Comparative analysis of amino acid profiles from the 13 mtDNA protein-coding genes in New Zealand White and Indonesia local rabbits

Abstract

This study aimed to characterize the amino acid profiles of 13 mtDNA protein-coding genes in Indonesian local rabbits and New Zealand White (NZW) rabbits. Genomic DNA (gDNA) was extracted from liver tissue to obtain complete mtDNA sequences using long-read sequencing technology (Nanopore). The mtDNA sequences were aligned to identify amino acid variations in the 13 mtDNA protein-coding genes, including ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2, COX3, ATP6, ATP8, and CYTB. Results showed that the amino acid composition in both strains was largely conserved, with leucine as the dominant residue. Minor variations were observed, such as higher phenylalanine in Indonesia local rabbits and slightly lower isoleucine in NZW rabbits, suggesting potential differences in energy metabolism and physiological adaptation. Low proportions of cysteine, arginine, and aspartate were found in both strains, reflecting their limited structural role. Overall, the amino acid composition patterns of mtDNA were highly conserved (dominated by Leu, Ile, Phe, and Ser), although small but significant differences in certain genes, such as ND4L, COX1, and ND2, may be associated with genetic adaptation, domestication history, and physiological performance of the two strains.