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
Vvi1g191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g00792 . . . . Cma15g01429 . . . . Bhi12g00829 . . . Hepe02g2694 . Lcy10g1478 Cla01g00568 Cam01g0592 Cec01g0583 Cco01g0607 Clacu01g0587 Cmu01g0557 Cre09g1950 Lsi09g00616 . . .
Vvi1g192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g197 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 25356803 25357823 - XM_039019490.1 Bhi12g00829 829
6 40568896 40570682 - Bma023805.1 Bma06g00792 792
1 6388716 6389375 - CaPI482276_01g005920.1 Cam01g0592 592
1 6113811 6114470 - CcPI632755_01g006070.1 Cco01g0607 607
1 6157171 6157830 - CePI673135_01g005830.1 Cec01g0583 583
1 6033807 6034466 - ClG42_01g0058700.10 Clacu01g0587 587
1 6371348 6372007 - ClCG01G005820.1 Cla01g00568 568
15 9058282 9061115 - CmaCh15G014290.1 Cma15g01429 1429
1 5990560 5991219 - CmPI595203_01g005570.1 Cmu01g0557 557
9 38347711 38348370 + CrPI670011_09g019500.1 Cre09g1950 1950
2 74801818 74802810 + Hsped.02g26940.1 Hepe02g2694 2694
10 38872447 38873100 + Maker00006953 Lcy10g1478 1478
9 6751781 6752440 - Lsi09G006160.1 Lsi09g00616 616
1 1887738 1890871 + Vvi1g191 Vvi1g191 191
1 1891401 1898953 - Vvi1g192 Vvi1g192 192
1 1902381 1918897 - Vvi1g193 Vvi1g193 193
1 1923582 1928032 + Vvi1g194 Vvi1g194 194
1 1929405 1932533 + Vvi1g195 Vvi1g195 195
1 1932547 1958549 + Vvi1g196 Vvi1g196 196
1 1959015 1964386 + Vvi1g197 Vvi1g197 197
1 1967826 1973352 + Vvi1g198 Vvi1g198 198
1 1973841 1978367 + Vvi1g199 Vvi1g199 199
1 1989809 1993774 + Vvi1g200 Vvi1g200 200
       

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