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
Vvi1g1091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy10g00053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1093 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1094 . . . . . . Bma14g01740 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy10g00052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1095 . . . . . . Bma14g01739 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1096 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1097 . . . . . . Bma14g01738 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g01730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1098 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1099 . . . . . . Bma14g01737 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g01727 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 37332974 37333915 + Bma012503.1 Bma14g01737 1737
14 37356178 37357137 - Bma012504.1 Bma14g01738 1738
14 37375870 37376913 + Bma012506.1 Bma14g01739 1739
14 37379297 37380091 - Bma012507.1 Bma14g01740 1740
11 13620938 13621963 - Bpe005042.1 Bpe11g01727 1727
11 13649518 13650925 - Bpe005045.1 Bpe11g01730 1730
10 1295853 1297025 + Chy10G172460.1 Chy10g00052 52
10 1309998 1311137 - Chy10G172470.1 Chy10g00053 53
1 18557850 18558676 + Vvi1g1091 Vvi1g1091 1091
1 18566882 18567791 + Vvi1g1092 Vvi1g1092 1092
1 18582982 18583441 + Vvi1g1093 Vvi1g1093 1093
1 18601358 18606800 - Vvi1g1094 Vvi1g1094 1094
1 18621156 18622440 + Vvi1g1095 Vvi1g1095 1095
1 18632671 18633953 + Vvi1g1096 Vvi1g1096 1096
1 18638900 18641794 + Vvi1g1097 Vvi1g1097 1097
1 18645673 18653975 - Vvi1g1098 Vvi1g1098 1098
1 18657362 18658552 - Vvi1g1099 Vvi1g1099 1099
1 18668410 18669651 + Vvi1g1100 Vvi1g1100 1100
       

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