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.
Fgf1a in the zebrafish genome on chromosome 14 —
PhyloView, rooted at the Neopterygii ancestor
The red square node shows that a duplication of the ancestral Fgf1a
gene took place in the ancestral Osteoglossocephalai genome. The zebrafish
paralog of Fgf1a is on chromosome 21 (Fgf1b), but the display shows
that all other fish also contain two copies, Fgf1a and Fgf1b. Most
strikingly, many gene that are neighbours of Fgf1a also have paralogs
in the neighborhood of its paralog Fgf1b, and this is true in all
sequenced fish genomes. One can therefore conclude 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, Fgf1 in tetrapodes is also
surrounded by many genes that are still in the vicinity of the
zebrafish Fgf1a and Fgf1b gene.
PhyloView, rooted at the Euteleostomi 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) .