Egyptian river buffalo (Bubalus bubalis) mitogenome sequence: characterization and analysis of variations in protein- and transfer RNA-coding genes

Abstract Background Genetic analysis of the mitochondrial genome (mitogenome) has become essential for breed characterization, population genetics, and taxonomic studies in livestock. Genetic variations in mitochondrial DNA protein- and transfer RNA-coding genes have been associated with utility traits in cattle and sheep. The present study focused on characterizing the mitogenome of 29 river buffalo (Bubalus bubalis) from northern and southern Egypt as a population sample, with particular attention to sequence variations in protein- and transfer RNA-coding genes. Results The Egyptian buffalo mitogenome is 16,357 − 16,359 base pairs long, including a non-coding control region (D-loop) and 37 coding genes as in a typical mammalian genome. Alignment of the investigated buffalo mitogenomes revealed 24 haplotypes with nucleotide diversity of 0.1%. Results indicated 44 variations in protein-coding genes and three variations in transfer RNA-coding genes. Significantly, two non-synonymous variations in the protein-coding genes ATP8 (m.7874 A > T) and ND5 (m.12083 C > T) were predicted to result in intolerant amino acid substitutions. Consequently, these substitutions: p.asparagine36tyrosine (p.N36Y) and p.proline112leucine (p.P112L) were predicted to reduce the structural stability of ATP8 and ND5 protein subunits, respectively. The three variations in tRNA-Ile (m.3746T > C), tRNA-Lys (m.7767G > A), and tRNA-Pro (m.15379 A > G) were located away from anticodons and did not alter internal base pairing in tRNAs. The phylogenetic tree of the mitogenome sequence indicated that neither northern nor southern buffalo haplotypes clustered into distinct clades, and no shared mitogenome haplotypes were detected between them. Conclusion Mitogenome sequence analysis demonstrated that Egyptian buffalo share stop codons in protein-coding genes and anticodons in transfer RNAs with all Bubalus species. Differences in start codons of ND2 and ND4L were observed among Bubalus species. Compared with published river buffalo mitogenomes, nucleotide variation m.7874 A > T has been previously detected in Indian river buffalo. In contrast, m.12,083 C > T, m.3746T > C, and m.15,379 A > G represent novel variations identified for the first time in the Egyptian buffalo mitogenome. The phylogenetic analysis suggests that the northern and southern buffalo samples have mixed origins. Further research on the mitogenome using a larger sample size is expected to elucidate the relationship between mtDNA variation and key utility traits and provide clear insights into the genetic diversity of the Egyptian buffalo.