Whole-Genome Resequencing Reveals Genetic Variation and Selection Signals in Fusarium acuminatum Causing Astragalus Root Rot

Astragalus root rot is a soil-borne disease primarily caused by Fusarium spp., which severely hampers the sustainable development of the Astragalus industry. F. acuminatum is a predominant pathogen causing this disease. To elucidate the genetic variation and adaptive evolutionary characteristics of F. acuminatum from different geographical origins, this study conducted whole-genome resequencing analysis on 28 isolates of F. acuminatum collected from four major Astragalus production regions. Approximately 124.9 Gb of high-quality sequencing data were obtained, and a large number of single-nucleotide polymorphisms (SNPs) were detected. Population genetic analysis revealed that strains from different regions did not form strictly geographically specific clusters, exhibiting a complex mixed distribution pattern. Nucleotide polymorphism analysis indicated that the Dingxi, Gansu (GD) population possessed the highest nucleotide diversity (π) value, reflecting the richest genetic diversity. Fixation index (Fst) analysis revealed significant genetic differentiation (Fst > 0.15) among populations from different provinces, suggesting that geographic isolation may be a contributing factor to restricted gene flow between pathogenic isolates in these regions. Tajima’s D positive values suggest a deviation from neutrality, consistent with balancing selection or population contraction. Ka/Ks analysis further revealed that the majority of genes exhibited Ka/Ks > 1, differing from the typical pattern of purifying selection dominance. This study revealed the genetic variation and selection signals of F. acuminatum isolates from different geographical origins, observed significant genetic differentiation between the Gansu and Ningxia populations, and identified a large number of genes that may be subject to positive selection.