High-resolution genome assembly and linkage mapping in Meloidogyne hapla reveal non-canonical telomere repeats and recombination hotspots associated with effector proteins.

Root-knot nematodes (Meloidogyne spp.) are among the most destructive agricultural pests that cause significant yield losses across a wide range of crops. Meloidogyne hapla is a valuable model for studying root-knot nematodes due to its parasitic diversity, small diploid genome, and a reproductive strategy that facilitates genetic analysis. Here, we report the most contiguous genome assembly to date for any plant-parasitic nematode built using PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C sequencing. Genetic linkage analysis of F2 populations derived from crosses between M. hapla strains validated the assembly but also revealed anomalies indicating chromosome structure differences between parental isolates such as fissions, fusions, and rearrangements. Strikingly, we identified sharply delimited zones with extraordinarily high recombination on most chromosomes. Notably, several of these high recombination zones were significantly enriched for genes encoding secreted proteins, many of which contribute to parasitism. These findings suggest that meiotic recombination facilitates effector diversification and offer insight into how these parasites diversify their effector protein repertoire to change or expand their extraordinary host range. We further report the discovery of a novel 16-nucleotide tandem repeat and lack of canonical telomere repeats at chromosome ends. The localization of this 16-nt repeat at chromosome ends highlights a potentially divergent mechanism of chromosome-end maintenance in this nematode group. Overall, our study integrates high-resolution structural genomics, genetic mapping, and functional inference to uncover links between genome architecture, recombination landscapes, and host-parasite interactions.