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
Vvi18g1420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1421 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00034 . . .
Vvi18g1422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1423 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1424 Blo01g01706 . . . . . . . . . . Cma09g01112 . . . . . . . . . . . . . . . . . . . Cone4ag1210 . . . . . . . . . . . . . . . . . Cmo09g01118 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1425 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 56824745 56827629 - BLOR01706 Blo01g01706 1706
9 6098294 6103921 - CmaCh09G011120.1 Cma09g01112 1112
9 6352818 6358473 - CmoCh09G011180.1 Cmo09g01118 1118
4 10154299 10160313 - Conep04aG0125600.1 Cone4ag1210 1210
8 849912 862269 - Lsi08G000340.1 Lsi08g00034 34
18 20806773 20807814 + Vvi18g1420 Vvi18g1420 1420
18 20835992 20839675 + Vvi18g1421 Vvi18g1421 1421
18 20839815 20855197 - Vvi18g1422 Vvi18g1422 1422
18 20855586 20865341 - Vvi18g1423 Vvi18g1423 1423
18 20935210 20942470 - Vvi18g1424 Vvi18g1424 1424
18 20963969 20970885 - Vvi18g1425 Vvi18g1425 1425
18 20989272 20993698 - Vvi18g1426 Vvi18g1426 1426
18 21049251 21050534 - Vvi18g1427 Vvi18g1427 1427
18 21096663 21096914 + Vvi18g1428 Vvi18g1428 1428
18 21103611 21103912 + Vvi18g1429 Vvi18g1429 1429
       

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