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
Vvi19g364 . . . . Bpe09g00255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi11g00710 . . . . . . . . . . . . . . . . .
Vvi19g365 . . . . . . . . . . . . . . . . Cpe02g00733 . . . . . . . . . . . . . . . Cone9ag0121 . . Lsi04g01266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g368 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g370 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01265 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 18305973 18308805 + XM_039050018.1 Bhi11g00710 710
9 1868286 1870820 - Bpe023926.1 Bpe09g00255 255
9 528827 532607 - Conep09aG0012100.1 Cone9ag0121 121
2 4677073 4677903 + Cp4.1LG02g01440.1 Cpe02g00733 733
4 19877028 19881085 - Lsi04G012650.1 Lsi04g01265 1265
4 19919294 19924423 - Lsi04G012660.1 Lsi04g01266 1266
19 4722227 4722965 - Vvi19g364 Vvi19g364 364
19 4723053 4725550 - Vvi19g365 Vvi19g365 365
19 4729361 4732605 - Vvi19g366 Vvi19g366 366
19 4745382 4749486 - Vvi19g367 Vvi19g367 367
19 4788585 4790378 - Vvi19g368 Vvi19g368 368
19 4797273 4799404 - Vvi19g369 Vvi19g369 369
19 4799620 4801550 - Vvi19g370 Vvi19g370 370
19 4811256 4812384 - Vvi19g371 Vvi19g371 371
19 4833433 4836507 + Vvi19g372 Vvi19g372 372
19 4851074 4855125 - Vvi19g373 Vvi19g373 373
       

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