Comparative Genomics Analysis and Pathogenicity Assessment of Colletotrichum siamense Strain JDA-12 on Multiple Strawberry Cultivars

Strawberry crown rot (SCR) disease poses a significant threat to strawberry production in Zhejiang Province, China. In our previous study, we identified Colletotrichum siamense strain JDA-12 as the dominant causal agent of SCR disease in samples collected from Zhejiang. However, the factors associated with this phenomenon remain unclear. In this study, a comparative analysis of JDA-12 and other documented Colletotrichum species revealed that the gene families AbiEii and CBM24-GH71, together with two annotated RiPP-like secondary metabolite biosynthetic clusters, are specifically expanded or uniquely present in JDA-12. These lineage-specific genomic features may represent genomic signatures associated with ecological adaptation and host-associated interactions of JDA-12. Additionally, we assessed the pathogenicity of JDA-12 on major strawberry cultivars grown in Zhejiang. The findings demonstrated that ‘Benihoppe’ exhibited high susceptibility, while ‘Fenyu No.1′ showed comparatively strong resistance. Furthermore, we evaluated the impact of environmental factors on pathogenicity and found that short-day conditions (10L:14D), high temperature (~30 °C), and high humidity (≥90%) constitute the optimal environment for JDA-12 infection in strawberries, at least under conditions representative of Zhejiang. This study provides genomic insights into the ecological adaptation and pathogenic potential of JDA-12, while revealing environmental conditions favorable for SCR development, facilitating the development of effective disease management strategies.