Pangenome analysis of nine Soybean Cyst Nematode genomes reveal hidden variation contributing to diversity and adaptation

Background Soybean cyst nematode (SCN) poses a persistent challenge to soybean production. SCN populations repeatedly overcome resistant cultivars, resulting in crop yield loss. Reference-genome driven analysis limits our knowledge of intraspecific diversity, impeding our understanding of virulence evolution and host adaptation. Here, we leverage high-fidelity long-read sequencing and comparative analysis to generate a pangenome from nine SCN populations differing in their pathotypes. Results In this study we compared 9 SCN genomes, including 8 new assemblies at the chromosome level. We identified over 19,000 orthologous gene families, with nearly 50% comprising the conserved core genome. A large portion of the core genome (40%) exhibited signatures of more rapid evolution in a positive selection analysis, particularly in domains related to host interaction and immune evasion. Structural variants in genomic regions under selection suggest population-specific haplotypes that may underlie differential virulence. Furthermore, the secretome, comprising ~ 1,400 genes per genome, revealed dynamic effector content across accessions. Conclusions Our study highlights the power of pangenomics in revealing hidden genetic diversity in SCN. The dynamic nature of both core and accessory genomes, shaped by selection and structural rearrangements, illustrates the genomic evolutionary arms race between SCN and soybean. These insights provide a foundational resource for resistance breeding and pathogen surveillance, with broader implications for managing rapidly evolving crop pathogens.