Teknonaturalist

Teknonaturalist provides a Snakemake pipeline for rapid detection and classification of pathogenic and endophytic fungi from plant genomic DNA, targeting the ITS region for taxonomic assignment with methods for maximizing query sequence length and taxon-specific local cut-off and confidence scores.

Key Features:

• ITS region targeting: Targets the internal transcribed spacer (ITS) region, a fungal barcode standard, for taxonomic assignment of fungi.
• Query sequence length maximization: Maximizes query sequence length to give higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region.
• Taxon-specific scoring: Provides taxon-specific local cut-off and confidence scores for classification.
• Computational efficiency: Classifies fungi within minutes to a few hours per host individual.

Scientific Applications:

• Cryptic pathogen detection: Detects cryptic fungal pathogens from existing plant genomic sequence data.
• Endophytic microbiome characterization: Helps characterize the endophytic fungal microbiome of plants.
• Bioprospecting: Supports bioprospecting for commercially useful fungal species.
• Host range determination: Determines the plant host range of fungi by mining publicly available plant genomic DNA.
• Fungal diversity assessment: Assesses fungal diversity from plant genome bycatch, including detection of fungi with no prior record of association with particular hosts.

Methodology:

The pipeline uses Snakemake for workflow management and targets the ITS region for fungal classification from plant genomic DNA, with methods for maximizing query sequence length and providing taxon-specific local cut-off and confidence scores.