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
Vvi5g1039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1040 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1043 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1044 . . . . . Bpe14g01052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g02120 . . . . . Lcy13g0893 . . . . . . . . . . Cme11g02217
Vvi5g1045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe13g00846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1046 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1048 . . . . Bpe04g00937 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00473 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4978491 4979993 - Bda005212.1 Bda11g00473 473
12 66011237 66012989 + XM_039020156.1 Bhi12g02120 2120
4 6288996 6291994 - Bpe015600.1 Bpe04g00937 937
13 14662614 14663776 + Bpe010536.1 Bpe13g00846 846
14 7879025 7879255 - Bpe014426.1 Bpe14g01052 1052
11 29397648 29399077 + MELO3C021154.2.1 Cme11g02217 2217
13 15740609 15741973 + Maker00026330 Lcy13g0893 893
5 18498542 18499178 + Vvi5g1039 Vvi5g1039 1039
5 18540774 18541924 - Vvi5g1040 Vvi5g1040 1040
5 18545099 18546540 + Vvi5g1041 Vvi5g1041 1041
5 18570161 18570552 - Vvi5g1042 Vvi5g1042 1042
5 18570883 18609930 - Vvi5g1043 Vvi5g1043 1043
5 18614166 18615558 - Vvi5g1044 Vvi5g1044 1044
5 18634352 18636084 - Vvi5g1045 Vvi5g1045 1045
5 18653163 18653382 + Vvi5g1046 Vvi5g1046 1046
5 18718169 18750726 + Vvi5g1047 Vvi5g1047 1047
5 18760945 18763626 - Vvi5g1048 Vvi5g1048 1048
       

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