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
Vvi4g642 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g643 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g644 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g645 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g647 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g648 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g649 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g650 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g651 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
18 2472502 2481325 - BLOR08734 Blo18g00246 246
18 2559804 2563297 - BLOR08736 Blo18g00248 248
18 2590478 2596093 - BLOR08737 Blo18g00249 249
18 2607047 2610605 - BLOR08738 Blo18g00250 250
4 27460551 27464837 + Lsi04G020340.1 Lsi04g02034 2034
4 8285868 8291277 + Vvi4g642 Vvi4g642 642
4 8358355 8364248 + Vvi4g643 Vvi4g643 643
4 8446666 8446942 + Vvi4g644 Vvi4g644 644
4 8454239 8455121 + Vvi4g645 Vvi4g645 645
4 8461865 8466086 + Vvi4g646 Vvi4g646 646
4 8473897 8482145 - Vvi4g647 Vvi4g647 647
4 8484122 8513037 + Vvi4g648 Vvi4g648 648
4 8597275 8598256 + Vvi4g649 Vvi4g649 649
4 8600288 8616390 + Vvi4g650 Vvi4g650 650
4 8622022 8624152 + Vvi4g651 Vvi4g651 651
       

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