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
Vvi18g1720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1721 . . . . . . . . . . . . . . Sed03g0696 . . Bhi04g02547 Tan11g0050 Cmetu03g0396 . Hepe02g3464 . Lcy10g2356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00794 Cam11g0828 Cec11g0811 Cco11g0815 Clacu11g1030 Cmu11g0891 Cre11g1272 . . . .
Vvi18g1722 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1723 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1725 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1726 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1727 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1728 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1729 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 68419048 68428005 - XM_039029159.1 Bhi04g02547 2547
11 10556414 10563887 - CaPI482276_11g008280.1 Cam11g0828 828
11 9354146 9361577 - CcPI632755_11g008150.1 Cco11g0815 815
11 9610770 9618122 - CePI673135_11g008110.1 Cec11g0811 811
11 12732545 12740023 + ClG42_11g0103000.10 Clacu11g1030 1030
11 11457366 11465253 - ClCG11G008300.1 Cla11g00794 794
3 26054192 26061779 - PI0017848.1 Cmetu03g0396 396
11 12061593 12069073 + CmPI595203_11g008910.1 Cmu11g0891 891
11 11240804 11248340 - CrPI670011_11g012720.1 Cre11g1272 1272
2 83947777 83955530 - Hsped.02g34640.1 Hepe02g3464 3464
10 47156576 47164233 - Maker00039364 Lcy10g2356 2356
3 4158151 4165976 - Sed0005744.1 Sed03g0696 696
11 766776 773763 + Tan0002109.1 Tan11g0050 50
18 28184066 28198137 - Vvi18g1720 Vvi18g1720 1720
18 28208995 28216173 + Vvi18g1721 Vvi18g1721 1721
18 28239145 28241275 - Vvi18g1722 Vvi18g1722 1722
18 28260002 28262148 - Vvi18g1723 Vvi18g1723 1723
18 28267993 28270421 - Vvi18g1724 Vvi18g1724 1724
18 28271404 28273634 - Vvi18g1725 Vvi18g1725 1725
18 28282936 28284029 + Vvi18g1726 Vvi18g1726 1726
18 28286786 28287068 - Vvi18g1727 Vvi18g1727 1727
18 28294817 28296663 + Vvi18g1728 Vvi18g1728 1728
18 28305574 28309440 - Vvi18g1729 Vvi18g1729 1729
       

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