Comprehensive mitochondrial genomics of from Sudan: insights into genetic diversity, evolutionary dynamics, and host adaptation.

Introduction: This study presents a comprehensive analysis of the complete mitochondrial genomes of isolated from cattle, sheep, and goats in Sudan, aiming to provide new insights into genetic diversity, evolutionary dynamics, and host adaptation.

Methods: Mitochondrial genomes were sequenced using high-throughput Illumina MiSeq technology, yielding sequences of 14,483 bp, slightly longer than the reference genome (14,478 bp). A sliding window analysis was conducted to assess nucleotide diversity, and phylogenetic analyses were performed using complete mitochondrial sequences, including and excluding non-coding regions.

Results: Key genetic variations were observed, including a non-canonical start codon (GTG) in the ND5 gene and an alternative stop codon (TAA) in ND4. Length polymorphisms in ND4L and suggested potential mitochondrial efficiency adaptations. Non-coding regions showed minor length differences, with the long non-coding region extending by 20 bp and the short by 4 bp. Sliding window analysis identified ND4 and ND5 as the most variable genes, while , were the most conserved. Phylogenetic analysis showed distinct clustering of Sudanese isolates with strong bootstrap support. Excluding the D-loop preserved phylogenetic structure, while D-loop-specific analysis revealed high variability, particularly in the sheep isolate.

Discussion: These findings highlight significant genetic variation and evolutionary divergence among isolates in Sudan. The observed diversity, particularly within non-coding and variable coding regions, underscores the influence of regional evolutionary pressures and host-associated adaptations. This work enhances understanding of 's genetic landscape and supports the development of more targeted molecular surveillance and control strategies for fascioliasis in endemic regions.