu11g1616 . Hepe08g0623 . . . . . . . . . . Csa06g01179 Chy11g01014 Cme01g01539
Vvi19g1010 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g01809 Cam02g1912 Cec02g1932 Cco02g1976 Clacu02g1894 Cmu02g1839 Cre02g2156 . . . . . . . Cme11g01581 Blo15g00603 . . . . . . . Sed05g3285 . . . . . . . . Bhi10g00977 Tan05g0619 Cmetu11g1548 . . . . . . . . . . . . Csa06g01178 Chy11g01015 .
Vvi19g1011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1012 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g01810 Cam02g1914 Cec02g1935 Cco02g1979 Clacu02g1896 Cmu02g1841 Cre02g2158 . . . . . . . Cme11g01583 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01177 . .
Vvi19g1013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 36433106 36434602 - Bda009268.1 Bda12g00774 774
5 62319939 62321538 - XM_039032925.1 Bhi05g02031 2031
10 19999613 20002722 + XM_039044368.1 Bhi10g00977 977
10 20027390 20028512 - XM_039044809.1 Bhi10g00978 978
15 14277965 14279682 + BLOR06996 Blo15g00602 602
15 14325253 14326429 - BLOR06997 Blo15g00603 603
12 27473867 27474639 - Bma007798.1 Bma12g00622 622
13 38897408 38899496 - Bma009967.1 Bma13g00893 893
2 32167499 32168510 + CaPI482276_02g019110.1 Cam02g1911 1911
2 32182363 32185184 - CaPI482276_02g019120.1 Cam02g1912 1912
2 32193088 32196265 - CaPI482276_02g019140.1 Cam02g1914 1914
7 29361510 29361917 - CaPI482276_07g014720.1 Cam07g1472 1472
11 29735025 29735432 + CaPI482276_11g017050.1 Cam11g1705 1705
2 32675318 32675999 + CcPI632755_02g019750.1 Cco02g1975 1975
2 32691933 32693819 - CcPI632755_02g019760.1 Cco02g1976 1976
2 32701921 32706357 - CcPI632755_02g019790.1 Cco02g1979 1979
7 25363833 25364240 + CcPI632755_07g011630.1 Cco07g1163 1163
11 30123123 30123530 + CcPI632755_11g017270.1 Cco11g1727 1727
2 37172659 37173700 + CePI673135_02g019310.1 Cec02g1931 1931
2 37189910 37191779 - CePI673135_02g019320.1 Cec02g1932 1932
2 37200543 37203726 - CePI673135_02g019350.1 Cec02g1935 1935
7 27253010 27254763 + CePI673135_07g011860.1 Cec07g1186 1186
11 31574694 31575101 + CePI673135_11g017310.1 Cec11g1731 1731
7 15692675 15694757 + Chy7G139040.1 Chy07g01074 1074
11 14322232 14330793 + Chy11G195940.1 Chy11g01014 1014
11 14335381 14338122 - Chy11G195950.1 Chy11g01015 1015
2 32425854 32426856 + ClG42_02g0189300.10 Clacu02g1893 1893
2 32441137 32443918 - ClG42_02g0189400.10 Clacu02g1894 1894
2 32451860 32455031 - ClG42_02g0189600.10 Clacu02g1896 1896
7 25433169 25433576 + ClG42_07g0108800.10 Clacu07g1088 1088
11 29755647 29756054 + ClG42_11g0186100.10 Clacu11g1861 1861
2 33113817 33114867 + ClCG02G018470.1 Cla02g01808 1808
2 33129917 33132980 - ClCG02G018480.1 Cla02g01809 1809
2 33134579 33148945 - ClCG02G018490.2 Cla02g01810 1810
7 26781794 26790057 + ClCG07G010880.1 Cla07g01033 1033
11 30083400 30083807 + ClCG11G016790.1 Cla11g01639 1639
1 9548659 9549192 + CmaCh01G013320.1 Cma01g01332 1332
4 3152197 3152604 - CmaCh04G006160.1 Cma04g00616 616
16 2466579 2469177 + CmaCh16G004860.1 Cma16g00486 486
1 20443752 20445840 - MELO3C012628.2.1 Cme01g01539 1539
7 5966460 5967150 + MELO3C026403.2.1 Cme07g00692 692
11 23447082 23449263 + MELO3C019673.2.1 Cme11g01580 1580
11 23466574 23469085 - MELO3C019670.2.1 Cme11g01581 1581
11 23495891 23497556 - MELO3C019668.2.1 Cme11g01583 1583
1 7554086 7556285 - PI0025577.1 Cmetu01g2586 2586
11 9175084 9178982 + PI0024260.1 Cmetu11g1548 1548
11 9191631 9192669 - PI0023590.1 Cmetu11g1616 1616
1 10954119 10954526 + CmoCh01G013880.1 Cmo01g01388 1388
4 3294916 3295323 - CmoCh04G006620.1 Cmo04g00662 662
9 3467714 3469580 - CmoCh09G007030.1 Cmo09g00703 703
16 2547989 2550129 + CmoCh16G005270.1 Cmo16g00527 527
2 32288231 32289230 + CmPI595203_02g018380.1 Cmu02g1838 1838
2 32303472 32306251 - CmPI595203_02g018390.1 Cmu02g1839 1839
2 32314199 32317370 - CmPI595203_02g018410.1 Cmu02g1841 1841
7 25683659 25684066 + CmPI595203_07g010760.1 Cmu07g1076 1076
11 29008436 29008843 + CmPI595203_11g016730.1 Cmu11g1673 1673
6 1275499 1277362 + Conep06aG0027800.1 Cone6ag0276 276
4 7881190 7883535 + Cp4.1LG04g02300.1 Cpe04g00854 854
2 35124200 35125197 + CrPI670011_02g021550.1 Cre02g2155 2155
2 35141066 35142885 - CrPI670011_02g021560.1 Cre02g2156 2156
2 35151069 35154252 - CrPI670011_02g021580.1 Cre02g2158 2158
7 29610537 29610944 + CrPI670011_07g014520.1 Cre07g1452 1452
11 32677469 32677876 + CrPI670011_11g020880.1 Cre11g2088 2088
6 9940476 9945545 + CsaV3_6G013750.1 Csa06g01177 1177
6 9945760 9948942 + CsaV3_6G013760.1 Csa06g01178 1178
6 9958663 9960142 - CsaV3_6G013770.1 Csa06g01179 1179
7 11583959 11586508 + CsaV3_7G022700.1 Csa07g01181 1181
2 478310 479809 - Hsped.02g00320.1 Hepe02g0032 32
8 5487758 5489007 + Hsped.08g06230.1 Hepe08g0623 623
12 9169252 9170468 + Lag0015253.1 Lac12g0881 881
4 26406071 26410891 + Lsi04G019210.1 Lsi04g01921 1921
1 5473607 5474986 + Sed0011131.2 Sed01g0743 743
5 32009812 32012127 - Sed0026558.1 Sed05g1856 1856
5 42222459 42226598 - Sed0013658.1 Sed05g3285 3285
2 867886 869672 - Tan0008912.1 Tan02g0066 66
5 4568283 4572026 + Tan0013939.2 Tan05g0619 619
5 4584647 4586332 - Tan0017641.1 Tan05g0620 620
19 19813959 19816800 + Vvi19g1004 Vvi19g1004 1004
19 19846205 19847357 + Vvi19g1005 Vvi19g1005 1005
19 19894726 19903429 + Vvi19g1006 Vvi19g1006 1006
19 19906332 19906912 + Vvi19g1007 Vvi19g1007 1007
19 19907420 19915676 + Vvi19g1008 Vvi19g1008 1008
19 19941483 19950657 - Vvi19g1009 Vvi19g1009 1009
19 19951145 19968808 - Vvi19g1010 Vvi19g1010 1010
19 19970562 19972299 + Vvi19g1011 Vvi19g1011 1011
19 19972383 19975720 - Vvi19g1012 Vvi19g1012 1012
19 20024721 20025572 - Vvi19g1013 Vvi19g1013 1013
       

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