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
Vvi19g844 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g845 . . . . . . . Bma13g00912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00676 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g846 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0233 . . . . . . . . . . . . . . . . . Cmo09g00677 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00678 . . Car04g00605 . . . . . . . . . . . . . . . . . . . . .
Vvi19g848 . . . . . . . . . Cmo04g00701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00972 Blo10g00714 Bda05g00818 Bda12g00808 . . . . . . . Cma04g00653 . . . . Cpe01g00589 . . . . . . . . . . . . . . . . . .
Vvi19g849 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g850 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g851 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g853 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56689968 56691242 - Bda021976.1 Bda05g00818 818
12 37256720 37257637 + Bda009317.1 Bda12g00808 808
7 29185603 29186413 + BLOR18904 Blo07g00972 972
10 22734181 22737057 + BLOR02504 Blo10g00714 714
13 39534550 39535457 - Bma009989.1 Bma13g00912 912
4 3471979 3476185 - Carg13100-RA Car04g00605 605
4 3336026 3345509 - CmaCh04G006530.1 Cma04g00653 653
4 3479202 3483094 - CmoCh04G007010.1 Cmo04g00701 701
9 3358471 3363491 - CmoCh09G006760.1 Cmo09g00676 676
9 3365428 3367489 - CmoCh09G006770.1 Cmo09g00677 677
9 3368556 3371715 - CmoCh09G006780.1 Cmo09g00678 678
6 1078537 1080092 - Conep06aG0023500.1 Cone6ag0233 233
9 1146817 1148424 - Conep09aG0027200.1 Cone9ag0269 269
1 3404293 3408670 - Cp4.1LG01g00590.1 Cpe01g00589 589
19 12437323 12438413 + Vvi19g844 Vvi19g844 844
19 12496228 12500010 - Vvi19g845 Vvi19g845 845
19 12608003 12612293 + Vvi19g846 Vvi19g846 846
19 12661107 12663417 + Vvi19g847 Vvi19g847 847
19 12760339 12761747 - Vvi19g848 Vvi19g848 848
19 12826741 12829288 - Vvi19g849 Vvi19g849 849
19 12834088 12834905 - Vvi19g850 Vvi19g850 850
19 12837509 12837996 - Vvi19g851 Vvi19g851 851
19 12924113 12928461 + Vvi19g852 Vvi19g852 852
19 12999414 13001085 - Vvi19g853 Vvi19g853 853
       

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