In Silico Analyses of B-LG Gene in some Mammalian Species

O.M. Momoh, Samuel Ter Vincent, A. Yakubu

Abstract


This study investigates in silico the genetic diversity of B-Lg and their evolutionary and differentiation within and among selected species; and also examines the attendant effects of polymorphism on the functionality of the gene. A total of 21 B-Lg gene sequences with corresponding amino acids belonging to 6 species [cattle (4), buffalo (4), sheep (3), goat (3), pig (3) and horse (4)] were retrieved from GenBank (www.ncbi.nlm.nih.gov). All sequences were trimmed to equal length (500bp) corresponding to the same region. Sequences alignment, translation and comparison were done with ClustalW using IUB substitution matrix, gap open penalty of 15 and gap extension penalty of 6.66. The alignment revealed high polymorphism of sequences among extant. The Dxy inferred using p-distance revealed that sheep and goat had the lowest distance of 0.05 with a maximum distance of 0.65 between goat and horse. The hypothesis of strict neutrality (dN=dS) was rejected for all extant as allelic sequence evolution was driven by both purifying and positive selection. Only pig and buffalo were driven by positive selection. In-silico functional analysis of non-synonymous mutations using PANTHER revealed that, all the 12 amino acid substitutions (10 in cattle and 2 in sheep) did not impair protein function. The Neighbour-Joining phylogeny revealed trans-species evolution, but was species-wise phylogeny was obtained with consensus sequences. Thus, all probed SNPs from this study have no deleterious effect and can be tolerated by breeders when selecting stocks for milk improvement.


Keywords


Single Nucleotide Polymorphism, Phylogeny, Alignment, Variants

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