Macrophomina phaseolina expresses sequential waves of effector, secondary metabolite, and CAZyme genes during strawberry infection, suggesting a hemibiotrophic lifestyle.

Macrophomina phaseolina causes crown and root rot disease in strawberry (Fragaria ananassa) and has become more damaging with increasing temperatures in strawberry-growing areas worldwide. Little is known about the molecular events during M. phaseolina infection in strawberry, such as transcriptional changes at elevated temperatures and different stages of infection. To fill this knowledge gap, we analyzed transcriptional changes during M. phaseolina infection in strawberry plants grown in controlled environments with high (30°C) and low (23°C) daytime temperature regimes. At high temperatures, plants had more severe crown/root necrosis, wilting, and accelerated disease progress compared to plants incubated at low temperature. Based on the composite analysis of the temperature treatments, transcriptional changes in M. phaseolina and strawberry were greatly influenced by disease stage, with each stage having distinct expression patterns of specific gene classes. In M. phaseolina, effector-encoding genes were highly enriched and expressed at the early disease stage, whereas during necrotrophy at mid-infection, secondary metabolite-encoding genes were highly upregulated. Carbohydrate active enzyme (CAZyme) expression was enriched at late infection. These patterns of gene enrichment and expression suggest M. phaseolina has a hemibiotrophic lifestyle during strawberry infection. Under high temperature, M. phaseolina pathogenicity-associated genes were upregulated while immunity-related genes in strawberry were downregulated, suggesting that increased disease severity under this treatment is at least partially attributed to susceptibility-related plant responses. Our study is the first to characterize the M. phaseolina-strawberry interaction using transcriptomics and to investigate mechanisms by which high temperature affects M. phaseolina pathogenesis.