LAUSR

Charcoal rot is a disease that is becoming more and more prevalent in sesame and is brought on by the fungus Macrophomina phaseolina. It significantly reduces yields all over the world. Understanding the pathogen's diversity at the crop field level is essential for managing the disease effectively and for understanding the epidemiology of the disease and host–pathogen interactions. This study investigates the genetic diversity among Macrophomina isolates (MAC S01–MAC S08) through comprehensive analysis of RNA secondary structures, phylogenetic relationships and structural divergence. Distinctive folding patterns, including variations in helices, loops and base‐pair stability, were observed, indicating structural and functional diversity. Consensus RNA structures revealed conserved helices crucial for stability and function, alongside flexible variable regions indicative of adaptive roles. Phylogenetic analysis highlighted distinct evolutionary clusters, with MAC S05 emerging as an outlier due to significant divergence. Structural divergence heatmaps quantified pairwise differences, aligning with phylogenetic findings, with mismatch values ranging from 247 to 413 mismatches. Geographic distribution underscored the influence of environmental diversity, with isolates from similar regions displaying structural similarities, while isolates from distinct locations exhibited divergence. Principal component analysis further captured key variability patterns, linking structural features to environmental and evolutionary pressures. These findings provide insights into the adaptive mechanisms and evolutionary dynamics of Macrophomina spp. in diverse ecological contexts. Accordingly, the results indicated that secondary structure analysis can provide new insights for the determination of genetic diversity among various strains isolated from different geographical origins.