HISS

HISS implements Snakemake workflows to identify and characterize plant disease resistance genes from RenSeq data by assembling PacBio HiFi reads, performing k-mer–based association genetics, and diagnosing candidate gene presence/absence.

Key Features:

• Snakemake-based workflows: Uses Snakemake to orchestrate reproducible execution of complex RenSeq analysis steps.
• SMRT-RenSeq assembly: Assembles enriched PacBio HiFi reads from resistant accessions to generate contigs containing candidate resistance genes.
• AgRenSeq (association genetics RenSeq): Applies k-mer–based association genetics across panels of resistant and susceptible accessions to identify contigs associated with resistance traits.
• dRenSeq (diagnostic RenSeq): Performs graphical genotyping to assess presence or absence of candidate genes on identified contigs across the accession panel.
• Contig-level candidate identification: Produces contigs that serve as targets for downstream candidate gene characterization and validation.

Scientific Applications:

• Resistance gene discovery: Identification and characterization of novel plant disease resistance genes from RenSeq-enriched sequencing data.
• Association genetics of resistance traits: Detection of contigs associated with disease resistance using k-mer–based association across resistant and susceptible accessions.
• Diagnostic genotyping: Assessment of candidate gene presence/absence across germplasm panels to support validation and breeding decisions.

Methodology:

Workflows use Snakemake to run SMRT-RenSeq assembly of enriched PacBio HiFi reads, k-mer–based AgRenSeq association genetics across resistant and susceptible accession panels to identify associated contigs, and dRenSeq graphical genotyping to assess candidate gene presence/absence.