Cryptic host-associated differentiation and diversity: unravelling the evolutionary dynamics of the plant pathogen Lasiodiplodia

<i>Lasiodiplodia</i>, a genus within the <i>Botryosphaeriaceae</i> family, comprises significant plant pathogens with a broad host range and global distribution, posing a substantial threat to agricultural production. Our recent study revealed the complexity of this genus by identifying numerous potential cryptic species within the seemingly generalist <i>L.theobromae</i>. To fully understand this species' complexity, higher-resolution genetic markers are required. Therefore, this study employed a comprehensive analysis of multiple transferable microsatellite markers to verify <i>Lasiodiplodia</i> species delimitation and examine the fine-scale genetic structure and diversity of <i>Lasiodiplodia</i> species, particularly <i>L.theobromae</i>. The study identified four distinct genetic groups within <i>L.theobromae</i>, each showing high genetic diversity. The phylogenetic relationships of these groups align with the evolutionary history of their host plants. This finding suggests that host-pathogen co-evolution is shaped by shared ancestral variation, limited gene flow, isolation and natural selection. These insights enhance our understanding of managing economically important <i>Lasiodiplodia</i> plant pathogens and highlight the significance of genetic diversity and host preferences in developing effective control measures.