Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry

Summary Rapid adaptation in fungal plant pathogens is often attributed to sexual recombination, yet many important pathogens are largely clonal. We investigated how genetic and phenotypic diversity arises in the predominantly asexual fungus Colletotrichum nymphaeae , the main cause of strawberry anthracnose in Europe and North America. We performed comparative genomics on 36 C. nymphaeae genomes and 45 other Colletotrichum genomes sampled from strawberry or from closely related species, assessing population structure, transposable element (TE) content, genome compartmentalisation and signatures of horizontal transfer, and linked these features to phenotypic variation and virulence. Colletotrichum nymphaeae consists of three major lineages, with a globally distributed clonal lineage showing high variability in morphology and virulence. Extensive variation in TE content was detected among and within lineages. Genomes are compartmentalised into core regions and TE‐rich accessory regions (ARs) that cluster by lineage and are enriched for gene duplications, genes under relaxed selection and genes linked to stress, virulence and fungicide resistance. We identified a Starship element and a 2 kb region containing two effector genes that were horizontally acquired. TE‐rich ARs and horizontal gene transfer drive diversification in this largely asexual pathogen, shaping its evolution and posing challenges for durable strawberry anthracnose management.