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
Vvi2g172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0874 . . . Cme07g01533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g173 . . . . . . . Bma14g00108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01130 .
Vvi2g174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01532 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g175 . . . . . . . . . Cmo16g00583 . . . . . . . . . . . . . . Cla07g01084 Cam07g1416 Cec07g1246 Cco07g1222 Clacu07g1148 Cmu07g1128 Cre07g1505 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01129 .
Vvi2g176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g177 Blo02g01161 Blo03g00259 . Bda08g00456 Bpe05g00706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00928 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g178 . . . Bda08g00455 . . . . . Cmo16g00580 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01531 . . . . . . . . . . . . Cma16g00532 . . . . . . . . . . . . . . . . . . . . Chy07g01128 .
Vvi2g179 . . . . . . . . . . . . . . . . . . . . . . . . Cla07g01083 Cam07g1417 Cec07g1245 Cco07g1220 Clacu07g1147 Cmu07g1127 Cre07g1504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g181 . . . . . . . . . Cmo16g00579 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01526 . . . . . . . . . . . . Cma16g00531 Car06g00531 . . . . . . . . . . . . . . . . . . . Chy07g01127 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 4721290 4722918 + Bda024906.2 Bda08g00455 455
8 4735004 4736242 - Bda024908.1 Bda08g00456 456
2 43262871 43264156 - BLOR10891 Blo02g01161 1161
3 5474864 5478352 - BLOR11440 Blo03g00259 259
14 1466252 1468674 + Bma010513.1 Bma14g00108 108
5 20634286 20635532 - Bpe025824 Bpe05g00706 706
7 28698094 28705472 + CaPI482276_07g014160.1 Cam07g1416 1416
7 28708462 28712299 + CaPI482276_07g014170.1 Cam07g1417 1417
6 2986491 2989661 + Carg16283-RA Car06g00531 531
7 26061946 26066049 - CcPI632755_07g012200.1 Cco07g1220 1220
7 26082056 26089503 - CcPI632755_07g012220.1 Cco07g1222 1222
7 27965120 27970869 - CePI673135_07g012450.1 Cec07g1245 1245
7 27985074 27992523 - CePI673135_07g012460.1 Cec07g1246 1246
7 16178995 16182507 - Chy7G139570.1 Chy07g01127 1127
7 16184436 16194185 - Chy7G139580.1 Chy07g01128 1128
7 16208741 16212274 - Chy7G139590.1 Chy07g01129 1129
7 16226933 16235885 - Chy7G139600.1 Chy07g01130 1130
7 26135029 26140756 - ClG42_07g0114700.10 Clacu07g1147 1147
7 26152159 26159655 - ClG42_07g0114800.10 Clacu07g1148 1148
7 27516887 27522845 - ClCG07G011410.1 Cla07g01083 1083
7 27536293 27548513 - ClCG07G011420.1 Cla07g01084 1084
16 2712426 2715313 - CmaCh16G005310.1 Cma16g00531 531
16 2715744 2720019 - CmaCh16G005320.1 Cma16g00532 532
7 21090782 21094818 - MELO3C016263.2.1 Cme07g01526 1526
7 21157235 21161825 - MELO3C016267.2.1 Cme07g01531 1531
7 21173860 21178527 - MELO3C016268.2.1 Cme07g01532 1532
7 21179853 21184914 - MELO3C016269.2.1 Cme07g01533 1533
2 5700632 5703452 + CmoCh02G009280.1 Cmo02g00928 928
16 2807018 2810102 - CmoCh16G005790.1 Cmo16g00579 579
16 2810291 2812475 - CmoCh16G005800.1 Cmo16g00580 580
16 2818984 2820352 - CmoCh16G005830.1 Cmo16g00583 583
7 26344601 26354503 - CmPI595203_07g011270.1 Cmu07g1127 1127
7 26377876 26383596 - CmPI595203_07g011280.1 Cmu07g1128 1128
9 4246718 4249569 + Conep09aG0089500.1 Cone9ag0874 874
7 30300114 30304788 - CrPI670011_07g015040.1 Cre07g1504 1504
7 30307710 30315821 - CrPI670011_07g015050.1 Cre07g1505 1505
2 1711562 1715073 + Vvi2g172 Vvi2g172 172
2 1715551 1732689 + Vvi2g173 Vvi2g173 173
2 1733794 1737112 + Vvi2g174 Vvi2g174 174
2 1738782 1744976 + Vvi2g175 Vvi2g175 175
2 1746545 1777292 + Vvi2g176 Vvi2g176 176
2 1777415 1779497 - Vvi2g177 Vvi2g177 177
2 1780006 1787739 + Vvi2g178 Vvi2g178 178
2 1788233 1792130 + Vvi2g179 Vvi2g179 179
2 1792281 1793558 + Vvi2g180 Vvi2g180 180
2 1794322 1801778 + Vvi2g181 Vvi2g181 181
       

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