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
Vvi17g746 . . . . . . . Bma12g01035 . . . Cma11g00095 Car10g00115 Car11g00095 . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00057 Blo15g00268 . . . . . . . . Cmo11g00095 . . . . . . . . . . . . . . . . . . . . . . . Cme02g01981
Vvi17g747 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g752 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0139 . . . . . . . . . . . . Bma08g00166 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g754 . . . . Bpe12g00595 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme02g01982
Vvi17g755 . . Bda06g00597 . . . . Bma12g01037 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0140 . . . . . Blo15g00267 . . Bpe07g00838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8201172 8201753 + Bda023861.1 Bda06g00597 597
13 866282 880826 + BLOR05338 Blo13g00057 57
15 2882185 2882766 - BLOR06661 Blo15g00267 267
15 2897427 2901135 - BLOR06662 Blo15g00268 268
8 2053810 2055002 - Bma027166.1 Bma08g00166 166
12 42428588 42432305 + Bma008383.1 Bma12g01035 1035
12 42443630 42444211 + Bma008385.1 Bma12g01037 1037
7 14580058 14580639 + Bpe021682.1 Bpe07g00838 838
12 11687038 11691430 + Bpe005858.1 Bpe12g00595 595
10 545212 548955 - Carg10347-RA Car10g00115 115
11 547700 552822 - Carg18131-RA Car11g00095 95
11 517114 521651 - CmaCh11G000950.1 Cma11g00095 95
2 26082129 26086437 - MELO3C026291.2.1 Cme02g01981 1981
2 26087380 26091588 - MELO3C026290.2.1 Cme02g01982 1982
11 511533 515990 - CmoCh11G000950.1 Cmo11g00095 95
13 807969 809148 + Conep13aG0014400.1 Cone13ag0139 139
19 750954 753984 + Conep19aG0014500.1 Cone19ag0139 139
19 765943 767594 - Conep19aG0014600.1 Cone19ag0140 140
17 9600463 9610562 - Vvi17g746 Vvi17g746 746
17 9614843 9616885 - Vvi17g747 Vvi17g747 747
17 9616918 9618379 - Vvi17g748 Vvi17g748 748
17 9618399 9624140 - Vvi17g749 Vvi17g749 749
17 9661924 9664617 + Vvi17g750 Vvi17g750 750
17 9687219 9689610 + Vvi17g751 Vvi17g751 751
17 9690037 9700367 + Vvi17g752 Vvi17g752 752
17 9703425 9704372 - Vvi17g753 Vvi17g753 753
17 9713268 9720426 - Vvi17g754 Vvi17g754 754
17 9720549 9722116 + Vvi17g755 Vvi17g755 755
       

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