DYOGEN group

web-code version: 2009-10-07
database version: 56.01

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Here are examples of queries in Genomicus that illustrate key features of the browser and highlight the benefits of examining comparative genomic data in a broad phylogenetic perspective.

• Fgf8a in the zebrafish genome on chromosome 13 — PhyloView, rooted at the Euteleostomi ancestor
  
  The red square node shows that a duplication of the ancestral Fgf8a gene took place in the ancestral Clupeocephala genome. The zebrafish paralog of Fgf8a is on chromosome 1 (Fgf8b), but the display shows that all other fish also contain two copies, Fgf8a and Fgf8b. Most strikingly, many gene that are neighbours of Fgf8a also have paralogs in the neighborhood of its paralog Fgf8b, and this is true in all sequenced fish genomes. One can therefore conclude (as in the Krox20 example in mouse, above) that this situation is reminiscent of a large segmental duplication - or in this case - of the whole genome duplication that took place in the ancestor of ray-finned fish (so- called «3R» duplication). Interestingly, Fgf8 in tetrapodes is also surrounded by many genes that are still in the vicinity of the zebrafish Fgf8a and Fgf8b gene.
  
  
• Phox2b in the ancestral amniote genome — PhyloView, rooted at the Amniota ancestor
  
  One notices that this region is remarkably well conserved in the descendents of the ancestral amniota, and that Phox2b is surrounded by a high density of conserved non coding elements (CNEs) identified between chicken and several mammals (red symbols in intergenic regions).
  
  
• Unc-50 in C-elegans on chromosome III — PhyloView, rooted at the Bilateria ancestor
  
  This relatively simple situation shows that the Unc-50 gene (green) possesses orthologs in most vertebrates and that a neighbouring gene NP_499273.3 (blue) also has an ortholog in these same species, and that both remains nearly adjacent in all these genomes, except in fish. This is remarkable given the very large cumulated evolutionary distance that separate the different extant genomes.
  
  
• Krox20 (Egr2) in the mouse genome on chromosome 10 — PhyloView, rooted at the Olfactores ancestor
  
  The three red square nodes shows three successive duplications of the ancestral Krox20 gene in the ancestral bony vertebrate (Euteleostomi) genome. By following the branch leading to the most recent copy on mouse chromosome 14 (gene Egr3), one immediately see that this locus contains many other paralogs of genes that are neighbours of Krox20 (colored genes with white outlines). This strongly suggest that the two regions on mouse chromosome 14 and 10 originate from a single event that duplicated all the genes in the ancestral region. This situation is a typical signature of the whole genome duplication(s) that took place just before the bony vertebrate radiation (so-called «2R» duplications).