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
Vvi4g822 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag0653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g823 . . . . . . . . . . . . . . . Cpe07g00789 . . . . . . . . . . . . . . . . . . Cone3ag0649 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g824 . . . . . . . . . . . . . . . Cpe07g00787 . . . . . . . . . . . . . . . Cone5ag0927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g825 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g826 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g827 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g828 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g831 . . . . . . . . . . . . . . . Cpe07g00786 . . . . . . . . . . . . . . . . . Cone10ag0613 Cone3ag0640 . . . . . . . . . . . . . . . . . . Car05g00704 . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 4806971 4814368 + Carg19833-RA Car05g00704 704
3 3172659 3177654 - Conep03aG0065800.1 Cone3ag0640 640
3 3251245 3253605 + Conep03aG0066700.1 Cone3ag0649 649
3 3274664 3279334 - Conep03aG0067100.1 Cone3ag0653 653
5 3971268 3974722 - Conep05aG0095300.1 Cone5ag0927 927
10 2910258 2914206 - Conep10aG0063000.1 Cone10ag0613 613
7 6991127 6999400 + Cp4.1LG07g07860.1 Cpe07g00786 786
7 7000128 7004430 - Cp4.1LG07g07910.1 Cpe07g00787 787
7 7012593 7022542 - Cp4.1LG07g07920.1 Cpe07g00789 789
4 16186695 16227869 + Vvi4g822 Vvi4g822 822
4 16238301 16252399 + Vvi4g823 Vvi4g823 823
4 16253356 16258888 + Vvi4g824 Vvi4g824 824
4 16283372 16291482 - Vvi4g825 Vvi4g825 825
4 16320400 16320930 + Vvi4g826 Vvi4g826 826
4 16325050 16325705 + Vvi4g827 Vvi4g827 827
4 16329841 16330786 + Vvi4g828 Vvi4g828 828
4 16332208 16334957 - Vvi4g829 Vvi4g829 829
4 16349084 16351046 + Vvi4g830 Vvi4g830 830
4 16391581 16402392 + Vvi4g831 Vvi4g831 831
       

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