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
Vvi18g1610 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00847 Cam11g0877 Cec11g0878 Cco11g0873 Clacu11g0985 Cmu11g0836 Cre11g1321 . . . .
Vvi18g1612 . . . . Bpe02g00277 . . . . . . . . . . . . Bhi04g02592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1204 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1616 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1617 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 69617937 69623534 + XM_039029114.1 Bhi04g02592 2592
2 1856804 1866075 + Bpe008121.1 Bpe02g00277 277
11 12059010 12064116 + CaPI482276_11g008770.1 Cam11g0877 877
11 11031074 11036170 + CcPI632755_11g008730.1 Cco11g0873 873
11 11404551 11409635 + CePI673135_11g008780.1 Cec11g0878 878
11 11239275 11244386 - ClG42_11g0098500.10 Clacu11g0985 985
11 13021658 13026769 + ClCG11G008830.1 Cla11g00847 847
11 10567317 10572423 - CmPI595203_11g008360.1 Cmu11g0836 836
4 10115176 10117426 - Conep04aG0125000.1 Cone4ag1204 1204
11 12943533 12951237 + CrPI670011_11g013210.1 Cre11g1321 1321
18 26248387 26249251 - Vvi18g1610 Vvi18g1610 1610
18 26257298 26262353 - Vvi18g1611 Vvi18g1611 1611
18 26310664 26319306 - Vvi18g1612 Vvi18g1612 1612
18 26339439 26341510 + Vvi18g1613 Vvi18g1613 1613
18 26355120 26358597 - Vvi18g1614 Vvi18g1614 1614
18 26388225 26396921 + Vvi18g1615 Vvi18g1615 1615
18 26399781 26401436 - Vvi18g1616 Vvi18g1616 1616
18 26414511 26416346 + Vvi18g1617 Vvi18g1617 1617
18 26421125 26423185 - Vvi18g1618 Vvi18g1618 1618
18 26433782 26458644 - Vvi18g1619 Vvi18g1619 1619
       

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