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
Vvi4g772 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme05g01066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g773 . . . . . . . . . . . . . . . Cpe07g00820 . . . . . . . . . . . . . . . . . Cone10ag0627 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme05g01070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01092 Cam03g1138 Cec03g1154 Cco03g1135 Clacu03g1115 Cmu03g1694 Cre03g1403 . . . .
Vvi4g778 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g779 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0267 Cone5ag1581 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g780 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g781 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g00757 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 22176141 22177543 + CaPI482276_03g011380.1 Cam03g1138 1138
3 21664820 21666222 + CcPI632755_03g011350.1 Cco03g1135 1135
3 25293593 25294984 + CePI673135_03g011540.1 Cec03g1154 1154
3 20975944 21023672 + ClG42_03g0111500.10 Clacu03g1115 1115
3 21867987 21928798 + ClCG03G011350.2 Cla03g01092 1092
5 16372938 16429698 - MELO3C008660.2.1 Cme05g01066 1066
5 16554492 16559733 + MELO3C008666.2.1 Cme05g01070 1070
3 21348757 21350159 + CmPI595203_03g016940.1 Cmu03g1694 1694
1 1782650 1786260 - Conep01aG0028500.1 Cone1ag0267 267
5 11060374 11063618 + Conep05aG0162900.1 Cone5ag1581 1581
10 2985368 2987079 - Conep10aG0064300.1 Cone10ag0626 626
10 2990987 2993612 - Conep10aG0064400.1 Cone10ag0627 627
7 7420542 7426102 + Cp4.1LG07g08190.1 Cpe07g00820 820
3 26366838 26368234 + CrPI670011_03g014030.1 Cre03g1403 1403
6 14146610 14232999 + Lsi06G007570.1 Lsi06g00757 757
4 14291917 14374501 - Vvi4g772 Vvi4g772 772
4 14427680 14430561 + Vvi4g773 Vvi4g773 773
4 14434730 14448837 + Vvi4g774 Vvi4g774 774
4 14527353 14529566 + Vvi4g775 Vvi4g775 775
4 14598140 14599841 + Vvi4g776 Vvi4g776 776
4 14621964 14683043 + Vvi4g777 Vvi4g777 777
4 14692221 14705180 - Vvi4g778 Vvi4g778 778
4 14706472 14710080 - Vvi4g779 Vvi4g779 779
4 14713069 14730236 + Vvi4g780 Vvi4g780 780
4 14742964 14866094 + Vvi4g781 Vvi4g781 781
       

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