Genomic insights and comparative analysis of Colletotrichum species associated with anthracnose fruit rot and crown rot of strawberry in North Carolina

<i>Colletotrichum</i> is a large genus of fungal phytopathogens responsible for significant economic losses in numerous crops globally. These pathogens exhibit varying host specificities; some have a broad host range, while others are more limited. To explore the genetic composition and underlying factors of fungal virulence and pathogenicity, we sequenced the genomes of seven isolates of <i>Colletotrichum</i> spp.: three from the <i>C. acutatum</i> and four from the <i>C. gloeosporioides</i>. These isolates were sourced from anthracnose fruit rot and crown rot of strawberry in North Carolina. Phylogenetic and phylogenomic analyses classified the isolates within the <i>C. acutatum</i> as <i>C. nymphaeae</i>, while those in the <i>C. gloeosporioides</i> were identified as <i>C. siamense</i>. The genome sizes of the <i>C. nymphaeae</i> isolates ranged from 50.3 Mb to 50.7 Mb, with 14,235 to 14,260 predicted protein-coding gene models. In contrast, the genome sizes of the <i>C. siamense</i> isolates ranged from 55.7 Mb to 58.6 Mb, with predicted protein-coding gene models ranging from 17,420 to 17,729. The GC content across all genomes spanned from 51.9 to 53.7%. The predicted gene models included effectors (339 to 480), secondary metabolic gene clusters (67 to 90), and carbohydrate-active enzymes (800 to 1,060), with <i>C. siamense</i> isolates exhibiting the highest numbers in these categories. The genomic resources from this study will aid in resolving taxonomic challenges associated with <i>Colletotrichum</i> spp., elucidate their evolutionary history, and enhance the understanding of fungal biology and ecology, which is crucial for developing effective disease management strategies.