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

Sparganum proliferum is an enigmatic, highly proliferative cestode that causes fatal sparganosis. We present a 681 Mb chromosome-level genome assembled from Oxford Nanopore, PacBio HiFi, Illumina, and Hi-C data, yielding nine chromosome-length scaffolds consistent with 2n = 18. The assembly exhibits strong intra-chromosomal Hi-C contact signals and a repeat content of 55.8%, dominated by LINEs. We annotated 29 231 protein-coding genes, including 6316 transposable element-associated loci, with BUSCO completeness scores of 91% (eukaryota_odb10) and 73% (metazoa_odb10). Macrosynteny is well conserved with Echinococcus granulosus and Hymenolepis microstoma, moderately conserved with the trematode Schistosoma mansoni, but largely disrupted in the free-living flatworm Schmidtea mediterranea, revealing lineage-specific genome reorganization among flatworms. To enable functional genetics, we identified candidate genomic safe harbours-intergenic loci within transcriptionally active neighborhoods, separated from adjacent genes by 2-10 kb gene-free buffers, flanked by convergently oriented genes, and containing CRISPR/Cas9 PAM motifs (NGG)-and compiled housekeeping promoters for stable transgene expression. Together, these resources provide a reference framework for chromosome evolution and parasitic adaptation in Diphyllobothriidea and establish practical entry points for CRISPR-based functional studies in cestodes.