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
Vvi3g956 . . . . . . . . Cmo19g00492 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g00595 . . . . . . . . . . . . . . Cma19g00475 . Car19g00350 . . . . . . . . . Cla09g01571 Cam09g1583 Cec09g1725 Cco09g1786 . . Cre09g1620 . . Chy01g00215 .
Vvi3g957 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g958 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi03g00702 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g961 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g962 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g963 . . . . . . . . . . . . . . . . . Bhi05g00929 . . . . . . . . . . . . . . . . . . Csa07g00589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g964 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 32568970 32571573 - XM_039031340.1 Bhi05g00929 929
9 26809522 26809985 + CaPI482276_09g015830.1 Cam09g1583 1583
19 5391161 5404787 - Carg22814-RA Car19g00350 350
9 30526242 30526725 - CcPI632755_09g017860.1 Cco09g1786 1786
9 32326637 32327111 - CePI673135_09g017250.1 Cec09g1725 1725
1 1451095 1472244 - Chy1G002150.1 Chy01g00215 215
9 31214768 31262072 - ClCG09G016000.2 Cla09g01571 1571
19 5685284 5702646 - CmaCh19G004750.1 Cma19g00475 475
19 5857286 5877665 - CmoCh19G004920.1 Cmo19g00492 492
12 8479505 8481372 + Conep12aG0102500.1 Cone12ag0997 997
9 33150933 33154399 - CrPI670011_09g016200.1 Cre09g1620 1620
7 4269757 4272578 - CsaV3_7G006880.1 Csa07g00589 589
7 4326875 4349597 + CsaV3_7G006940.1 Csa07g00595 595
3 9220274 9230068 - Lsi03G007020.1 Lsi03g00702 702
3 14652186 14683330 - Vvi3g956 Vvi3g956 956
3 14771548 14773578 - Vvi3g957 Vvi3g957 957
3 14783386 14784221 + Vvi3g958 Vvi3g958 958
3 14784224 14797327 - Vvi3g959 Vvi3g959 959
3 14836669 14838402 + Vvi3g960 Vvi3g960 960
3 14838440 14853111 + Vvi3g961 Vvi3g961 961
3 14881927 14882711 - Vvi3g962 Vvi3g962 962
3 14960608 14980498 - Vvi3g963 Vvi3g963 963
3 14993697 14993826 + Vvi3g964 Vvi3g964 964
3 15013568 15014879 + Vvi3g965 Vvi3g965 965
       

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