Mutational and Evolutionary Analyses of Bovine Reprimo Gene

Abstract

Bovine reprimo (RPRM) gene is a pleiotropic gene involved in cancer suppression, regulation of mitotic cell cycle, cell cycle arrest, survival and fertility. This study used in silico approach to analyse single nucleotide polymorphisms (SNPs) and indels in bovine RPRM gene in order to identify mutations which can be used in marker assisted selection when working with the gene in cattle. The evolution of the gene was also studied to infer its relatedness with RPRM gene of other species. Nucleotide and amino acid sequences of bovine RPRM gene were downloaded from GenBank. Amino acid sequences of RPRM gene of other animals were also downloaded from GenBank and Universal Protein Resources database. The SNPs and indels in the bovine RPRM gene were identified and analysed using HaploSNPer software. The percent identity and similarity between the amino acid sequences of bovine RPRM and RPRM genes of other species was determined by conducting a pair wise comparison of the sequences using Comparing two or more sequences option of Basic Local Alignment Search Tool. The Molecular Evolution and Genetic Analysis (MEGA5) software was used to determine the phylogenetic relationship between bovine RPRM and RPRM genes of other species. Four (4) reliable transition SNPs and 5 indels were identified in the gene with D-value of 0.4677. The reliable transitions identified were 890G>A, 901A>G, 1216C>T and 1245C>T. The indels were 845C/-,878G/-, 1229-/T, 1230-/T and 1264-/A. The percent identity and similarity between the amino acid sequence of bovine RPRM and RPRM genes of other mammals were higher than 90% (91-100% and 94-100%, respectively), except in the duckbill platypus where percent identity and similarity indices were 78% and 81%, respectively. Phylogenetic analysis of the gene revealed that there was high relatedness between bovine RPRM and RPRM genes of other mammals. It can therefore be concluded that bovine RPRM gene contained 4 transition mutations and 5 indels that can be used in marker assisted selection. Evolutionary findings also demonstrated the existence of a divergent evolution between bovine RPRM gene and RPRM gene of fishes and frog.

Keywords: Identity, phylogeny, reprimo gene, similarity, single nucleotide polymorphism