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
Vvi18g1460 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1462 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1464 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1466 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g00041 Cam08g0040 Cec08g0212 Cco08g0093 Clacu08g0056 Cmu08g0054 Cre08g0044 . . . . . . . . . . . . . . . . Sed10g2126 . . . . . . . . Bhi06g00236 Tan10g2035 Cmetu09g1975 . . . . . . . . . . . Lsi08g00031 . . .
Vvi18g1467 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 5651960 5658999 + XM_039034250.1 Bhi06g00236 236
8 916588 923345 - CaPI482276_08g000400.1 Cam08g0040 40
8 1526611 1534124 - CcPI632755_08g000930.1 Cco08g0093 93
8 3918846 3925239 + CePI673135_08g002120.1 Cec08g0212 212
8 1328673 1335253 - ClG42_08g0005600.10 Clacu08g0056 56
8 1160703 1167398 - ClCG08G000400.1 Cla08g00041 41
9 21646071 21652095 + PI0004880.1 Cmetu09g1975 1975
8 1247192 1253773 - CmPI595203_08g000540.1 Cmu08g0054 54
8 1132646 1139230 - CrPI670011_08g000440.1 Cre08g0044 44
8 831092 838531 - Lsi08G000310.1 Lsi08g00031 31
10 37705368 37714177 + Sed0004336.4 Sed10g2126 2126
10 64670304 64677955 + Tan0003232.1 Tan10g2035 2035
18 22105716 22125120 - Vvi18g1460 Vvi18g1460 1460
18 22181939 22182371 - Vvi18g1461 Vvi18g1461 1461
18 22217637 22217847 + Vvi18g1462 Vvi18g1462 1462
18 22271553 22273738 - Vvi18g1463 Vvi18g1463 1463
18 22331770 22347176 - Vvi18g1464 Vvi18g1464 1464
18 22386903 22392771 - Vvi18g1465 Vvi18g1465 1465
18 22395058 22396523 + Vvi18g1466 Vvi18g1466 1466
18 22416677 22417853 + Vvi18g1467 Vvi18g1467 1467
18 22454189 22454823 + Vvi18g1468 Vvi18g1468 1468
18 22472565 22473188 + Vvi18g1469 Vvi18g1469 1469
       

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