Genome-wide survey of Crataegus scabrifolia provides new insights into its genetic evolution and adaptation mechanisms

Crataegus scabrifolia is a significant botanical resource in Southwest China, renowned for its medicinal properties and high potential for development due to its rich medicinal components. However, genomic research on C. scabrifolia remains limited. This study conducted a comprehensive genome-wide survey of C. scabrifolia, employing flow cytometry in conjunction with genome K-mer analysis to assess its genomic characteristics in detail. Our findings reveal that despite a genome size similar to cultivated hawthorn (Crataegus pinnatifida var. major), C. scabrifolia exhibits a significantly lower heterozygosity rate of 0.5% compared to 1.77% observed in cultivated varieties. Additionally, we identified transposable elements comprising 51.79% of the assembled genome, with retrotransposons accounting for 35.05% of the total genome. Furthermore, this study identified numerous simple sequence repeat (SSR) marker loci and conducted a polymorphism analysis. Subsequently, we annotated the functions of single-copy genes, providing insights into the adaptive strategies and genetic stability of C. scabrifolia under varying environmental conditions. These findings offer crucial tools and resources for further genotype selection, genetic analysis, and breeding improvement.