Chromosome-scale genome assembly and population genomic analysis of Phomopsis asparagi pathogen reveal genetic diversity among geographical populations

Background Asparagus stem blight, caused by Phomopsis asparagi, is one of the most destructive diseases affecting asparagus production worldwide, leading to stem cankers, wilting, and plant death. Although draft genome sequences of P. asparagi have previously been reported, a high-quality reference genome and comprehensive insights into the genetic diversity of regional pathogen populations are still lacking. Results In this study, we isolated nine P. asparagi strains from different asparagus-growing regions in China. Comparative phenotypic analysis revealed significant inter-strain variation in mycelial growth rates and tolerance to abiotic stresses. The HX-1 isolate from Huixian was sequenced using PacBio HiFi and Hi-C technologies, resulting in a high-quality chromosome-scale genome assembly of 89.24 Mb, with 98.28% BUSCO completeness. Using the HX-1 genome as the reference, whole-genome resequencing was conducted for the remaining eight regional strains. Population genomic analysis identified 754,148 single nucleotide polymorphisms (SNPs), 80,396 insertions and deletions (InDels), and 6,159 structural variations (SVs) across the eight strains. Notably, a subset of SNPs was located within genes associated with cell wall integrity, stress response, and virulence, suggesting a potential genetic basis for the phenotypic variation observed among isolates and providing candidate targets for further functional studies. Conclusions The chromosome-scale reference genome and population genomic resources generated in this study establish a valuable foundation for future studies of P. asparagi biology, pathogenicity, and population diversity, and will facilitate the development of effective disease management strategies for asparagus cultivation.