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
Vvi5g319 . . . . . . . . . . . Cma14g01622 . Car14g01447 . . . Bhi01g01001 . . . Hepe05g1452 . Lcy11g1419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g320 . . . . . . . Bma05g00958 . . . . . . Sed02g1185 . . Bhi01g01000 Tan10g1000 Cmetu06g0377 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo14g01659 . . . . . Cpe17g00072 . . . . . . . . . . . . . . . . . .
Vvi5g321 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g322 . . . . Bpe04g01133 . Bma04g01106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01522 . . Blo02g00508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g323 . . . . . Bpe14g01129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01521 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g325 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0058 Cone19ag0061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01519 . . . . . . Bpe05g00765 . . . . . . . . . . . Cpe17g00025 . . . . . . . . . . . . . . . . . .
Vvi5g328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 18270189 18279377 - XM_039026560.1 Bhi01g01000 1000
1 18270707 18273524 + XM_039026580.1 Bhi01g01001 1001
2 8020658 8027026 + BLOR10238 Blo02g00508 508
4 25950104 25950416 + Bma019804.1 Bma04g01106 1106
5 47837892 47839250 + Bma022104.1 Bma05g00958 958
4 9940261 9941809 - Bpe015814.1 Bpe04g01133 1133
5 21022780 21029053 + Bpe025829 Bpe05g00765 765
14 8402016 8402399 - Bpe014504.1 Bpe14g01129 1129
14 12122912 12124081 - Carg20111-RA Car14g01447 1447
14 12169264 12170702 - CmaCh14G016220.1 Cma14g01622 1622
6 5008271 5013950 - PI0010655.2 Cmetu06g0377 377
14 13103837 13109717 + CmoCh14G016590.1 Cmo14g01659 1659
13 359828 361177 - Conep13aG0006100.1 Cone13ag0058 58
19 383202 385184 - Conep19aG0006500.1 Cone19ag0061 61
17 166662 172454 + Cp4.1LG17g00680.1 Cpe17g00025 25
17 417449 420802 + Cp4.1LG17g00240.1 Cpe17g00072 72
6 12751769 12758126 - CsaV3_6G017170.1 Csa06g01519 1519
6 12760556 12763802 - CsaV3_6G017190.1 Csa06g01521 1521
6 12771046 12773599 + CsaV3_6G017200.1 Csa06g01522 1522
5 63835891 63837211 - Hsped.05g14520.1 Hepe05g1452 1452
11 38020372 38021583 - Maker00031753 Lcy11g1419 1419
2 48858314 48869166 + Sed0015229.1 Sed02g1185 1185
10 8824062 8829986 - Tan0005818.2 Tan10g1000 1000
5 3158390 3159842 + Vvi5g319 Vvi5g319 319
5 3160875 3165959 - Vvi5g320 Vvi5g320 320
5 3167516 3178049 - Vvi5g321 Vvi5g321 321
5 3179043 3181240 - Vvi5g322 Vvi5g322 322
5 3181985 3182859 + Vvi5g323 Vvi5g323 323
5 3183730 3190850 - Vvi5g324 Vvi5g324 324
5 3190855 3194069 - Vvi5g325 Vvi5g325 325
5 3197069 3199170 + Vvi5g326 Vvi5g326 326
5 3203017 3217695 + Vvi5g327 Vvi5g327 327
5 3217985 3244322 - Vvi5g328 Vvi5g328 328
       

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