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
Vvi4g1352 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1353 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1354 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0924 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0963 Cone12ag0931 . . . . . . . . . Bda14g00948 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1360 . . Bda04g00387 Bda10g00408 . . Bma09g00443 Bma15g00774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo05g00524 Blo06g00185 . . Bpe10g00268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy02g01137 .
Vvi4g1361 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 50894782 50907453 - Bda019335.1 Bda04g00387 387
10 36240863 36243874 - Bda007239.1 Bda10g00408 408
14 7617604 7620574 + Bda027735.1 Bda14g00948 948
5 9635994 9641193 + BLOR15486 Blo05g00524 524
6 7767998 7778576 + BLOR16768 Blo06g00185 185
9 38321933 38333633 - Bma029451.1 Bma09g00443 443
15 16369849 16383474 + Bma013849.1 Bma15g00774 774
10 9985184 10002016 - Bpe002604.1 Bpe10g00268 268
2 8046142 8049227 - Chy2G034040.1 Chy02g01137 1137
8 8906478 8913396 - Conep08aG0095000.1 Cone8ag0924 924
8 9112981 9113613 - Conep08aG0099100.1 Cone8ag0963 963
12 8143135 8143764 - Conep12aG0095900.1 Cone12ag0931 931
4 23692719 23693812 + Vvi4g1352 Vvi4g1352 1352
4 23718053 23723233 + Vvi4g1353 Vvi4g1353 1353
4 23723364 23737176 - Vvi4g1354 Vvi4g1354 1354
4 23750422 23756493 - Vvi4g1355 Vvi4g1355 1355
4 23760777 23765255 + Vvi4g1356 Vvi4g1356 1356
4 23766044 23774373 - Vvi4g1357 Vvi4g1357 1357
4 23774950 23783516 + Vvi4g1358 Vvi4g1358 1358
4 23794824 23796668 - Vvi4g1359 Vvi4g1359 1359
4 23798588 23816120 - Vvi4g1360 Vvi4g1360 1360
4 23834849 23834978 - Vvi4g1361 Vvi4g1361 1361
       

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