Unveiling Cryptic Species Diversity and Genetic Variation of <i>Lasiodiplodia</i> (Botryosphaeriaceae, Botryosphaeriales) Infecting Fruit Crops in Taiwan

The genus <i>Lasiodiplodia</i>, a member of the family Botryosphaeriaceae, is an important fungal disease genus in agriculture. However, the <i>Lasiodiplodia</i> species survey and genetic diversity in Taiwan remain unclear. This study aimed to investigate the <i>Lasiodiplodia</i> species associated with various fruit species to explore the cryptic <i>Lasiodiplodia</i> species diversity, validate species delimitation, and unveil cryptic genetic diversity. Overall, six <i>Lasiodiplodia</i> species were identified, with several new records of infection identified. Additionally, phylogenetic analyses indicated that the relations of all isolates of <i>L. theobromae</i> might be paraphyletic. They were grouped with <i>L. brasiliense</i> based on Automatic Barcode Gap Discovery (ABGD), Automatic Partitioning (ASAP) and structure-based clustering analyses. These analyses did not provide conclusive evidence for <i>L. brasiliensis</i> as a stable species. It may be necessary to gather more information to clarify the species delineation. The multiple new records of <i>Lasiodiplodia</i> species with high genetic diversity and differentiation revealed that the diversity of <i>Lasiodiplodia</i> in Taiwan was underestimated in the past. We found that <i>L. theobromae</i> has the highest number of haplotypes but the lowest number of haplotype and nucleotide diversities, indicating a recent population expansion. This was supported by the significant negative Tajima’s <i>D</i> and Fu and Li’s <i>D</i>* tests. The high genetic diversity, low gene flow, and host-associated differentiation of <i>Lasiodiplodia</i> species indicate that they might harbour powerful evolutionary potential in Taiwan. This study provided critical insights into genetic variation, host-associated differentiation, and demography of <i>Lasiodiplodia</i> species, which would be helpful for disease management of related pathogens.