FoEC2

FoEC2 identifies and analyzes putative effector proteins in Fusarium oxysporum genomes to classify strains into formae speciales by leveraging presence/absence variation and hierarchical clustering of predicted effector sequences.

Key Features:

• Effector identification and clustering: Identifies putative effectors across Fusarium oxysporum genome assemblies and classifies strains into formae speciales using presence/absence variation and hierarchical clustering of predicted effector sequences.
• Parallelization: Supports multithreading to scale analyses across large genome datasets.
• Snakemake pipeline: Implemented as a Snakemake workflow to manage reproducible bioinformatics analyses.
• Subtype delineation: Detects and delineates subtypes within formae speciales based on differences in effector repertoires.
• Scalability: Capable of analyzing hundreds of genomes, demonstrated on 537 publicly available Fusarium oxysporum genomes.

Scientific Applications:

• Formae speciales classification: Classifies F. oxysporum isolates into formae speciales based on effector presence/absence profiles and clustering.
• Pathogenicity and host-range studies: Supports investigation of effector repertoires relevant to fungal pathogenicity mechanisms and host specificity.
• Population genomics and subtype analysis: Enables delineation of genetic subtypes within formae speciales using effector-based comparisons.
• Crop protection research: Provides effector repertoire data to inform studies of host–pathogen interactions relevant to crop protection strategies.

Methodology:

Hierarchical clustering of predicted effector sequences derived from genome assemblies using presence/absence variation, implemented as a Snakemake pipeline.