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
Vvi4g812 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01065 Cam03g1103 Cec03g1117 . . . Cre03g1368 . . . .
Vvi4g813 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g814 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0921 Cone1ag1676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g818 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g819 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g820 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0616 Cone3ag0656 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 20886123 20907141 - CaPI482276_03g011030.1 Cam03g1103 1103
3 23504384 23520887 - CePI673135_03g011170.1 Cec03g1117 1117
3 20474743 20521724 - ClCG03G011070.2 Cla03g01065 1065
1 57893978 57897679 - Conep01aG0173900.1 Cone1ag1676 1676
3 3291232 3297132 + Conep03aG0067400.1 Cone3ag0656 656
5 3943056 3947172 - Conep05aG0094700.1 Cone5ag0921 921
10 2939379 2945077 + Conep10aG0063300.1 Cone10ag0616 616
10 2955819 2959800 + Conep10aG0063600.1 Cone10ag0619 619
3 24768957 24770195 - CrPI670011_03g013680.1 Cre03g1368 1368
4 15826161 15887813 + Vvi4g812 Vvi4g812 812
4 15919427 15925004 - Vvi4g813 Vvi4g813 813
4 15930192 15931579 + Vvi4g814 Vvi4g814 814
4 15933939 15957362 + Vvi4g815 Vvi4g815 815
4 15962926 15963850 + Vvi4g816 Vvi4g816 816
4 16020905 16021763 + Vvi4g817 Vvi4g817 817
4 16084014 16085284 - Vvi4g818 Vvi4g818 818
4 16085318 16105882 - Vvi4g819 Vvi4g819 819
4 16120034 16124634 - Vvi4g820 Vvi4g820 820
4 16164434 16185831 + Vvi4g821 Vvi4g821 821
       

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