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" (https://doi.org/10.1038/s41467-023-43702-4). 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