An optimised phylogenetic method sheds more light on the main branching events of rhodopsin-like superfamily.
The comparative genomics between different rhodopsin-like family groups (α, β, γ and δ) is not well studied. We used a combination of phylogenetic analysis and statistical genomic methods to compare rhodopsin-like family proteins in species likely symbolic of this family's evolutionary progression. For intra-cluster relationships, we applied mathematical optimisation to enhance the tree search produced by the neighbour joining method (NJ) and compared it with maximum likelihood (ML) method. To infer inter-clusters relationships, we used Needleman-Wunsch analysis (NW), HHsearch, ancestral sequence reconstruction and phylogenetic network analysis. Using this workflow, we were able to identify key evolutionary events in the rhodopsin-like family receptors. We found that α rhodopsin-like group gave rise to the β group, while the γ rhodopsin-like group diverged from the β group. We tracked the diversification of every cluster, revealing that fungal opsin is the most ancient member of the α group, while adenosine receptors could be the first member to diverge in the MECA (melanocortin, endothelial differentiation sphingolipid, cannabinoid, and adenosine receptors) subfamily and that histamine receptors could be the parent of the amines receptors, while hypocretin receptors might be the most ancient member of the β group. SOG (somatostatin, opioid, galanin) receptors formed the most ancient members of the γ group. Our analysis indicated that basal receptors might be playing a role in early evolution of the nervous system. This is evident in Trichoplax adhaerens genome, where we located histamine receptors and adenosine receptors.
Functional Pharmacology Group, Department of Neuroscience, Uppsala University, Biomedical Centre, Uppsala, Sweden; Research Group For Computational System Biology, German Centre of Neurodegenerative Diseases, Gottingen, Germany. Electronic address: michel.edwar77@gmail.com.
Michel E
ME
Mickael
Research Group For Computational System Biology, German Centre of Neurodegenerative Diseases, Gottingen, Germany.
Ashish
A
Rajput
Faculty of Natural Sciences, School of Computing and Mathematics, Keele University, Keele ST5 5BG, UK.
Jannetta
J
Steyn
Functional Pharmacology Group, Department of Neuroscience, Uppsala University, Biomedical Centre, Uppsala, Sweden.
Lyle
L
Wiemerslage
Dept. of Biomedicine, University of Basel, Switzerland.
Thomas
T
Bürglin
D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010802:Phylogeny; D012243:Rhodopsin / Q000145:classification* / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
D012243:Rhodopsin