Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14

Abstract

Pseudomonas aeruginosa is a ubiquitous pathogen. There is much diversity among P. aeruginosa strains, including two divergent but well-studied strains, PAO1 and PA14.

Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia

“…In this study, we focused on creating RNA-seq compendia of 2,333 samples all mapped to both the PAO1 and PA14 cDNA reference genomes and validating these compendia using expression patterns from gene sets comprised of core genes present in both strains. We analyze the relationships between the expression of core genes and accessory genes in both strains PAO1 and PA14 in the companion article by Lee et al ( 18 ).…”

“…As it is more likely that these differences are at least partly driven by technical or sequence-driven differences in the alignment, expression differences for these loci require additional consideration by investigators. An in-depth analysis of differences in gene expression patterns between PAO1- and PA14-specific compendia is pursued in the companion article by Lee and coauthors ( 18 ), who identify strain-stable and strain-variable patterns in core and accessory genes in PAO1 and PA14.…”

“…These loci were among those that had multiple paralogs in one genome but not the other, and thus, they were not considered further ( Data Set S1 ). In the companion article that examines compendia of all public PAO1 and PA14 samples, Lee and coauthors show via principal-component analysis (PCA) that there was not a strong separation of PAO1- and PA14-derived samples (using both core and accessory genes) and that the distributions of sample types were very similar in PCA plots generated for both compendia regardless of whether the PAO1 or PA14 reference genome was used ( 18 ). These findings strongly support the notion that gene expression analyses can be performed across strains (at least for PAO1 and PA14) and that transcriptional patterns reflect the expression of highly similar core genes that strains have in common.…”

“…With computationally efficient methods, it is possible to use pangenomes, which capture wide ranges of genetic material from multiple strains ( 27 ). In the companion article to this one, Lee et al explore differences in transcriptional patterns between core and accessory genes of strains PAO1 and PA14, taking an important step in integrating strain-aware analyses with transcriptional profiling ( 18 ).…”

“…Thus, we present a method to build uniform compendia from public data and demonstrate its success using P. aeruginosa gene expression profiles. This method and the resultant compendia are utilized in a companion paper wherein Lee and coauthors use PAO1- and PA14-specific compendia to identify strain-stable gene expression patterns and interrogate transcriptional relationships among and between core and accessory genes ( 18 ).…”