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
Vvi1g1061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1062 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1064 . . . . . . . . . Cmo18g00714 . Cma18g00728 . Car18g00676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1065 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1067 . . Bda01g01783 . . . . . . . . . . . . . Cpe01g01881 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g01960 . Bma06g00591 . Cmo04g02270 . Cma04g02171 . Car04g02100 . . . Bhi12g01016 . . . . . . Cla01g00691 . . . . . Cre09g1825 Lsi09g00749 Csa05g01326 . .
Vvi1g1068 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01195 . .
Vvi1g1070 . . . . . . . . Cmo04g01062 . Cma04g00986 . Car04g00924 . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo11g01001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01194 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54046039 54047741 - Bda004072.1 Bda01g01783 1783
12 30919002 30924429 - XM_039019676.1 Bhi12g01016 1016
11 25199172 25201034 + BLOR03877 Blo11g01001 1001
6 31643626 31646212 + Bma023518.1 Bma06g00591 591
2 21488562 21494336 - Bpe009784.1 Bpe02g01960 1960
4 5289747 5291814 + Carg00099-RA Car04g00924 924
4 17140570 17144844 - Carg17707-RA Car04g02100 2100
18 7958874 7961771 + Carg27654-RA Car18g00676 676
1 8133094 8137478 - ClCG01G007070.2 Cla01g00691 691
4 5067266 5093612 + CmaCh04G009860.1 Cma04g00986 986
4 15189388 15193993 - CmaCh04G021710.1 Cma04g02171 2171
18 6577123 6582176 + CmaCh18G007280.1 Cma18g00728 728
4 5316865 5318940 + CmoCh04G010620.1 Cmo04g01062 1062
4 16934268 16938299 - CmoCh04G022700.1 Cmo04g02270 2270
18 8972843 8975681 + CmoCh18G007140.1 Cmo18g00714 714
1 16117268 16121976 - Cp4.1LG01g18920.1 Cpe01g01881 1881
9 36636728 36639818 + CrPI670011_09g018250.1 Cre09g1825 1825
5 12419415 12423841 + CsaV3_5G015180.1 Csa05g01194 1194
5 12428997 12430929 - CsaV3_5G015190.1 Csa05g01195 1195
5 14038245 14044250 - CsaV3_5G017490.1 Csa05g01326 1326
9 8582242 8587779 - Lsi09G007490.1 Lsi09g00749 749
1 17754739 17755128 - Vvi1g1061 Vvi1g1061 1061
1 17760879 17762318 - Vvi1g1062 Vvi1g1062 1062
1 17826901 17827540 - Vvi1g1063 Vvi1g1063 1063
1 17836173 17836991 + Vvi1g1064 Vvi1g1064 1064
1 17879904 17881773 + Vvi1g1065 Vvi1g1065 1065
1 17884031 17888603 - Vvi1g1066 Vvi1g1066 1066
1 17913957 17930657 + Vvi1g1067 Vvi1g1067 1067
1 17939354 17940260 + Vvi1g1068 Vvi1g1068 1068
1 17946852 17950054 + Vvi1g1069 Vvi1g1069 1069
1 17965018 17966964 - Vvi1g1070 Vvi1g1070 1070
       

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