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
Vvi1g1071 . . . . . . Bma14g01626 Bma15g00252 Cmo04g01061 Cmo18g01016 Cma04g00985 Cma18g01004 Car04g00922 Car18g00926 . Cpe09g00316 Cpe01g01333 . . . . . . . . . . . . . . Cone13ag0662 Cone19ag0659 . . Lsi04g00237 Csa05g02631 Chy10g01166 Cme10g00239 . . . . Bpe11g01621 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01191 . .
Vvi1g1072 . . . . . . . Bma15g00053 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0663 Cone19ag0660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1073 . . . . . . Bma14g01625 . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0665 Cone19ag0662 . . . . . . . . Bda07g01448 . Bpe11g01619 . . . . . Cmo15g00895 . Cma15g00860 . Car15g00811 . . . . . . . . . . . . . . . . . . Chy09g00445 Cme09g01240
Vvi1g1074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1075 Blo01g00385 . . . . . . . . . . . . . . . . Bhi07g00153 . . . Hepe01g0358 . . . . . . . . . . . . . . . Chy10g00095 Cme10g01125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01008 . .
Vvi1g1076 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1077 . . Bda01g02198 . . . Bma14g01624 . Cmo04g01053 . . . Car04g00918 . . . . Bhi07g00090 . . . . . . . . . . . . . Cone13ag0666 . . . . . . Cme10g01366 . . . . Bpe11g01617 . Bma01g00029 . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00964 . .
Vvi1g1078 . . . . . . Bma14g01623 Bma15g00051 . . . . . . . . . Bhi07g00089 . . . . . . . . . . . . . Cone13ag0667 Cone19ag0663 . . . . . Cme10g01363 . . . . Bpe11g01616 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00962 . .
Vvi1g1079 . . . . . . . . Cmo04g01052 . Cma04g00976 . Car04g00917 . . . . Bhi07g00087 . . . . . . . . . . . . . . . . . . . . Cme10g01362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00958 . .
Vvi1g1080 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma15g00864 . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57890277 57891733 + Bda004538.1 Bda01g02198 2198
7 26943135 26947268 + Bda028276.1 Bda07g01448 1448
7 4778167 4781864 - XM_039036435.1 Bhi07g00087 87
7 4869583 4875356 - XM_039035442.1 Bhi07g00089 89
7 4891532 4902800 - XM_039036485.1 Bhi07g00090 90
7 8162452 8165743 + XM_039037287.1 Bhi07g00153 153
1 4386882 4396151 - BLOR00385 Blo01g00385 385
1 395317 396736 + Bma030163 Bma01g00029 29
14 34219764 34223682 - Bma012330.1 Bma14g01623 1623
14 34253079 34261567 + Bma012331.1 Bma14g01624 1624
14 34280225 34284587 + Bma012332.1 Bma14g01625 1625
14 34297610 34305903 + Bma012333.1 Bma14g01626 1626
15 673307 676125 - Bma013025.1 Bma15g00051 51
15 710461 712734 + Bma013027.1 Bma15g00053 53
15 2515983 2517930 + Bma013237.1 Bma15g00252 252
11 12299737 12303868 - Bpe004933.1 Bpe11g01616 1616
11 12308888 12316796 + Bpe024852 Bpe11g01617 1617
11 12336107 12339907 + Bpe024853 Bpe11g01619 1619
11 12354878 12359824 + Bpe004936.1 Bpe11g01621 1621
4 5242340 5245927 - Carg00092-RA Car04g00917 917
4 5246731 5256203 - Carg00093-RA Car04g00918 918
4 5282794 5287025 + Carg00097-RA Car04g00922 922
15 4584120 4588782 + Carg01344-RA Car15g00811 811
18 10004979 10007310 + Carg19052-RA Car18g00926 926
9 3953594 3960617 + Chy9G161610.1 Chy09g00445 445
10 2430798 2431804 - Chy10G172890.1 Chy10g00095 95
10 16515367 16517886 - Chy10G183600.1 Chy10g01166 1166
4 5020393 5033633 - CmaCh04G009760.1 Cma04g00976 976
4 5060054 5064200 + CmaCh04G009850.1 Cma04g00985 985
15 4344900 4349479 + CmaCh15G008600.1 Cma15g00860 860
15 4355842 4360824 + CmaCh15G008640.1 Cma15g00864 864
18 8432568 8436336 + CmaCh18G010040.1 Cma18g01004 1004
9 17317288 17323825 + MELO3C005206.2.1 Cme09g01240 1240
10 1574589 1577523 + MELO3C012266.2.1 Cme10g00239 239
10 10532955 10534684 + MELO3C000047.2.1 Cme10g01125 1125
10 15774239 15778338 - MELO3C022593.2.1 Cme10g01362 1362
10 15808025 15812209 - MELO3C022596.2.1 Cme10g01363 1363
10 15840764 15851647 - MELO3C022598.2.1 Cme10g01366 1366
4 5262162 5266097 - CmoCh04G010520.1 Cmo04g01052 1052
4 5268105 5278525 - CmoCh04G010530.1 Cmo04g01053 1053
4 5308080 5313711 + CmoCh04G010610.1 Cmo04g01061 1061
15 4523668 4528225 + CmoCh15G008950.1 Cmo15g00895 895
18 10990716 10999687 + CmoCh18G010160.1 Cmo18g01016 1016
13 6608801 6612824 - Conep13aG0068600.1 Cone13ag0662 662
13 6613604 6615914 - Conep13aG0068700.1 Cone13ag0663 663
13 6619158 6622622 - Conep13aG0068900.1 Cone13ag0665 665
13 6625270 6628314 - Conep13aG0069000.1 Cone13ag0666 666
13 6629443 6632241 + Conep13aG0069100.1 Cone13ag0667 667
19 5611580 5615598 - Conep19aG0068000.1 Cone19ag0659 659
19 5615987 5618719 - Conep19aG0068100.1 Cone19ag0660 660
19 5621440 5639248 - Conep19aG0068300.1 Cone19ag0662 662
19 5640122 5642910 + Conep19aG0068400.1 Cone19ag0663 663
1 8022491 8025247 + Cp4.1LG01g13900.1 Cpe01g01333 1333
9 1877589 1879858 - Cp4.1LG09g03140.1 Cpe09g00316 316
5 8061089 8065304 - CsaV3_5G012550.1 Csa05g00958 958
5 8113279 8116836 - CsaV3_5G012590.1 Csa05g00962 962
5 8127869 8133541 - CsaV3_5G012610.1 Csa05g00964 964
5 9518646 9520478 - CsaV3_5G013140.1 Csa05g01008 1008
5 12337268 12343923 - CsaV3_5G015150.1 Csa05g01191 1191
5 27428234 27429917 - CsaV3_5G034500.1 Csa05g02631 2631
1 53254698 53262411 + Hsped.01g03580.1 Hepe01g0358 358
4 2405835 2408855 + Lsi04G002370.1 Lsi04g00237 237
1 17986242 17994297 - Vvi1g1071 Vvi1g1071 1071
1 18001133 18011125 - Vvi1g1072 Vvi1g1072 1072
1 18012151 18020938 - Vvi1g1073 Vvi1g1073 1073
1 18021455 18021599 + Vvi1g1074 Vvi1g1074 1074
1 18082561 18106134 - Vvi1g1075 Vvi1g1075 1075
1 18125556 18125798 + Vvi1g1076 Vvi1g1076 1076
1 18125930 18140256 - Vvi1g1077 Vvi1g1077 1077
1 18163362 18172933 + Vvi1g1078 Vvi1g1078 1078
1 18179461 18184021 + Vvi1g1079 Vvi1g1079 1079
1 18206571 18208242 + Vvi1g1080 Vvi1g1080 1080
       

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