Comparative genomics of different haplotypes in Ditylenchus destructor provides insights into their host preferences

The nematode Ditylenchus destructor comprises multiple haplotypes with distinct host preferences, while the genetic basis remains unclear. We generate three genomes (Haplotypes A, B, and C) using hybrid assembly and conduct comparative analysis with two published Haplotype A genomes. Integrating haplotype-resolved phylogeny, whole-genome alignments, functional annotation, orthogroup profiling, and secretome analysis shows Haplotypes B and C are more similar to each other than to Haplotype A. We identify several key genomic differences that may underlie host adaptation: Haplotype A features expanded chemosensory GPCR repertoires and GH31 glycoside hydrolases. Haplotype B possesses an abundance of cytochrome P450 domain proteins and secretory pectate lyases. Haplotype C harbors more genes encoding NADPH reductases, oxidoreductases, ABC transporters, secreted animal haem peroxidases, C-type lectins, and Astacins. We propose that these genomic variations facilitate the nematode’s adaptation to different host plants. Collectively, our findings establish a genomic framework for understanding host adaptation in D. destructor. The genetic basis of Ditylenchus destructor haplotypes with host preferences remains unclear. This study investigates the genomes of three distinct haplotypes and identifies key genomic variations that may underlie host adaptation.