Genetic and phenotypic diversity of six Colletotrichum lupini strains isolated from a single field

Colletotrichum lupini, the causal agent of anthracnose in white lupin (Lupinus albus L.), is a specialized ascomycete pathogen responsible for severe yield losses worldwide. Despite the predominance of the highly clonal pandemic lineage II, the extent of diversity within local populations remains poorly understood. This study examined genetic and phenotypic diversity among isolates from a single geographic location and their association with differences in aggressiveness.

A collection of 150 monosporal isolates was obtained from symptomatic white lupin plants collected in a single field in the Bryansk region, Russia. Six isolates displaying contrasting fitness and aggressiveness (Samad et al., 2023) were selected for comparative genomic and phenotypic analyses.

Whole-genome sequencing confirmed that all six isolates belonged to lineage II. However, comparison with publicly available genomes revealed clear differentiation between the Bryansk isolates and global lineage II accessions (Hudson’s FST = 0.44), with highly differentiated genomic regions enriched in genes involved in metabolism and intracellular transport. The most aggressive isolates investigated in this study formed a distinct subgroup and carried missense mutations in predicted virulence-associated genes.

Profiling of extracellular enzyme activities (lipase, protease, cellulase and polygalacturonase) in fungal cultures grown with or without root extracts from white lupin cultivars differing in anthracnose resistance revealed isolate-specific responses to host-derived metabolites, with protease activity showing the strongest association with aggressiveness.

The substantial genetic, physiological and biochemical differentiation observed among the isolates highlights the diversity within local C. lupini populations and provides candidate traits for further investigation of fungal aggressiveness and host–pathogen interactions.