Complete mitochondrial genome assembly and analysis of a Neotropical lineage of Ligula intestinalis reveals evolutionary and phylogenetic insights

Ligula intestinalis (Cestoda: Diphyllobothriidea) is a cosmopolitan tapeworm parasite characterized by a complex life cycle that includes freshwater fish infection. Ligula disrupts host reproduction, and causes ecological imbalances. Despite its broad geographic distribution and ecological significance, molecular data for South American populations have been lacking, leaving a critical gap in understanding its genetic diversity and evolutionary history. To address this, we conducted the first molecular characterization of L. intestinalis plerocercoid larvae isolated from the native fish Orestias agassizii in Lake Titicaca, Peru. Using Illumina next-generation sequencing, we assembled a complete mitochondrial genome of 13,657 bp, containing 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. The mitogenome exhibited an A + T-rich composition (66.3%) and contained over 580 repetitive elements, primarily concentrated within its control region. Comparative analyses with European and Asian mitogenomes revealed substantial regional differences in nucleotide diversity and amino acid composition, with closer similarity observed between South American and Asian lineages. Genes atp6, nad5, and nad6 showed the highest variability, whereas cox1 demonstrated significant intercontinental divergence yet remained conserved within South America, reflecting both phylogeographic patterns and strong functional constraints. Phylogenetic inference based on mitochondrial markers (cytb, cox1, and nd1) confirmed the Titicaca specimen as a distinct South American lineage, closely related to the Nearctic lineage. These findings enhance our understanding of L. intestinalis mitogenomic diversity, emphasize the importance of geographic isolation in parasite diversification, and provide an essential genomic resource for future evolutionary and ecological research in high-altitude ecosystems.