A chromosome-level genome resource for the lethal tapeworm Sparganum proliferum, with candidate genomic safe harbours for functional genetics

Abstract

Sparganum proliferum is an enigmatic and highly proliferative cestode known for its ability to form invasive larval infections in mammalian hosts. Here, we present the first chromosome-level genome assembly for a member of the order Diphyllobothriidea, generated using a hybrid sequencing approach that integrates Oxford Nanopore/PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C scaffolding. The final genome assembly spanned approximately 681 megabases (Mb) across nine chromosomes. BUSCO analysis revealed 81.9% completeness, whereas repeat annotation identified 55.8% of the genome as repetitive elements. Gene annotation uncovered approximately 29,000 protein-coding genes including [~]6200 transposon associated genes, highlighting the complex genomic landscape underlying parasitic lifestyles. Synteny analysis with other cestode linages including Echinococcus and Hymenolepis provided insights into the structural organisation and evolutionary trajectory of S. proliferum. In addition, we identified candidate genomic safe harbour (GSH) loci and promoters from housekeeping genes, offering potential for stable transgene integration. This high-quality genome serves as a critical resource for studying parasite evolution, host adaptation mechanisms, and the molecular basis of invasive proliferation in cestodes.