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
Vvi3g1096 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1097 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1098 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1099 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00651 . . . . . . Cpe01g00548 . . . . . . . . . . . . . . . . . .
Vvi3g1101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00542 . . . . Cpe14g00420 . . . . . . . . . . . . . . . . . . .
Vvi3g1102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00543 . . . . Cpe14g00422 . . . . . . . . . . . . . . . . . . .
Vvi3g1103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 3227619 3231993 - CmoCh04G006510.1 Cmo04g00651 651
16 2633087 2635880 - CmoCh16G005420.1 Cmo16g00542 542
16 2636864 2642110 + CmoCh16G005430.1 Cmo16g00543 543
1 3153800 3155563 - Cp4.1LG01g01150.1 Cpe01g00548 548
14 2631146 2635326 - Cp4.1LG14g02940.1 Cpe14g00420 420
14 2636350 2641592 + Cp4.1LG14g03020.1 Cpe14g00422 422
4 30422607 30428790 + Lsi04G023220.1 Lsi04g02322 2322
3 19070426 19072521 + Vvi3g1096 Vvi3g1096 1096
3 19077044 19089362 - Vvi3g1097 Vvi3g1097 1097
3 19092610 19104472 + Vvi3g1098 Vvi3g1098 1098
3 19106478 19108923 + Vvi3g1099 Vvi3g1099 1099
3 19131621 19132932 + Vvi3g1100 Vvi3g1100 1100
3 19133600 19138570 - Vvi3g1101 Vvi3g1101 1101
3 19173480 19192428 + Vvi3g1102 Vvi3g1102 1102
3 19194573 19201576 - Vvi3g1103 Vvi3g1103 1103
3 19264108 19321764 - Vvi3g1104 Vvi3g1104 1104
4 2348 12360 + Vvi4g1 Vvi4g1 1
       

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