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
Vvi3g1066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1067 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00855 Cam10g0875 Cec10g0905 Cco10g0858 Clacu10g0900 Cmu10g1692 Cre10g1063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1068 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00652 . . . . . . Cpe01g00550 . . . . . . . . . . . . . . . . . .
Vvi3g1069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00538 . . . . Cpe14g00419 . . . . . . . . . . . . . . . . . . .
Vvi3g1071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1072 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1075 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 19628109 19629615 - CaPI482276_10g008750.1 Cam10g0875 875
10 17973912 17976146 - CcPI632755_10g008580.1 Cco10g0858 858
10 19975826 19977332 - CePI673135_10g009050.1 Cec10g0905 905
10 18753344 18754850 - ClG42_10g0090000.10 Clacu10g0900 900
10 19576698 19578932 - ClCG10G008950.1 Cla10g00855 855
4 3235812 3242519 + CmoCh04G006520.1 Cmo04g00652 652
16 2628087 2630329 + CmoCh16G005380.1 Cmo16g00538 538
10 19373429 19375663 - CmPI595203_10g016920.1 Cmu10g1692 1692
1 3162198 3169100 + Cp4.1LG01g01250.1 Cpe01g00550 550
14 2627811 2629761 + Cp4.1LG14g03010.1 Cpe14g00419 419
10 20980095 20981601 - CrPI670011_10g010630.1 Cre10g1063 1063
3 18320398 18321759 - Vvi3g1066 Vvi3g1066 1066
3 18336897 18341110 + Vvi3g1067 Vvi3g1067 1067
3 18343141 18371399 - Vvi3g1068 Vvi3g1068 1068
3 18402494 18403698 + Vvi3g1069 Vvi3g1069 1069
3 18407104 18409640 + Vvi3g1070 Vvi3g1070 1070
3 18414316 18417667 + Vvi3g1071 Vvi3g1071 1071
3 18431657 18446321 + Vvi3g1072 Vvi3g1072 1072
3 18452317 18460134 + Vvi3g1073 Vvi3g1073 1073
3 18523066 18524555 + Vvi3g1074 Vvi3g1074 1074
3 18544551 18544851 + Vvi3g1075 Vvi3g1075 1075
       

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