Mining natural history collections for molecular treasures: mitogenomes and nuclear ribosomal transcription units of proteocephalid tapeworms (Onchoproteocephalidea) via genome skimming

Abstract

The potential of natural history collections to address biological questions has been increasingly recognized with the advent of high-throughput sequencing (HTS) and museomics approaches. However, their use remains largely underexplored for most taxonomic groups. This is particularly true for proteocephalid cestodes (Onchoproteocephalidea I), for which extensive material is available in helminthological collections. Here, we subjected ethanol-preserved specimens deposited in two helminthological collections to HTS using a genome skimming approach. This allowed us to recover dozens of mitogenomes and nuclear ribosomal transcription units (rTUs) and to place them within a phylogenetic framework. We generated 88 complete or partial mitogenomes and rTUs. These samples correspond to 78 species in 43 genera from all continents except Antarctica, including parasites of fishes (86 %), snakes, monitor lizards, and the common opossum. Comparative analyses revealed highly conserved mitochondrial content and architecture, following the typical pattern recognized for proteocephalid cestodes. Phylogenetic reconstructions based on concatenated mitogenomes and rTUs datasets were largely concordant with the most comprehensive phylogenies published to date, with several informal clades also recognized in this study: the “Proteocephalus-aggregate”, the “African fish clade”, Clade K of the “cosmopolitan reptilian clade”, and the “Neotropical fish superclade”. However, improved resolution was obtained in the parsimony analyses for early-diverging lineages represented by Old World cestodes of the subfamilies Acanthotaeniinae and Gangesiinae. Also, we identified the MT-ND5 gene as the most informative under the parsimony criterion, whereas the most frequently sampled MT-CO1 proved far less phylogenetically informative. The data generated here provide a solid foundation for future multilocus phylogenetic and comparative studies of cestodes and highlight the value of genome skimming using decades-old archived samples. New avenues for exploring the evolutionary history of proteocephalid cestodes are discussed.