https://phaidra.vetmeduni.ac.at/o:5399 Chromosome-scale nuclear genome and proteome of Anoplocephala perfoliata elucidate lineage-specific features of a ‘neglected’ equine tapeworm Young, Neil D. Neil D. Young Wang, Tao Tao Wang Ang, Ching-Seng Ching-Seng Ang Lale, Dilara Dilara Lale 0000-0002-8575-7402 University of Veterinary Medicine Vienna. Clinical Centre for Equine Health and Research Fuehrer, Hans-Peter Hans-Peter Fuehrer 0000-0002-4178-0133 University of Veterinary Medicine Vienna. Centre of Pathobiology Sumanam, Sunita B. Sunita B. Sumanam Korhonen, Pasi K. Pasi K. Korhonen Chang, Bill C. H. Bill C. H. Chang Gasser, Robin B. Robin B. Gasser Springer journal article open access eng Background Anoplocephala perfoliata is the most prevalent and pathogenic tapeworm (cestode) of horses worldwide, yet it remains molecularly understudied. Here, we present the mitochondrial and chromosome-scale nuclear genomes and matched somatic proteome for this parasite, establishing the first high-resolution molecular resource for the family Anoplocephalidae. Results This parasite was first characterised morphologically and then by its mitochondrial genome (size: 13,776 bp). Its complete nuclear genome (size: 372.3 Mb) was assembled and characterised; it encodes 9,711 protein-coding genes, 78.2% of which were functionally annotated and ~ 80% supported by transcriptomic evidence. Proteomic analysis confirmed 758 proteins in previously-analysed excretory/secretory (ES) products from adult worms, including highly expressed components of the ubiquitin–proteasome system, stress response families – e.g., translationally controlled tumour proteins (TCTPs) and universal stress proteins (USPs) – and cytoskeletal scaffolds. Approximately 6.5% of the genome contains retroelements, predominantly LINEs. Comparative genomic analyses revealed a relatively conserved synteny with members of the family Taeniidae (Echinococcus granulosus, E. multilocularis and Taenia multiceps) and a pronounced structural divergence from Hymenolepis microstoma (Hymenolepididae), reflecting mosaic genome evolution within the order Cyclophyllidea. Classification of proteins inferred from the genome identified GTPases, kinases, peptidases and secretome-associated proteins among the most abundant groups. A subset of proteins exhibited signal peptides or extracellular localisation, suggesting their role as parasite-derived proteins (PDPs) involved in host–parasite communication and immune evasion. Conclusion This integrated genomic and proteomic framework reveals lineage-specific molecular adaptations in A. perfoliata and provides a foundation for future functional and translational investigations of this and closely related cestodes. Anoplocephala Perfoliata Anoplocephalidae Equine Tapeworm Cestode Molecular Biology Chromosome-scale Genome Proteome Comparative Genomics Host–parasite Interactions http://creativecommons.org/licenses/by-nc-nd/4.0/ https://phaidra.vetmeduni.ac.at/api/object/o:5399/download 10.1186/s12864-026-12554-9 https://phaidra.vetmeduni.ac.at/o:605 application/pdf BMC Genomics issn:1471-2164 VoR BMC Genomics 27 1 1.87 MB 2026