engleski

Cattle mitogenome sequence analyses revels the presence of selection

Mitochondria have DNA maternal inheritance in vertebrates and has 37 genes, 13 encodes subunits of oxidative phosphorylation (OXPHOS) metabolic pathway, 22 for mitochondrial tRNA, 2 for rRNA and highly variable non-functional D-loop region. While mitochondrial genome controls one of the most important processes in cell, production of energy, it is often modelled assuming constant mutation rate and equilibrium neutral model of molecular evolution. We analysed 799 complete mitogenomes, belonging to >100 breeds. Mitogenome was split in 18 partitions: CYTB, COX1-3, ATP6, ATP8, ND1-6, ND4L, 12S rRNA, 16S rRNA, 22 tRNAs merged in one partition, start and end D-loop region. In the calculation of molecular clock BEAST 2.4.8. software package was used. The estimation of selection pressure, calculated by HyPhy software within Datamonkey platform, was analysed by Fixed Effects Likelihood, Detect Individual Sites Subject to Episode Diversifying Selection and Fast, Unconstrained Bayesian AppRoximation for Inferring Selection. The highest molecular clock rate was observed in non-functional D-loop region, specifically in end part while rRNAs and tRNAs seems to be quite conserved. In the OXPHOS subunit coding region the highest molecular clock (3.84×10-7 and 3.63×10-7 mutations/per base/per year) and percentage of pervasive negative/purifying selection (0.0561 and 0.0525 sites/base) was observed in ND5 and CYTB, respectively. Evidence of pervasive positive/diversifying selection was observed in CYTB (1 site), ND5 (2 sites) and COX3 (1 site). Our results will help better phylogenetic modelling and identification of mitogenome detrimental mutations.

mitochondrial genome, cattle, BEAST, Datamonkey platform, molecular clock rate, selection

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