Available online 18 December 2025, 104762

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Genome skimming enabled efficient molecular prospecting of decades-old museum specimens.

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Mitogenomes and nuclear ribosomal transcription unit sequence data were generated from 88 archived proteocephalid samples.

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We generated the most character-rich phylogeny to date for proteocephalids (Onchoproteocephalidea I).

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The general tree topologies are consistent with the phylogenies of previous studies.

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The dataset generated here provides a foundation for future multi-locus phylogenetic and comparative studies of cestodes.

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.

Graphical abstractDownload: Download high-res image (196KB)Download: Download full-size imageKeywords

Onchoproteocephalidea I

High-throughput sequencing

Mitochondrial genome

Nuclear ribosomal DNA

Phylogenetics

Museomics

Data availabilityAll relevant data supporting our findings are provided in the main text and supplementary files. The complete and partial mitochondrial genomes and nuclear ribosomal transcription unit datasets are available at GenBank (PX326266–PX326326, PX395790–PX395815, and PX283208–PX283293 for the complete mitogenomes, partial mitogenomes, and rTUs, respectively). Genomic readpools are deposited in the Sequence Read Archive (SRA) under BioProject PRJNA1309085, with BioSample accession nos. SAMN50734482–SAMN50734569.

© 2025 The Author(s). Published by Elsevier Ltd on behalf of Australian Society for Parasitology.