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
Vvi19g324 . . Bda07g00265 . . . . . . . . . . . . Cpe06g00728 Cpe02g00732 . . . . . . . . . . . . . . Cone6ag0104 Cone9ag0124 . . Lsi04g01267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g325 . . . . . . . . . . Cma01g01172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g331 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g332 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01226 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g333 . . . . . . . . Cmo16g00922 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe01g00368 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3721010 3721582 + Bda025345.1 Bda07g00265 265
1 2314013 2316206 + Bpe000357.1 Bpe01g00368 368
1 8518748 8520133 + CmaCh01G011720.1 Cma01g01172 1172
1 9848866 9850854 + CmoCh01G012260.1 Cmo01g01226 1226
16 5616846 5620190 + CmoCh16G009220.1 Cmo16g00922 922
6 507294 508767 + Conep06aG0010400.1 Cone6ag0104 104
9 544375 545477 + Conep09aG0012400.1 Cone9ag0124 124
2 4671120 4672733 - Cp4.1LG02g01330.1 Cpe02g00732 732
6 4551660 4553673 - Cp4.1LG06g07400.1 Cpe06g00728 728
4 20001468 20002891 + Lsi04G012670.1 Lsi04g01267 1267
19 4194433 4200262 - Vvi19g324 Vvi19g324 324
19 4224219 4232990 + Vvi19g325 Vvi19g325 325
19 4233864 4234385 + Vvi19g326 Vvi19g326 326
19 4271943 4272189 + Vvi19g327 Vvi19g327 327
19 4272422 4275796 + Vvi19g328 Vvi19g328 328
19 4277011 4277346 + Vvi19g329 Vvi19g329 329
19 4278164 4280582 + Vvi19g330 Vvi19g330 330
19 4296663 4298294 + Vvi19g331 Vvi19g331 331
19 4300427 4304176 + Vvi19g332 Vvi19g332 332
19 4309212 4314290 + Vvi19g333 Vvi19g333 333
       

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