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
Vvi4g1222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1223 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1224 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1225 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1227 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi01g01126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g02809 Chy02g01024 .
Vvi4g1228 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme08g01049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1230 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1231 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0679 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
2 6964902 6979694 + Chy2G032910.1 Chy02g01024 1024
8 6850257 6854318 + MELO3C008027.2.1 Cme08g01049 1049
5 2895027 2903827 - Conep05aG0070300.1 Cone5ag0679 679
6 24496090 24500590 - CsaV3_6G041950.1 Csa06g02809 2809
1 9362548 9386619 + Lsi01G011260.1 Lsi01g01126 1126
4 21120002 21127168 + Vvi4g1222 Vvi4g1222 1222
4 21129634 21141708 + Vvi4g1223 Vvi4g1223 1223
4 21142198 21144587 + Vvi4g1224 Vvi4g1224 1224
4 21152723 21154968 + Vvi4g1225 Vvi4g1225 1225
4 21163785 21172634 + Vvi4g1226 Vvi4g1226 1226
4 21178400 21181027 + Vvi4g1227 Vvi4g1227 1227
4 21199522 21230747 + Vvi4g1228 Vvi4g1228 1228
4 21234507 21237843 + Vvi4g1229 Vvi4g1229 1229
4 21237940 21239744 - Vvi4g1230 Vvi4g1230 1230
4 21239772 21242831 + Vvi4g1231 Vvi4g1231 1231
       

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