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
Vvi18g1470 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g1817 . . . . . . . . Bhi06g00237 Tan10g2036 . . . . . . . . . . . . . . . .
Vvi18g1471 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1473 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1474 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00156 . . Bda13g01449 . Bpe14g00407 . Bma02g00192 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1476 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1477 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1478 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1479 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 37195668 37201304 - Bda000282.1 Bda13g01449 1449
6 5651960 5658304 + XM_039034248.1 Bhi06g00237 237
17 1456830 1462295 - BLOR15977 Blo17g00156 156
2 1786538 1797989 - Bma030858 Bma02g00192 192
14 3802852 3808376 + Bpe007061.1 Bpe14g00407 407
20 4268182 4271366 + Conep20aG0070800.1 Cone20ag0687 687
5 31796471 31804678 + Sed0001549.1 Sed05g1817 1817
10 64670304 64677955 + Tan0003232.2 Tan10g2036 2036
18 22487870 22493242 + Vvi18g1470 Vvi18g1470 1470
18 22524257 22527030 - Vvi18g1471 Vvi18g1471 1471
18 22543842 22544496 + Vvi18g1472 Vvi18g1472 1472
18 22552354 22552665 - Vvi18g1473 Vvi18g1473 1473
18 22618199 22638670 + Vvi18g1474 Vvi18g1474 1474
18 22714887 22715312 - Vvi18g1475 Vvi18g1475 1475
18 22766636 22767234 - Vvi18g1476 Vvi18g1476 1476
18 22806789 22808514 - Vvi18g1477 Vvi18g1477 1477
18 22922147 22923585 + Vvi18g1478 Vvi18g1478 1478
18 22937009 22942889 + Vvi18g1479 Vvi18g1479 1479
       

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