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
Vvi1g1281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0657 Cone15ag0667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0656 Cone15ag0666 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0655 Cone15ag0665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1289 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 3288360 3291340 + Conep14aG0066900.1 Cone14ag0655 655
14 3291606 3294106 - Conep14aG0067000.1 Cone14ag0656 656
14 3304769 3310904 - Conep14aG0067100.1 Cone14ag0657 657
15 3500449 3503505 + Conep15aG0067800.1 Cone15ag0665 665
15 3503525 3506382 - Conep15aG0067900.1 Cone15ag0666 666
15 3512628 3518191 - Conep15aG0068000.1 Cone15ag0667 667
1 21582289 21584461 - Vvi1g1281 Vvi1g1281 1281
1 21601486 21610278 + Vvi1g1282 Vvi1g1282 1282
1 21612647 21615897 + Vvi1g1283 Vvi1g1283 1283
1 21626787 21633564 + Vvi1g1284 Vvi1g1284 1284
1 21636776 21647857 + Vvi1g1285 Vvi1g1285 1285
1 21648792 21648906 + Vvi1g1286 Vvi1g1286 1286
1 21666019 21669215 + Vvi1g1287 Vvi1g1287 1287
1 21672317 21676640 - Vvi1g1288 Vvi1g1288 1288
1 21682874 21685163 - Vvi1g1289 Vvi1g1289 1289
1 21696689 21699186 + Vvi1g1290 Vvi1g1290 1290
       

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