Comprehensive mitochondrial genome profile of New Zealand white rabbit (Oryctolagus cuniculus) using Nanopore sequencing technology.

Abstract

This study was aimed to discover, identify, and comprehensively explore the characteristics of the complete mitochondrial DNA genomes of the NZW rabbit (Oryctolagus cuniculus). This study utilized genomic DNA (gDNA) which was extracted from New Zealand White (NZW) rabbit's liver tissue. The extracted gDNA was rigorously evaluated for both quality and quantity to ensure optimal suitability for mitochondrial DNA enrichment. The sequencing process was carried out using whole genome sequencing (WGS) analysis with Nanopore technology, employing the Oxford Nanopore Technologies GridION platform and bioinformatic tools. Data analysis was carried out using the MEGA11 software to uncover potential mutations, assess genetic diversity, genetic distance and visualize the phylogenetic relationships. The NZW rabbit mtDNA genome spans 17,374 bp, with adenine (31.5%) and thymine (28.3%) as the dominant nucleotides. Leucine is the most abundant amino acid (15.82%), while cysteine is the least abundant (0.61%). The s-rRNA and l-rRNA genes are 957 bp and 1,581 bp long, respectively. The 2,000 bp D-loop region contains two repetitive elements: a 20-bp sequence repeated 14 times and a 153-bp sequence repeated 5 times, which differs from that previously reported in other rabbit mtDNA genomes, thus becoming a specific characteristic and a novel finding of this study.