Manuscript code repository

This repository contains the packages used, commands issued, and raw files to generate figures 1A, S1B, and S2 for the manuscript titled "Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis". The goal of this repository is to increase transparency and reproducibility.

Genome assembly and annotation

Raw files and commands issued for reference genome assembly and annotation:

• genome_assembly_workflow.md markdown file containing the commands issued to assemble and annotate the genomes used in this study. And the commands issued to generate figure 1A.

Includes additional file information for SRRaccessions.txt , many_bwa.mem.sh , and many_prokka.sh

Phylogenetic analyses

Input files and commands issued to generate phylogenetic trees:

• LuxI_orthologue_workflow.md markdown file containing the commands issued to generate supplemental figure S1B.
• RhlI_PA_workflow.md markdown file containing the commands issued to generate figure S2.

Citation information

List of packages, versions used, citations, and relevant links.

TrimGalore v0.6.7 doi.org/10.5281/zenodo.7598955

SAMtools v1.1.2 Li, H. et al. The Sequence Alignment/Map format and samtools. Bioinformatics 25, 2078 (2009). doi:10.1093/bioinformatics/btp352

BCFtools v1.1.0.2 Danececk, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, 1-4 (2021). doi:10.1093/gigascience/giab008

Cutadapt v2.8.0 Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 17, 10-12 (2011). doi:10.14806/ej.17.1.200

Prokka v1.14 Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069 (2014). doi:10.1093/bioinformatics/btu153

MUSCLE v.3.8.1551 Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32, 1792–1797 (2004). doi:10.1186/1471-2105-5-113

trimAL v.1.4.1 Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009). doi:10.1093/bioinformatics/btp348

IQ-TREE v1.6.12 Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol Biol Evol 32, 268–274 (2015). doi:10.1093/molbev/msu300

iTOL v.6.7.1 Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49, W293–W296 (2021). doi:10.1093/nar/gkab301