Assembly, annotation and analysis of the complete mitochondrial genome of a neotropic lineage of Ligula intestinalis (Cestoda: Diphyllobothriidea): Insights into Evolution and Phylogenetics

This study reports the first record and molecular characterisation of Ligula intestinalis (Linnaeus, 1758) (Cestoda: Diphyllobothriidea) in Lake Titicaca, the world's highest navigable lake, located in the Puno Province of Peru. Plerocercoid larvae were isolated from the native fish Orestias agassii (Cyprinodontiformes), and analyzed using next-generation sequencing (Illumina technology) to assemble the complete mitochondrial genome (mitogenome). The assembled mitogenome is a 13,657 bp circular DNA molecule containing 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions (NCR1 and NCR2). This genomic structure aligns with that of other diphyllobothriidean species. A notable A + T bias (66.32%) with negative AT skew (-0.310) and positive GC skew (0.222) was observed, alongside conventional cloverleaf structures for most tRNAs except trnS1, trnR, and trnC. Over 580 repetitive sequences were detected, including seven simple sequence repeats (SSRs) and several tandem repeats and stem-loop structures in the control region. Comparative analyses of nucleotide diversity and amino acid compositions across global populations (South America, Europe, Asia) showed substantial regional variability, especially in genes atp6, nad5, and nad6. Phylogenetic analyses using Bayesian Inference and Maximum Likelihood methods indicated that the Titicaca specimen represents a distinct lineage closely related to the Nearctic lineage, emphasizing geographical isolation as a key driver of evolutionary diversification. The characterization of the mitogenome presented here represents a significant step toward elucidating the evolutionary relationships of this cestode and provides a valuable resource for further research on parasitic biodiversity in South America.