Genome-wide analyses reveal divergent evolutionary lineages of Colletotrichum godetiae shared among almond and other hosts

Abstract Colletotrichum godetiae is the primary causal agent of almond anthracnose in Mediterranean regions. However, its evolutionary origin and population structure remain poorly understood. Here, we combined whole-genome sequencing, population genomics, phylogenomic and multilocus analysis to investigate the genetic diversity of C. godetiae from almond and other hosts. Seventeen genomes representing different hosts and geographic origins were analysed. Genomic analyses based on PCA, NeighborNet and ADMIXTURE, and phylogenomic analysis using single-copy orthologs, revealed three strongly supported lineages, with comparatively low genomic divergence within each lineage, and significant linkage disequilibrium both overall and within each lineage (standardised index of association r̄d = 0.088 for the pooled dataset, p = 0.001), consistent with predominantly clonal reproduction, while not excluding occasional recombination. Almond-associated isolates were distributed across two lineages: one comprised predominantly almond isolates, whereas the other also contained isolates from other hosts, including olive, a pattern consistent with the possibility of pathogen circulation between hosts. Genome-based screening identified highly variable loci, including Rsm22 , AKR , 4pyrrol-Mease and GroL , which showed higher nucleotide diversity than conventional multilocus markers; however, GroL and 4pyrrol-Mease , which were subsequently validated across the larger isolate collection, did not resolve the three lineages identified by genomic approaches. Results reveal that C. godetiae is composed of distinct evolutionary lineages whose existence is masked by the use of conventional markers, providing new insights into the evolution, epidemiology and population dynamics of the almond anthracnose pathogen.