Genomic and pathogenic insights of Colletotrichum viniferum, an emerging ripe rot pathogen in grapes

<title>Abstract</title> <p> Grape ripe rot caused by <italic>Colletotrichum</italic> species is a significant limitation on fruit quality and yield in viticulture and requires integrative pathogen characterisation for precise diagnosis and management. Symptomatic bunches harvested during the 2025 growing season from Maharashtra (Sangli) and Karnataka (Athni) showed typical anthracnose lesions of high field severity (PDI = 50–70%). Both isolates formed circular colonies on potato dextrose agar with regular radial expansion (~ 1.01 to 1.1 cm/day), grey-pigmented aerial mycelium, conidiomata, and hyaline, aseptate, cylindrical conidia measuring 12–16 × 4.6-6.0 µm. Pathogenicity assays revealed deep necrotic lesions at seven days post-inoculation (PDI = 30–46%), and re-isolation confirmed Koch's hypothesis. ITS amplification and neighbour-joining phylogeny resolved GRR1 and GRR2 within a strongly supported <italic>Colletotrichum viniferum</italic> clade—whole-genome sequencing of GRR1 assembled into a 69.88 Mb draft genome with 5,670 contigs. Annotation predicted 5,158 protein-coding genes, with a focus on amino acid (184 genes), carbohydrate (89 genes), energy (50 genes) and secondary metabolic (50 genes) pathways, while ANI analysis validated species identity. Comparative orthology classified 16,151 proteins into clusters, including 1,405 lineage-specific groups and identified 50 virulence-associated proteins, 29.8% of which are potential effectors, as well as several CAZyme families (GH5, GH13, GH43) involved in host cell wall breakdown. Secretome prediction identified signal peptides in 7.85% of proteins, highlighting their potential for host interactions. This study represents the first report of <italic>Colletotrichum viniferum</italic> infecting grapevine in India. These combined phenotypic, phylogenetic and genomic datasets identified both isolates as <italic>C. viniferum</italic> and provide a quantitative framework for studying pathogenic specialisation, evolution and disease management in grapevine pathosystems. </p>