Mitochondrial genome assembly of the Peruvian Paso horse through PacBio long-read sequencing.

The complete mitochondrial genome of the Peruvian Paso Horse was assembled using PacBio HiFi long reads, resulting in a high-quality circular genome of 16,617 bp comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition and gene structure were consistent with other equine mitogenomes. Codon usage analysis revealed a bias toward CUA (Leu), AUA and AUC (Ile), suggesting translational optimization. Thirty-five heteroplasmic variants were identified, predominantly located in RNA genes (12 S rRNA and tRNA-Phe), with allele frequencies between 0.10 and 0.60 and no substitutions in protein-coding genes, consistent with purifying selection. Repeat analysis detected a single 192 bp tandem repeat and two short tandem repeat (STR) motifs (CATAA and TCT) within the control region, supporting their functional role in mitochondrial replication. Comparative mitogenomic alignment with 14 representative breeds showed high collinearity and structural conservation, with localized variability in the control region (~ 16,000-16,600 bp) and minor divergence at positions ~ 1,500 and ~ 10,000 bp. Phylogenetic analysis positioned the Peruvian Paso Horse within a European breed clade, closely related to Westphalian, Maremmano, and individuals from Germany and Serbia with potential connections to Asian lineages. These results provide valuable insights for equine mitogenomics, conservation, and evolutionary studies.