Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola

In warm and humid regions, the productivity of sorghum is significantly limited by the fungal hemibiotrophic pathogen <i>Colletotrichum sublineola</i>, the causal agent of anthracnose, a problematic disease of sorghum (<i>Sorghum bicolor</i> (L.) Moench) that can result in grain and biomass yield losses of up to 50%. Despite available genomic resources of both the host and fungal pathogen, the molecular basis of sorghum-<i>C. sublineola</i> interactions are poorly understood. By employing a dual-RNA sequencing approach, the molecular crosstalk between sorghum and <i>C. sublineola</i> can be elucidated. In this study, we examined the transcriptomes of four resistant sorghum accessions from the sorghum association panel (SAP) at varying time points post-infection with <i>C. sublineola</i>. Approximately 0.3% and 93% of the reads mapped to the genomes of <i>C. sublineola</i> and <i>Sorghum bicolor</i>, respectively. Expression profiling of <i>in vitro</i> versus <i>in planta C. sublineola</i> at 1-, 3-, and 5-days post-infection (dpi) indicated that genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), and membrane transporters increased in expression during the transition from the biotrophic to the necrotrophic phase (3 dpi). The hallmark of the pathogen-associated molecular pattern (PAMP)-triggered immunity in sorghum includes the production of reactive oxygen species (ROS) and phytoalexins. The majority of effector candidates secreted by <i>C. sublineola</i> were predicted to be localized in the host apoplast, where they could interfere with the PAMP-triggered immunity response, specifically in the host ROS signaling pathway. The genes encoding critical molecular factors influencing pathogenicity identified in this study are a useful resource for subsequent genetic experiments aimed at validating their contributions to pathogen virulence. This comprehensive study not only provides a better understanding of the biology of <i>C. sublineola</i> but also supports the long-term goal of developing resistant sorghum cultivars.