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
Vvi4g862 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g863 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01018 Cam03g1070 Cec03g1071 Cco03g1062 Clacu03g1041 Cmu03g1631 Cre03g1332 Lsi06g00694 . . Cme02g00909
Vvi4g865 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00714 . . . . . . . . . Cla03g01017 Cam03g1069 Cec03g1070 Cco03g1061 Clacu03g1040 Cmu03g1630 Cre03g1331 Lsi06g00693 . . Cme02g00907
Vvi4g866 . . . Bda10g00323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g869 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g870 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0942 Cone1ag1699 Cone10ag0599 Cone3ag0625 . . . . . . . . . . . . . . . . . . Car05g00753 . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 33243304 33244213 + Bda007106.1 Bda10g00323 323
3 19705490 19709061 + CaPI482276_03g010690.1 Cam03g1069 1069
3 19765238 19766671 + CaPI482276_03g010700.1 Cam03g1070 1070
5 4912415 4919472 + Carg19843-RA Car05g00714 714
5 5660287 5668684 - Carg27759-RA Car05g00753 753
3 18532015 18535589 + CcPI632755_03g010610.1 Cco03g1061 1061
3 18602093 18603472 + CcPI632755_03g010620.1 Cco03g1062 1062
3 22211672 22215285 + CePI673135_03g010700.1 Cec03g1070 1070
3 22285761 22287186 + CePI673135_03g010710.1 Cec03g1071 1071
3 18540526 18544096 + ClG42_03g0104000.10 Clacu03g1040 1040
3 18605168 18606591 + ClG42_03g0104100.10 Clacu03g1041 1041
3 19349068 19353076 + ClCG03G010650.1 Cla03g01017 1017
3 19414202 19416234 + ClCG03G010660.1 Cla03g01018 1018
2 12479105 12483075 + MELO3C010053.2.1 Cme02g00907 907
2 12549829 12550640 + MELO3C010055.2.1 Cme02g00909 909
3 18924657 18928227 + CmPI595203_03g016300.1 Cmu03g1630 1630
3 18989244 18990667 + CmPI595203_03g016310.1 Cmu03g1631 1631
1 57959139 57960448 - Conep01aG0176000.1 Cone1ag1697 1697
1 57961584 57964197 + Conep01aG0176200.1 Cone1ag1699 1699
3 3091583 3095165 - Conep03aG0064300.1 Cone3ag0625 625
5 4029985 4033139 + Conep05aG0096800.1 Cone5ag0942 942
10 2820638 2824134 - Conep10aG0061600.1 Cone10ag0599 599
3 23572418 23575980 + CrPI670011_03g013310.1 Cre03g1331 1331
3 23645420 23649957 + CrPI670011_03g013320.1 Cre03g1332 1332
6 10998062 11001912 + Lsi06G006930.1 Lsi06g00693 693
6 11029609 11031481 + Lsi06G006940.1 Lsi06g00694 694
4 16779756 16780072 - Vvi4g862 Vvi4g862 862
4 16782059 16782353 - Vvi4g863 Vvi4g863 863
4 16788069 16801485 - Vvi4g864 Vvi4g864 864
4 16801743 16809442 - Vvi4g865 Vvi4g865 865
4 16811745 16815368 - Vvi4g866 Vvi4g866 866
4 16834851 16838222 + Vvi4g867 Vvi4g867 867
4 16845197 16845383 - Vvi4g868 Vvi4g868 868
4 16896540 16897919 + Vvi4g869 Vvi4g869 869
4 16950431 16953530 - Vvi4g870 Vvi4g870 870
4 16985684 16993625 + Vvi4g871 Vvi4g871 871
       

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