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
Vvi3g1026 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1027 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1028 . . . . . . . . . . . . . . . . . Bhi05g00826 . . . . . . . . . . . . . . . . . Lsi03g00755 Csa07g00559 . Cme01g00233 . . Bda15g00496 . . . . . . . . . Cma19g00464 . . . . . . . . . . . Cla09g01523 . . . . . . . . . .
Vvi3g1029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1032 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1033 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 8070389 8071918 - Bda012324.1 Bda15g00496 496
5 27474683 27477144 + XM_039032010.1 Bhi05g00826 826
9 30168335 30179050 + ClCG09G015530.1 Cla09g01523 1523
19 5552578 5554192 - CmaCh19G004640.1 Cma19g00464 464
1 1662279 1665359 - MELO3C018635.2.1 Cme01g00233 233
7 4085529 4096057 + CsaV3_7G006580.1 Csa07g00559 559
3 10359684 10363101 - Lsi03G007550.1 Lsi03g00755 755
3 17293807 17305617 - Vvi3g1026 Vvi3g1026 1026
3 17343351 17349004 - Vvi3g1027 Vvi3g1027 1027
3 17366988 17383201 + Vvi3g1028 Vvi3g1028 1028
3 17392362 17399497 + Vvi3g1029 Vvi3g1029 1029
3 17403196 17428076 - Vvi3g1030 Vvi3g1030 1030
3 17428661 17429476 - Vvi3g1031 Vvi3g1031 1031
3 17433234 17434221 + Vvi3g1032 Vvi3g1032 1032
3 17434756 17439101 + Vvi3g1033 Vvi3g1033 1033
3 17461170 17461983 - Vvi3g1034 Vvi3g1034 1034
3 17464311 17465298 + Vvi3g1035 Vvi3g1035 1035
       

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