Pseudomonas aeruginosa gene expression analysis using pangenome and PAO1 reference genomes

Abstract: Development in sequencing technologies has made the analyses of genetic material much more accessible. Processing sequenced data for an accurate analysis comes with its challenges, especially with the studies in microbial in clinical in vivo samples where difficulties in the collection of these samples for sequencing could lower the quality and contamination from the human host which might affect the accuracy of downstream analysis. In this project, we use RNA-seq and different reference genomes to look at the differential gene expression of Pseudomonas aeruginosa (PA), one of the most prevalent species of bacterial pathogens in the progression of chronic pulmonary diseases such as cystic fibrosis, due to its resistance to antimicrobial treatment. In this project, we created a pangenome from 21 strains of PA and explored the use of this, its subsets (core and soft-core gene sets) and a commonly used PA genome (PAO1) as reference genomes. We compared some of the differences and similarities in the results using the four gene sets, including mapping transcripts while developing a feasible pipeline to process raw sample reads from human sputum samples for differential expression and gene ontology enrichment analysis. From the analyses, we have found that differentially expressed genes upregulated in in vivo samples were related to biofilm, which plays a role in the difficulties in the treatment of PA infections, across most of the various genome reference-based results.