Mitochondrial Genome Assembly of the Peruvian Paso Horse Through PacBio Long-Read Sequencing

The Peruvian Paso Horse (PPH) is a unique breed recognized for its distinctive gait and cultural significance. Despite its importance, its mitochondrial genome (mitogenome) remains largely uncharacterized. This study presents the first complete mitogenome of the PPH, which was assembled using PacBio long-read sequencing. The resulting high-quality circular mitogenome (16,617 bp) contains 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region (D-loop). The Nucleotide composition was 24.44% A, 25.13% T, 25.62% C, and 24.81% G, consistent with other equine mitogenomes. Codon usage analysis revealed a bias toward CUA(Leu), AUC(Ile), and AUA(Ile), suggesting optimization for mitochondrial translation. The tRNA genes exhibited a typical cloverleaf secondary structure, except for tRNA ^Ser . The D-loop (1,152 bp) was positioned between tRNA ^Pro and tRNA ^Phe , serving as the primary site for mitochondrial replication and transcription. Phylogenetic analysis placed the PPH within a European breed clade, closely related to Westphalian and Maremmano and two individuals from Germany and Serbia. with potential connections to Asian lineages. These findings highlight the effectiveness of long-read sequencing for resolving complex mitochondrial regions, providing a valuable resource for equine genetics, breed conservation, and evolutionary studies.