ORPER

ORPER constrains phylogenetic placement of small subunit (SSU) rRNA sequences (16S rRNA) within a multilocus reference tree built from ribosomal protein genes extracted from public genomes to inform bacterial strain selection and reduce redundancy.

Key Features:

• Constrained SSU rRNA placement: Constrains 16S SSU rRNA sequences within a multilocus reference tree to link single-gene markers to genome-derived phylogenies.
• Multilocus reference tree construction: Builds a reference tree based on ribosomal protein genes extracted from public genomes.
• MLST integration: Integrates SSU rRNA data with multilocus sequence typing (MLST) derived from ribosomal proteins for constrained placement.
• Workflow implementation: Implemented as a Nextflow workflow.
• Containerization: Packaged using Singularity containers.
• Demonstrated case study: Applied to Cyanobacteria to place 152 strains from the BCCM/ULC collection within a multilocus reference tree.

Scientific Applications:

• Strain selection for sequencing: Inform selection of bacterial strains for future genome sequencing by identifying phylogenetic redundancy or novelty.
• Phylogenetic placement of 16S sequences: Place SSU rRNA sequences into a genome-informed multilocus phylogenetic context.
• Redundancy reduction in public genomes: Detect potential redundancy between candidate strains and existing public genomes.
• Microbial diversity and evolutionary analysis: Improve interpretation of microbial diversity and evolutionary relationships by linking 16S markers to ribosomal protein-based phylogenies.

Methodology:

Implemented in Nextflow and containerized with Singularity; constructs a multilocus reference tree from ribosomal protein genes extracted from public genomes; constrains SSU rRNA (16S) placement by integrating SSU rRNA sequences with MLST derived from ribosomal proteins.