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
Vvi4g92 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g93 Blo01g01463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g00263 . . . . . . . . . . . . . . . . . Cme07g00220
Vvi4g94 Blo01g01464 . . . . Bpe02g00338 . . . . . . Car09g00288 . . . Cpe06g00240 . . . . . . . Cla05g01574 . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00591 . . . . . Cpe02g00262 Bhi09g03147 . . . Hepe01g1884 . . . . . . . . . . . . .
Vvi4g95 . Blo12g01015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01778 . . . . . . Cpe02g00261 . . . . . . . . . . . . . . . . . .
Vvi4g96 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g97 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g98 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00519 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g99 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 80659001 80662458 + XM_039042139.1 Bhi09g03147 3147
1 53803380 53816561 + BLOR01463 Blo01g01463 1463
1 53823002 53829599 + BLOR01464 Blo01g01464 1464
12 28097102 28102192 + BLOR05034 Blo12g01015 1015
2 10346578 10347597 - Bma015022.1 Bma02g00519 519
2 2200872 2218613 - Bpe008179.1 Bpe02g00338 338
9 1551505 1554494 - Carg21733-RA Car09g00288 288
5 26733041 26736534 - ClCG05G015160.1 Cla05g01574 1574
7 1456692 1459150 + MELO3C016876.2.1 Cme07g00220 220
1 13140379 13144532 + CmoCh01G017780.1 Cmo01g01778 1778
9 2907414 2911576 - CmoCh09G005910.1 Cmo09g00591 591
20 1209198 1210534 - Conep20aG0028300.1 Cone20ag0272 272
2 1351414 1359034 + Cp4.1LG02g06080.1 Cpe02g00261 261
2 1354706 1361371 - Cp4.1LG02g06030.1 Cpe02g00262 262
2 1362081 1363966 - Cp4.1LG02g06010.1 Cpe02g00263 263
6 1279966 1286804 - Cp4.1LG06g02380.1 Cpe06g00240 240
1 83710598 83713713 - Hsped.01g18840.1 Hepe01g1884 1884
4 945472 948330 - Vvi4g92 Vvi4g92 92
4 953960 957028 + Vvi4g93 Vvi4g93 93
4 961662 979105 + Vvi4g94 Vvi4g94 94
4 979130 981610 - Vvi4g95 Vvi4g95 95
4 982055 986881 - Vvi4g96 Vvi4g96 96
4 991578 994919 + Vvi4g97 Vvi4g97 97
4 998107 1000178 - Vvi4g98 Vvi4g98 98
4 1004336 1006409 + Vvi4g99 Vvi4g99 99
4 1010388 1016584 - Vvi4g100 Vvi4g100 100
4 1029310 1029946 + Vvi4g101 Vvi4g101 101
       

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