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
Vvi19g864 . . . . . . . Bma13g00910 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda12g00806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g865 . . . . . . . Bma13g00909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda12g00804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g866 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g869 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g870 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g872 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g873 Blo03g00729 . . . . . . . . . . . . . . . . Bhi09g03596 . . . . . . . . . . . . . . . . . Lsi04g01950 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 37100499 37101757 + Bda009309.1 Bda12g00804 804
12 37180057 37180992 - Bda009312.1 Bda12g00806 806
9 89858068 89875679 - XM_039042022.1 Bhi09g03596 3596
3 30587469 30606558 - BLOR11910 Blo03g00729 729
13 39463942 39465168 + Bma009985.2 Bma13g00909 909
13 39481538 39482847 + Bma009986.1 Bma13g00910 910
4 26612851 26626112 + Lsi04G019500.1 Lsi04g01950 1950
19 13399161 13400570 - Vvi19g864 Vvi19g864 864
19 13464828 13467295 - Vvi19g865 Vvi19g865 865
19 13551126 13555600 + Vvi19g866 Vvi19g866 866
19 13603257 13607510 + Vvi19g867 Vvi19g867 867
19 13632901 13633389 - Vvi19g868 Vvi19g868 868
19 13633964 13645604 + Vvi19g869 Vvi19g869 869
19 13653086 13653826 + Vvi19g870 Vvi19g870 870
19 13983529 13983968 - Vvi19g871 Vvi19g871 871
19 13985237 13986407 + Vvi19g872 Vvi19g872 872
19 13989274 14016964 + Vvi19g873 Vvi19g873 873
       

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