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
Vvi19g914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g915 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g916 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g917 . . . . Bpe09g00277 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g918 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g920 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g921 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g922 . . . . Bpe09g00278 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01035 .
Vvi19g923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 22700971 22701936 - BLOR02500 Blo10g00710 710
10 22706160 22707096 - BLOR02502 Blo10g00712 712
9 2088881 2090094 - Bpe023948.1 Bpe09g00277 277
9 2101810 2103218 - Bpe023949.1 Bpe09g00278 278
7 15318582 15319611 + Chy7G138650.1 Chy07g01035 1035
19 16401286 16406784 + Vvi19g914 Vvi19g914 914
19 16413688 16414795 + Vvi19g915 Vvi19g915 915
19 16448661 16459547 - Vvi19g916 Vvi19g916 916
19 16531631 16532867 + Vvi19g917 Vvi19g917 917
19 16533380 16545164 + Vvi19g918 Vvi19g918 918
19 16545941 16556452 + Vvi19g919 Vvi19g919 919
19 16556999 16569957 - Vvi19g920 Vvi19g920 920
19 16570450 16572001 + Vvi19g921 Vvi19g921 921
19 16593567 16595273 + Vvi19g922 Vvi19g922 922
19 16609678 16610200 + Vvi19g923 Vvi19g923 923
       

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