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
Vvi2g802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g803 . . . . . . . . Cmo06g00616 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01143 . . Cme06g02419 . . . . . . . . . . . Cma06g00610 . Car06g00543 . . . . . . . . . . . . . . . . . . . . .
Vvi2g804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g805 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g809 . . . . . . . . . Cmo16g01254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g01207 . . . . . . . . . . . . . . . . . . . . . .
Vvi2g810 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g811 . . . . . . Bma07g00859 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 29648638 29655466 - Bma025918.1 Bma07g00859 859
6 3061100 3072555 + Carg16296-RA Car06g00543 543
6 2956146 2967956 + CmaCh06G006100.1 Cma06g00610 610
16 9154328 9166888 - CmaCh16G012070.1 Cma16g01207 1207
6 31315886 31327431 + MELO3C013803.2.1 Cme06g02419 2419
6 3047272 3059350 + CmoCh06G006160.1 Cmo06g00616 616
16 8935237 8949541 - CmoCh16G012540.1 Cmo16g01254 1254
7 16895415 16907622 + Lsi07G011430.1 Lsi07g01143 1143
2 13456564 13457349 - Vvi2g802 Vvi2g802 802
2 13478752 13525358 + Vvi2g803 Vvi2g803 803
2 13526996 13528253 - Vvi2g804 Vvi2g804 804
2 13595183 13673525 + Vvi2g805 Vvi2g805 805
2 13673927 13674737 - Vvi2g806 Vvi2g806 806
2 13681702 13716339 - Vvi2g807 Vvi2g807 807
2 13720782 13721456 + Vvi2g808 Vvi2g808 808
2 13744081 13747505 + Vvi2g809 Vvi2g809 809
2 13761814 13769172 - Vvi2g810 Vvi2g810 810
2 13772326 13858248 - Vvi2g811 Vvi2g811 811
       

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