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
Vvi2g792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g793 . . . . . . . Bma14g00074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g795 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g797 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g798 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00112 Cam10g0108 Cec10g0117 Cco10g0118 Clacu10g0114 Cmu10g0961 Cre10g0371 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00112 . .
Vvi2g799 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g800 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1774808 1775800 - Bda025211.1 Bda07g00145 145
14 889912 896189 + Bma010477.2 Bma14g00074 74
10 2666706 2668456 - CaPI482276_10g001080.1 Cam10g0108 108
10 1079502 1081252 - CcPI632755_10g001180.1 Cco10g0118 118
10 1092425 1094175 - CePI673135_10g001170.1 Cec10g0117 117
10 1393951 1395701 - ClG42_10g0011400.10 Clacu10g0114 114
10 1118452 1124802 - ClCG10G001090.2 Cla10g00112 112
10 1544215 1546815 - CmPI595203_10g009610.1 Cmu10g0961 961
10 2507679 2509429 - CrPI670011_10g003710.1 Cre10g0371 371
3 889425 893301 - CsaV3_3G001120.1 Csa03g00112 112
2 13051403 13055977 - Vvi2g792 Vvi2g792 792
2 13058117 13081615 - Vvi2g793 Vvi2g793 793
2 13170202 13171363 - Vvi2g794 Vvi2g794 794
2 13196757 13200394 - Vvi2g795 Vvi2g795 795
2 13229559 13231569 - Vvi2g796 Vvi2g796 796
2 13235349 13237726 + Vvi2g797 Vvi2g797 797
2 13345787 13348282 + Vvi2g798 Vvi2g798 798
2 13348292 13349583 + Vvi2g799 Vvi2g799 799
2 13406893 13407178 + Vvi2g800 Vvi2g800 800
2 13419773 13426129 + Vvi2g801 Vvi2g801 801
       

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