Genomic and Transcriptomic Insights into the Evolution and Parasitic Strategy of the Woody-Plant Nematode Pratylenchus vulnus

The root-lesion nematode Pratylenchus vulnus parasitizes a wide range of hosts including woody perennials such as walnut (Juglans regia) and grapevine (Vitis vinifera), significantly damaging roots and reducing yields. Here, we present a high-quality, chromosome-level genome assembly of P. vulnus (61.7 Mb across six chromosomes). Comparative genomic analysis revealed high collinearity in protein-coding genes between P. vulnus and the root-knot nematode Meloidogyne graminicola, indicating a closer evolutionary relationship with this sedentary endoparasite. Large chromosomal regions in P. vulnus lack synteny with other nematode genomes, have comparatively low GC content (<30%), and are enriched in genes with unique or lineage-specific functions. Transcriptome analysis highlighted dynamic, stage-specific expressions of genes involved in parasitism, development, and metabolism. Additionally, we identified an extensive repertoire of putative effector genes and characterized lineage-specific expansions of cell wall-degrading enzyme families. Overall, these findings provide insight into the genome organization, chromosome evolution, and parasitism-related gene repertoire in a woody-plant parasitizing nematode.