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
Vvi1g161 . . . . . . . . Cmo04g01631 . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0951 Lsi04g00318 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g162 . . . . . . . . . Cmo18g00534 . Cma18g00557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g166 Blo01g00908 . . . . . . . . . . Cma18g00559 . . . Cpe09g00681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g167 . . . . . . . . . Cmo18g00536 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g170 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 19572078 19577598 - BLOR00908 Blo01g00908 908
18 3650247 3659619 - CmaCh18G005570.1 Cma18g00557 557
18 3671672 3674403 - CmaCh18G005590.1 Cma18g00559 559
4 8332582 8337038 - CmoCh04G016310.1 Cmo04g01631 1631
18 3988272 3995326 - CmoCh18G005340.1 Cmo18g00534 534
18 4011383 4014443 - CmoCh18G005360.1 Cmo18g00536 536
15 7544084 7544834 - Conep15aG0097100.1 Cone15ag0951 951
9 5958464 5961841 + Cp4.1LG09g06810.1 Cpe09g00681 681
4 3258592 3262288 + Lsi04G003180.1 Lsi04g00318 318
1 1587041 1587956 - Vvi1g161 Vvi1g161 161
1 1589378 1597918 - Vvi1g162 Vvi1g162 162
1 1610161 1612639 + Vvi1g163 Vvi1g163 163
1 1620550 1621335 + Vvi1g164 Vvi1g164 164
1 1623154 1631283 - Vvi1g165 Vvi1g165 165
1 1634733 1639729 - Vvi1g166 Vvi1g166 166
1 1640449 1643813 + Vvi1g167 Vvi1g167 167
1 1646112 1646190 - Vvi1g168 Vvi1g168 168
1 1646532 1652442 + Vvi1g169 Vvi1g169 169
1 1652445 1676628 - Vvi1g170 Vvi1g170 170
       

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