Abstract
The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, IRF3 is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the IRF3 gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (Capra aegagrus). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats’ populations. Fu and Li tests were significantly positive but Tajima’s D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of IRF3 gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model dN/dS ratio for all goats was greater than one. Phylogenetic Analysis by Maximum Likelihood (PAML) gave a ω0 (dN/dS) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in IRF3 gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat IRF3 led us to conclude that the gene evolution may have been influenced by domestication processes in goats.
Highlights
Domesticated goats are very important livestock diversity; they play significant roles in the economy of many developing countries, as source of organic protein in food, and savings for poor rural farmers
To understand the pattern of evolution of the IRF3 gene in goats, we assembled IRF3 gene coding sequences in domesticated and wild goats from our resequencing data and we used the available sequences for the gene in public databases
Maximum likelihood (ML) tree showed that the IRF3 genes in different domesticated goats share a common ancestor, as illustrated in the length of the tree branches, suggesting single origin of domesticated goats
Summary
Domesticated goats are very important livestock diversity; they play significant roles in the economy of many developing countries, as source of organic protein in food, and savings for poor rural farmers. They are widely distributed across most continents of the world [1], over different ecological and geographic areas including humid tropical rain forest, hot desert regions, and cold to hypoxic high altitude regions, defying harsh environmental conditions and surviving under poor agrarian conditions [2]. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates along with cells reactions to stress [8]. Its activities have been associated with a number of health indices in humans, mice, sheep and cattle [15]
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