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
Vvi16g934 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g935 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g936 . . . . Bpe03g00221 . . . . . . . . . . . Cpe14g00002 . . . . . . . . . . . . . . . . . . . . . . Blo07g00302 . . . . . . . . . . . Cma18g01349 . . Cpe09g00002 . . . . . . . . . . . . . . . . . . .
Vvi16g937 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1042 Cone5ag0750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g938 . . . . . . . . . . . . . . . . Cpe14g00004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00003 . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g939 . . . . . . . . . . . . . . . . Cpe14g00005 . . . . . . . . . . . . . . Cone1ag1036 Cone5ag0747 . . . . . . . . . . . . . . . . . Cma16g00005 . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g940 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g941 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g942 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g01204 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g943 . . . . . . . . . . . . . . Sed07g0879 . Cpe14g00008 Bhi01g01526 Tan01g0051 Cmetu06g1634 . . . . . . . . . . . Cone1ag1033 . . . . . . . . . . . . . . . . . . Cma16g00008 Cma18g01348 . . Cpe09g00004 . Bhi12g00772 . . Lac11g0080 Hepe06g0729 . Lcy12g0062 . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31030944 31035321 - XM_039040441.1 Bhi01g01526 1526
12 23080111 23082368 + XM_039020247.1 Bhi12g00772 772
7 3737696 3739909 - BLOR18234 Blo07g00302 302
3 2758411 2758848 - Bpe012076.1 Bpe03g00221 221
16 22726 47630 - CmaCh16G000030.1 Cma16g00003 3
16 48586 50454 + CmaCh16G000050.1 Cma16g00005 5
16 53102 61263 - CmaCh16G000080.1 Cma16g00008 8
18 10235084 10237464 + CmaCh18G013480.1 Cma18g01348 1348
18 10237917 10245898 + CmaCh18G013490.1 Cma18g01349 1349
6 9514427 9515491 + MELO3C019416.2.1 Cme06g01204 1204
6 8406769 8406936 - PI0014068.1 Cmetu06g1634 1634
1 55174692 55176194 - Conep01aG0108100.1 Cone1ag1033 1033
1 55186083 55188554 - Conep01aG0108400.1 Cone1ag1036 1036
1 55201126 55201818 - Conep01aG0109000.1 Cone1ag1042 1042
5 3217760 3219247 - Conep05aG0077200.1 Cone5ag0747 747
5 3228258 3229371 - Conep05aG0077500.1 Cone5ag0750 750
9 10107 11669 - Cp4.1LG09g00150.1 Cpe09g00002 2
9 19099 21588 - Cp4.1LG09g00110.1 Cpe09g00004 4
14 19161 19598 - Cp4.1LG14g07000.1 Cpe14g00002 2
14 23950 48092 - Cp4.1LG14g06990.1 Cpe14g00004 4
14 48854 51175 + Cp4.1LG14g07070.1 Cpe14g00005 5
14 59221 61799 - Cp4.1LG14g06910.1 Cpe14g00008 8
6 53325851 53327751 - Hsped.06g07290.1 Hepe06g0729 729
11 705130 707164 - Lag0030718.1 Lac11g0080 80
12 930256 932761 - Maker00038447 Lcy12g0062 62
7 6353742 6362315 - Sed0009566.1 Sed07g0879 879
1 718947 723705 + Tan0008249.2 Tan01g0051 51
16 21043967 21050250 + Vvi16g934 Vvi16g934 934
16 21050288 21051593 - Vvi16g935 Vvi16g935 935
16 21059701 21062011 - Vvi16g936 Vvi16g936 936
16 21062994 21065000 + Vvi16g937 Vvi16g937 937
16 21066285 21076136 - Vvi16g938 Vvi16g938 938
16 21079041 21081111 + Vvi16g939 Vvi16g939 939
16 21082368 21083213 - Vvi16g940 Vvi16g940 940
16 21084820 21085998 + Vvi16g941 Vvi16g941 941
16 21086510 21089370 - Vvi16g942 Vvi16g942 942
16 21089926 21092709 - Vvi16g943 Vvi16g943 943
       

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