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
Vvi16g924 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g925 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g926 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1047 Cone5ag0757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1046 Cone5ag0756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g931 . Blo15g00003 . . . Bpe07g01106 . . . . Cma02g01149 Cma15g00993 . . . Cpe05g00574 . . . . . . . . . . . . . . . Cone1ag1044 Cone5ag0754 . . . Csa05g00015 Chy09g01465 . . . . . . . . . . . . . . . . . Cpe13g00341 . . . . . . . . . . . . . . . . . Cme09g02016
Vvi16g932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g933 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 29390 30357 - BLOR06397 Blo15g00003 3
7 16338869 16344899 + Bpe021944.1 Bpe07g01106 1106
9 16105839 16110462 + Chy9G171810.1 Chy09g01465 1465
2 6788459 6791733 + CmaCh02G011490.1 Cma02g01149 1149
15 5950575 5954955 - CmaCh15G009930.1 Cma15g00993 993
9 23855417 23860337 + MELO3C005915.2.1 Cme09g02016 2016
1 55207243 55209980 + Conep01aG0109200.1 Cone1ag1044 1044
1 55212696 55216224 + Conep01aG0109400.1 Cone1ag1046 1046
1 55216512 55219510 + Conep01aG0109500.1 Cone1ag1047 1047
1 55218792 55223322 - Conep01aG0109600.1 Cone1ag1048 1048
5 3235183 3237707 + Conep05aG0077900.1 Cone5ag0754 754
5 3241353 3243832 + Conep05aG0078100.1 Cone5ag0756 756
5 3244437 3246456 + Conep05aG0078200.1 Cone5ag0757 757
5 3479720 3483532 - Cp4.1LG05g05730.1 Cpe05g00574 574
13 3111890 3116424 + Cp4.1LG13g03400.1 Cpe13g00341 341
5 75640 90027 - CsaV3_5G000150.1 Csa05g00015 15
16 20939768 20940254 - Vvi16g924 Vvi16g924 924
16 20956386 20986185 - Vvi16g925 Vvi16g925 925
16 20987084 20993301 - Vvi16g926 Vvi16g926 926
16 20998714 21001887 - Vvi16g927 Vvi16g927 927
16 21004456 21010493 + Vvi16g928 Vvi16g928 928
16 21010766 21014022 - Vvi16g929 Vvi16g929 929
16 21017272 21022887 - Vvi16g930 Vvi16g930 930
16 21028690 21038014 - Vvi16g931 Vvi16g931 931
16 21040650 21042003 - Vvi16g932 Vvi16g932 932
16 21043159 21043959 + Vvi16g933 Vvi16g933 933
       

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