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
Vvi4g802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g803 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0624 . . . . Cme05g01090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1673 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01076 . . . . . . Lsi06g00730 . . Cme02g00934
Vvi4g805 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0623 Cone3ag0662 . . . Cme05g01092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0916 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g809 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g810 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 21194294 21208602 + ClCG03G011200.2 Cla03g01076 1076
2 13230987 13236931 - MELO3C029613.2.1 Cme02g00934 934
5 16883462 16887943 - MELO3C008674.2.1 Cme05g01090 1090
5 16929774 16936827 + MELO3C008677.2.1 Cme05g01092 1092
1 57879922 57882082 + Conep01aG0173600.1 Cone1ag1673 1673
3 3326538 3329787 - Conep03aG0068000.1 Cone3ag0662 662
5 3920853 3923126 + Conep05aG0094200.1 Cone5ag0916 916
10 2970442 2973691 - Conep10aG0064000.1 Cone10ag0623 623
10 2975774 2977333 + Conep10aG0064100.1 Cone10ag0624 624
6 12475073 12504393 - Lsi06G007300.1 Lsi06g00730 730
4 15584856 15587835 + Vvi4g802 Vvi4g802 802
4 15645007 15646649 + Vvi4g803 Vvi4g803 803
4 15655570 15657133 - Vvi4g804 Vvi4g804 804
4 15676482 15676833 + Vvi4g805 Vvi4g805 805
4 15677779 15678625 - Vvi4g806 Vvi4g806 806
4 15680402 15687686 + Vvi4g807 Vvi4g807 807
4 15699276 15713817 - Vvi4g808 Vvi4g808 808
4 15730839 15732344 + Vvi4g809 Vvi4g809 809
4 15766798 15766894 + Vvi4g810 Vvi4g810 810
4 15777314 15779531 - Vvi4g811 Vvi4g811 811
       

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