Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis

• Published in: Biochemical genetics Vol. 63; no. 1; pp. 43 - 66
• Main Authors: Arya, Mansi, Ghosh, Abhishek, Tyagi, Kaomud, Tyagi, Inderjeet, Bisht, Satpal Singh, Kumar, Vikas
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.02.2025; Springer Nature B.V
• Subjects: Altitude; Animals; Biochemistry; Biomedical and Life Sciences; Biomedicine; Bos frontalis; Cattle - genetics; Comparative analysis; Conservation genetics; Cyclooxygenase-2; data collection; Datasets; Evolution; Evolution & development; Evolution, Molecular; evolutionary adaptation; Evolutionary conservation; Evolutionary genetics; Genes; Genetics; Genome, Mitochondrial; Genomes; Genomic analysis; genomics; High altitude environments; Human Genetics; Medical Microbiology; Mitochondria; mitochondrial genome; mitochondrial proteins; Original Article; Oxidative phosphorylation; Phosphorylation; Phylogeny; Protein structure; Proteins; RNA, Transfer - genetics; Secondary structure; selection pressure; Selection, Genetic; species; zebu; Zoology; Selection pressure; Codon usage bias; Badri; Phylogeny; Mitogenome
• ISSN: 0006-2928; 1573-4927; 1573-4927
• DOI: 10.1007/s10528-024-10691-y

High-altitude mammals are often subject to specific environmental obstacles, which exert selective pressure on their physiological and morphological traits, hence driving their evolutionary processes. It is anticipated that these circumstances will lead to the adaptive evolution of protein-coding genes (PCGs) in the mitochondrial genome, which play a crucial role in the oxidative phosphorylation system. In this study, we have generated the complete mitochondrial genome of the Badri breed of Bos indicus inhabiting a high-altitude environment to test the signatures of adaptive evolution on PCGs and their phylogenetic relationships. The complete mitogenome of the Badri breed is 16,339 bp and most tRNAs showed typical clover-leaf secondary structure with a few exceptions, like trnS1 and trnS2 without DHU arm and trnK without DHU loop. Comparative analysis of PCGs indicated that cox1 is the most conserved, while atp6 is the most variable gene. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated the purifying selection (Ka/Ks < 1) in the protein-coding genes that shape the diversity in mitogenome of Bos indicus . Furthermore, Branch-site model (BSM) suggested that  cox1 , cox2 , nad3 , nad4L , and nad6 underwent stronger purifying selection (ω < 1) than other PCGs in 15 breeds of 4 species, including Badri. BSM also detected 10 positive sites in PCGs and one in 13 PCGs concatenated dataset. Additional analyses in Datamonkey indicated 11 positive sites and 23 purifying sites in the concatenated dataset, a relaxation of selection strength in  nad3 , and no evidence of episodic diversifying selection in any PCGs. Phylogeny revealed the sister relationship of the Badri with other breeds of Bos indicus as well as Bos frontalis (Gayal-2). The mitogenome of the Badri breed is an important genomic resource for conservation genetics of this species and also contributes to the understanding of the adaptive evolution of mitochondrial protein coding genes.