Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns

Strains of Pseudomonas aeruginosa , an opportunistic pathogen that causes difficult to treat infections, have significant genomic heterogeneity including the presence of diverse accessory genes that are only present in some strains or clades. Both core genes, which are conserved across strains, and accessory genes have been associated with traits such as biofilm formation and virulence. Much of what we know about core and accessory gene content comes from genome analyses. Here, we use a newly assembled transcriptome compendium to analyze the transcriptional patterns of core and accessory gene expression in PAO1 and PA14 strains across thousands of samples from hundreds of distinct experiments. We found that a subset of core genes were stable, having consistent correlated expression patterns across samples regardless of strain background, with a focus on strains PAO1 and PA14. These stable core genes had fewer co-expressed neighbors that were accessory genes. Significance Pseudomonas aeruginosa is a ubiquitous pathogen. There is a lot of diversity amongst P. aeruginosa strains, some which are clinically relevant. Understanding how these different strain-level traits manifest is important for identifying targets that regulate different traits of interest. With the availability of a PAO1-mapped and PA14-mapped RNA-seq compendium, which contain hundreds of strains, it is now possible to examine the effect of different strains on expression, which can mediate different traits. In this study we developed an approach to compare expression profiles across different P. aeruginosa gene groups – core and accessory genes. This approach revealed a subset of core genes with different transcriptional patterns across strains, which could contribute to trait differences.