Chromosome-level genome assembly of the nematophagous flatworm Luticola nematophagus: revealing molecular adaptations for predation and its biocontrol potential against nematode diseases

The soil-dwelling Rhabdocoela flatworm, Luticola nematophagus, recently identified as a specialized predator of plant-parasitic nematodes such as Meloidogyne incognita, demonstrates considerable potential as a biocontrol agent for agricultural nematode diseases. This study presents the first chromosome-level genome assembly of L. nematophagus, achieved by integrating PacBio HiFi long-read sequencing with Hi-C chromatin conformation capture. The assembled genome is approximately 899.92 Mb with a scaffold N50 of 231.83 Mb, comprising 50.08% repetitive sequences and 45,225 predicted protein-coding genes. Genome completeness was evaluated using CEGMA (94.76%) and BUSCO (85.49%) assessments. Comparative genomic analysis revealed notable expansions in gene families related to neural signaling, environmental adaptation, and nematode predation, including synaptic vesicle components, metalloendopeptidases, antioxidant enzymes, transmembrane transporters, peptidases, lipases, and detoxification mechanisms. These expansions suggest that L. nematophagus has evolved molecular adaptations favorable for thriving in soil ecosystems and for a specialized predation strategy, possibly aiding in the digestion of nematode cuticles and the neutralization of toxins. Interestingly, unlike Triclad flatworms such as Dugesia japonica and Schmidtea mediterranea, L. nematophagus has lost regenerative capabilities, instead allocating resources towards reproductive adaptations through self-fertilization and high fecundity. Controlled pot trials have experimentally validated its effectiveness in suppressing tomato root-knot nematode disease, underscoring its high reproductive output as critical for maintaining predator populations needed for effective biocontrol. This research provides essential genomic resources for understanding the evolutionary mechanisms of nematode predation within Platyhelminthes and promotes the development of L. nematophagus as a scalable biocontrol agent for managing nematode infections.