Buffalo and cattle sequence diversity and molecular evolution

Abstract Text: Identification of genes of importance regarding production traits in buffalo is impaired by a paucity of genomic resources although buffalo genome is sequenced. An alternative to fill this gap is to exploit the plenty of data available for cow including SNPchips. The cross-species application of comparative genomics tools i.e. microarrays and comparative sequencing to identify single nucleotide polymorphisms are potential gear to investigate the buffalo genome. However, both tools are dependent on nucleotide sequences similarity between the two species. Therefore, objective of this study was to explicate the sequence diversity between cattle and buffalo for comprehending buffalo genome using available cattle genomic resources. In this study gene diversity between buffalo and cattle was determined applying 86 gene orthologues taken from NCBI consisting of over 273 kb of aligned sequences using MEGA program V6.0. Results for relative rate test were assessed with the chi-squared test using all available sites (over 273 kb) using MEGA program V6.0. There was approximately 3% difference in all genes in term of nucleotide diversity; and 0.267±0.134 in amino acids indicating the possibility for successfully using cross-species strategies for genomic studies. There were significantly higher non synonymous substitutions both in cattle and buffalo. This higher rate of non-synonymous substitutions at similar level in buffalo and cattle indicates a similar positive selection pressure in both species. Results for relative rate test revealed no significance difference on unique mutations between cattle and buffalo lineages at synonymous sites. However, there was a significance difference on unique mutations for non synonymous sites. This indicated that the mutagenic process that generates substitutional mutation is taking place at approximately the same rate at silent sites in cattle and buffalo. However, there was greater variation in mutation rates at non-synonymous sites in both species. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of cattle and buffalo. The present study, for the first time, revealed that variable rates of molecular evolution may be present between cattle and buffalo suggesting usefulness in comparative genomics analysis.

Keywords: Buffalo, Cattle, gene diversity, molecular evolution