Uneven evolutionary rate of the melatonin-related receptor gene (GPR50) in primates

Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria

BACKGROUND

Speciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test whether Zan, which encodes the sperm acrosomal protein zonadhesin that mediates species-specific adhesion to the egg's zona pellucida, is a speciation gene in placental mammals.

RESULTS

Genomic ontogeny reveals that Zan arose by repurposing of a stem vertebrate gene that was lost in multiple lineages but retained in Eutheria on acquiring a function in egg recognition. A 112-species Zan sequence phylogeny, representing 17 of 19 placental Orders, resolves all species into monophyletic groups corresponding to recognized Orders and Suborders, with <5% unsupported nodes. Three other rapidly evolving germ cell genes (Adam2, Zp2, and Prm1), a paralogous somatic cell gene (TectA), and a mitochondrial gene commonly used for phylogenetic analyses (Cytb) all yield trees with poorer resolution than the Zan tree and inferior topologies relative to a widely accepted mammalian supertree. Zan divergence by intense positive selection produces dramatic species differences in the protein's properties, with ordinal divergence rates generally reflecting species richness of placental Orders consistent with expectations for a speciation gene that acts across a wide range of taxa. Furthermore, Zan's combined phylogenetic utility and divergence exceeds those of all other genes known to have evolved in Eutheria by positive selection, including the only other mammalian speciation gene, Prdm9.

CONCLUSIONS

Species-specific egg recognition conferred by Zan's functional divergence served as a mode of prezygotic reproductive isolation that promoted the extraordinary adaptive radiation and success of Eutheria.

Investigating molecular evolutionary forces and phylogenetic relationships among melatonin precursor-encoding genes of different plant species

A total of 53 plant species accessions from different geographic regions, including four melatonin precursor-coding genes obtained from Arachis hypogaea (ASMT1, 2, 3 and T5H) underwent extensive molecular evolutionary analyses. Evolutionary relationships were inferred and showed that dichotomous bifurcating trees did not reflect the true phylogeny since reticulate events took place due likely to recombination. Thus, a phylogenetic network was reconstructed for each type of enzyme and highlighted the presence of such incompatibilities. GARD algorithm pointed out that ASMT1, 2, and 3-coding gene sequences contained recombination sites with significant topological incongruence on both sides of the breakpoints (for ASMT1, and 2), while only on one side of the breakpoints for ASMT3. In contrast, no statistically recombination signal was recorded in T5H-coding gene. Furthermore, gene duplication was localized in the ancestor of a monophyletic group of Populus accessions. Selection pressure was assessed using several statistical models incorporated in HyPhy package through the datamonkey web server. It was demonstrated that numerous individual sites and tree branches experienced predominantly purifying selection. In contrast, the BUSTED model evidenced a gene-wide episodic diversifying selection in the phylogeny of only three enzyme-coding genes (ASMT, and 2, and T5H). Likewise, it was shown that Mixed Effects Model of Episodic Selection (MEME) model detected only episodic positively selected sites in all four melatonin enzymes-coding genes; whereas, REL model failed to detect neither positive nor negative selection in tested individual sites of ASMT3-coding gene.

Molecular characterization of GPR50 gene and study of its comparative genetic variability in sheep breeds adapted to different thermo-contrasting climatic regimens

GPR50, formerly known as a melatonin-related receptor, is one of the three subtypes of melatonin receptor subfamily, together with MTNR1A and MTNR1B. GPR50, despite its high identity with the melatonin receptor family, does not bind melatonin and is considered to be an ortholog of MTNR1C in mammals. GPR50-expressing cells have been found in the dorsomedial nucleus of the hypothalamus, the periventricular nucleus, and the median eminence. Genetic and functional evidence have been recently investigated linking GPR50 to adaptive thermogenesis and torpor, but still, it is an orphan receptor and is yet to be studied conclusively. The aims of the study were to characterize the GPR50 gene of sheep and to study the sequence variability of the gene in Indian sheep breeds of two different thermo-varied agroclimatic conditions. Genomic DNA isolation was done and a 791-bp sequence was amplified using self-designed primers and SNP profiling done out of samples of all the breeds to study the relative frequency of SNPs in each of the breed. Five important non-synonymous mutations were observed in the various breeds studied. T698G, G1097A, G1270A, G1318A, and C1334G lead to the following substitution: valine by glycine, arginine by glutamine, threonine by alanine, isoleucine by valine, and serine by cytosine, respectively. Two synonymous mutations (T663G and C888T) were also observed in some of the studied breeds. G1270A and C888T were the most prevalent SNPs observed in nearly all of the breeds. C888T SNPs were observed in higher prevalence in Chokla, Marwari, and Magra in comparison to Gaddi and Bharat Merino. A PolyPhen-2 analysis, which is used to assess the potential damaging nature of an SNP, revealed that mutation T698G and G1270A were benign while G1097A, G1318A, and C1334G were damaging with a score of 0.987, 0.993, and 0.739, respectively. A 3-D homology model of the protein was prepared using c4zwjA (UniProt sequence ID) as a template using the online version of Phyre2 protein modeling software. The structure demonstrated closed similarity with other G-coupled receptor and it had a 45 % α-helical content. G1270A and C888T may be taken up for SNP correlation in a larger population study for their association with heat stress protection.