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
Vvi19g624 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g625 . Blo03g01469 . Bda09g00417 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g01855 . . Cme06g02771 . . . . . . Bma07g01268 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0021 Cone9ag0020 . . Lsi02g01854 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g627 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g630 . . . . . . . . . . . Cma09g00988 . . . Cpe06g00799 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g631 . . . . . Bpe08g01103 . . . . . . . Car09g00899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g632 . . . . . . . . . . . . . . . . Cpe02g00807 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00991 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g633 . . . Bda09g00418 . Bpe08g01101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma07g01265 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 5209911 5215484 + Bda030997.1 Bda09g00417 417
9 5239190 5240847 + Bda030998.1 Bda09g00418 418
3 41326466 41331902 + BLOR12650 Blo03g01469 1469
7 48057991 48059625 - Bma026529.1 Bma07g01265 1265
7 48122944 48128301 - Bma026534.3 Bma07g01268 1268
8 13044695 13045712 - Bpe023225.1 Bpe08g01101 1101
8 13087887 13093429 - Bpe023230.1 Bpe08g01103 1103
9 5557404 5563703 + Carg12853-RA Car09g00899 899
9 5043668 5051233 + CmaCh09G009880.1 Cma09g00988 988
6 34982615 34983308 + MELO3C014120.2.1 Cme06g02771 2771
9 5263363 5270273 + CmoCh09G009910.1 Cmo09g00991 991
6 138565 144771 + Conep06aG0002100.1 Cone6ag0021 21
9 104129 109726 + Conep09aG0002000.1 Cone9ag0020 20
2 5168384 5174437 + Cp4.1LG02g00680.1 Cpe02g00807 807
6 5118047 5124698 + Cp4.1LG06g08570.1 Cpe06g00799 799
2 24293759 24299425 - Lsi02G018540.1 Lsi02g01854 1854
2 24302374 24308761 - Lsi02G018550.1 Lsi02g01855 1855
19 7871771 7903218 + Vvi19g624 Vvi19g624 624
19 7910838 7917664 - Vvi19g625 Vvi19g625 625
19 7925930 7935919 - Vvi19g626 Vvi19g626 626
19 7936172 7941661 - Vvi19g627 Vvi19g627 627
19 7962056 7965054 - Vvi19g628 Vvi19g628 628
19 7967802 7976826 - Vvi19g629 Vvi19g629 629
19 7977106 7983555 - Vvi19g630 Vvi19g630 630
19 8023416 8033145 - Vvi19g631 Vvi19g631 631
19 8033625 8034820 - Vvi19g632 Vvi19g632 632
19 8035821 8037817 - Vvi19g633 Vvi19g633 633
       

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