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
Vvi1g131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g132 . . . . . . . . . Cmo18g00250 . . . . . Cpe09g00929 . . . . . . . . . . . . . . . Cone2ag0800 . . . . . . . . . . . . Bpe02g02335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g134 Blo01g00399 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g135 . . . . . . . . . Cmo18g00564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00989 . Cec01g1007 Cco01g1062 Clacu01g1020 Cmu01g0969 Cre01g0893 . . . .
Vvi1g136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g137 . . . . . . . . . Cmo18g00251 . . . . . Cpe09g00928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g140 . . . . . . . . . Cmo18g00253 . . . . . Cpe09g00926 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 4520270 4529063 + BLOR00399 Blo01g00399 399
2 23919775 23920909 - Bpe010151.1 Bpe02g02335 2335
1 14025433 14028897 + CcPI632755_01g010620.1 Cco01g1062 1062
1 14170326 14173764 + CePI673135_01g010070.1 Cec01g1007 1007
1 13807617 13811039 + ClG42_01g0102000.10 Clacu01g1020 1020
1 14465063 14468814 + ClCG01G009940.2 Cla01g00989 989
18 1655442 1663866 + CmoCh18G002500.1 Cmo18g00250 250
18 1665206 1666168 + CmoCh18G002510.1 Cmo18g00251 251
18 1683325 1688326 - CmoCh18G002530.1 Cmo18g00253 253
18 4667435 4672337 + CmoCh18G005640.1 Cmo18g00564 564
1 13799968 13803392 + CmPI595203_01g009690.1 Cmu01g0969 969
2 34015139 34018117 - Conep02aG0182800.1 Cone2ag0800 800
9 8331449 8335733 + Cp4.1LG09g09130.1 Cpe09g00926 926
9 8353161 8354123 - Cp4.1LG09g09360.1 Cpe09g00928 928
9 8355473 8363284 - Cp4.1LG09g09390.1 Cpe09g00929 929
1 12421467 12424862 + CrPI670011_01g008930.1 Cre01g0893 893
1 1272688 1293994 - Vvi1g131 Vvi1g131 131
1 1303635 1315494 + Vvi1g132 Vvi1g132 132
1 1315727 1316069 - Vvi1g133 Vvi1g133 133
1 1316103 1326207 - Vvi1g134 Vvi1g134 134
1 1336617 1340485 + Vvi1g135 Vvi1g135 135
1 1340899 1343491 - Vvi1g136 Vvi1g136 136
1 1343519 1344663 - Vvi1g137 Vvi1g137 137
1 1353271 1355920 + Vvi1g138 Vvi1g138 138
1 1360443 1369503 + Vvi1g139 Vvi1g139 139
1 1386742 1417789 + Vvi1g140 Vvi1g140 140
       

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