Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates

Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain

“…Likewise, these results do not support a role for H3K27me3-mediated clustering in the evolutionary conservation of paralogous syntenies (23), as determined here for the Hox, Dlx, and Sp loci. Similarly, we found no evidence that the transcriptional activation of these specific genes relies upon contacts among each other, or with shared genomic elements.…”

“…Finally, we assessed whether the presence of closely located H3K27me3 domains may promote and/or enhance the establishment of long-range interactions. Such an effect, if associated with a functional outcome, could have participated in the maintenance of paralogous syntenic relationships, such as the conserved clustering of Hox, Dlx, and Sp genes, which is found on multiple chromosomes and thus predates the 2R genome duplications that occurred at the root of the vertebrate lineage (23,24). In both ES and forebrain cells, significant K27 BRICKs are unequally distributed, with clusters of multiple K27 BRICKs being separated by large intervals of several megabases (Fig.…”

Mu Opioids and Their Receptors: Evolution of a Concept

“…They have been identified in over 45 vertebrate species directly by molecular cloning or by bioinformatic analysis of available genomic sequence data. Phylogenetic analysis suggests two rounds of genome-wide duplication (paleoploidization) from a single ancestral opioid gene (unireceptor) (Ohno, 1999;Escriva et al, 2002;Lundin et al, 2003), with the first yielding the ancestral DOR-1/MOR-1 and ORL-1/KOR-1 genes. The duplication then led to DOR-1 and MOR-1, as well as KOR-1 and ORL-1 (Dreborg et al, 2008;Larhammar et al, 2009;Stevens, 2009).…”

Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup

“…Not only has extensive gene duplication occurred throughout the evolution of animals 22 , but in addition it is widely accepted that two rounds of whole-genome duplication occurred early in vertebrate evolution [23][24][25][26][27][28][29] ; most likely, one duplication occurred before the agnathans split from the vertebrate line and one occurred after (FIG. 1; for reviews, see .…”