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
Vvi18g1590 . . . . . . . . . . . . . . . Cpe06g01014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01323 . . . Car09g01153 . . . . . . . . . . . . . . . . . . . .
Vvi18g1591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g01024 . . . . . . . . . . . . . . . . . .
Vvi18g1593 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1594 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1595 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1596 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1597 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00315 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1599 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
2 3807160 3809472 - Bma014771.1 Bma02g00315 315
9 12156602 12157787 - Carg27175-RA Car09g01153 1153
9 11979069 11980609 - CmoCh09G013230.1 Cmo09g01323 1323
2 9394977 9398303 - Cp4.1LG02g10660.1 Cpe02g01024 1024
6 10487310 10500889 - Cp4.1LG06g10140.1 Cpe06g01014 1014
18 25838000 25839742 + Vvi18g1590 Vvi18g1590 1590
18 25847095 25853527 + Vvi18g1591 Vvi18g1591 1591
18 25876231 25883232 + Vvi18g1592 Vvi18g1592 1592
18 25886257 25888623 + Vvi18g1593 Vvi18g1593 1593
18 25889126 25897069 - Vvi18g1594 Vvi18g1594 1594
18 25899584 25904349 - Vvi18g1595 Vvi18g1595 1595
18 25905323 25934916 + Vvi18g1596 Vvi18g1596 1596
18 25936490 25946775 - Vvi18g1597 Vvi18g1597 1597
18 25979170 26009592 - Vvi18g1598 Vvi18g1598 1598
18 26017660 26020840 - Vvi18g1599 Vvi18g1599 1599
       

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