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
Vvi2g2 . . . . . . . . Cmo06g01102 . . . . . . Cpe14g00512 . . . . . . . . . . . . . . . . . Cone6ag0647 Cone9ag0652 . . . Cme07g01641 . . . . . . . . . . . Cma06g01087 . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0648 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0421 Cone12ag0406 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0405 Cone6ag0649 Cone9ag0653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7334632 7335810 + CmaCh06G010870.1 Cma06g01087 1087
7 22139736 22143705 - MELO3C016365.2.1 Cme07g01641 1641
6 8486791 8491695 + CmoCh06G011020.1 Cmo06g01102 1102
6 3271270 3275475 + Conep06aG0066900.1 Cone6ag0647 647
6 3275969 3278172 + Conep06aG0067000.1 Cone6ag0648 648
6 3279735 3280809 - Conep06aG0067100.1 Cone6ag0649 649
8 2617659 2620606 - Conep08aG0043700.1 Cone8ag0421 421
9 3100391 3104846 + Conep09aG0066900.1 Cone9ag0652 652
9 3110330 3111612 - Conep09aG0067000.1 Cone9ag0653 653
12 2381471 2382265 + Conep12aG0042000.1 Cone12ag0405 405
12 2382287 2385508 - Conep12aG0042100.1 Cone12ag0406 406
14 3239644 3243371 + Cp4.1LG14g02150.1 Cpe14g00512 512
2 19317 78024 + Vvi2g2 Vvi2g2 2
2 79687 80398 - Vvi2g3 Vvi2g3 3
2 94934 103571 + Vvi2g4 Vvi2g4 4
2 117103 118883 - Vvi2g5 Vvi2g5 5
2 125072 140057 + Vvi2g6 Vvi2g6 6
2 140184 142825 + Vvi2g7 Vvi2g7 7
2 143750 176185 + Vvi2g8 Vvi2g8 8
2 177604 178887 - Vvi2g9 Vvi2g9 9
2 197186 197651 - Vvi2g10 Vvi2g10 10
2 197960 209292 + Vvi2g11 Vvi2g11 11
       

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