# Genomic and Metabolic Characteristics of the Pathogenicity in Pseudomonas aeruginosa
## 3 Genome Structure in _Pseudomonas aeruginosa_  
The genetic repertoire of _P. aeruginosa_ reflects the adaptative character of this bacterial species [11]. The metabolic versatility is provided by genes encoding enzymes that participate in the metabolic pathways, transcriptional regulators, and regulatory systems [33]. The whole genome sequence of _P. aeruginosa_ strain type PAO1 was published by [PERSON] and other collaborators in 2000. Thereafter, several strains have had their whole genomes sequenced [34]. The _P. aeruginosa_ PAO1 genome is used as a reference for comparing with the genomes of other strains [34]. _P. aeruginosa_ PAO1 has a very large and complex genome, around 6.3 Mbp (G + C content 66.6%), encoding 5700 genes, including 5584 predictedopen read frames (ORFs) [34; 35]. In addition, it is estimated that 150 of the genes identified in _P. aeruginosa_ PAO1 encode outer membrane proteins related to adhesion, movement, antibiotics, and virulence factor output (Figure 1) which represents a much higher number when compared to other genomes [36]. _P. aeruginosa_ has a mosaic genome, composed of many core genes interspersed by strain-specific blocks of genes [37; 38]. As a result of comparative genomic studies within the species, the genome of _P. aeruginosa_ has been classified in three groups depending on its characteristics: the core genome, the accessory genome, and the pan-genome [18; 35; 37; 38; 39]. The core genome defines the region of the genome possessed by almost all _P. aeruginosa_ strains, interspersed with \"accessory\" genomic elements that are present in some, but absent in other strains of the same species [33; 35]. The core genome regions represent approximately 90% of the total _P. aeruginosa_ genome, display low levels of genetic diversity (0.5-0.7%), contain the majority of genes with housekeeping functions, and do not tolerate excessive changes over short evolutionary periods [40; 41; 42]. The accessory genome of _P. aeruginosa_ consists of non-conserved, variable-length stretches of DNA, generally located in extrachromosomal elements, and blocks of inserted DNA in certain loci [33; 43]. These DNA segments tend to cluster at certain loci, rather than being randomly distributed throughout the core genome [40]. These loci are often referred as genomic islands (>10 kb) [43]. This part of genome is very relevant for its clinical implications, since it harbors genes that encode proteins with homologies to virulence factors and genes that encode resistance to various classes of antibiotics [39; 44]. For example, genomic island of _P. aeruginosa_ PAPI-2 contain the gene encoding ExoU, a type-III secreted effector protein linked to increased virulence in animal models and human patients [35]. The intrinsic determinants of antibiotic resistance in _P. aeruginosa_, such as  
Figure 1: The circular representation of the _P. aeruginosa_ PAO1 genome generated with www.patrick.org (accessed in 8 May 2021). This genome contains about 6.3 Mbp. The pink circle that contains a black circle in the middle is the G + C content percentage (66.6%). The dark blue bars represent a drug target. Orange bars represent genes encoding virulence factors and the red bars genes encoding antimicrobial resistance. Cyan bars represent non-coding regions. The purple and dark green circle represent the reverse and forward coding regions of the genome, respectively. Finally, the blue circle that covers all regions represents the entire chromosome. efflux pumps and a \(\beta\)-lactamases, are located in the core genome. However, genes of acquired antibiotic resistance are present in the accessory genome [18; 31]. Indeed, the dissemination of multidrug-resistant strains is often due to the resistance genes present in the accessory genome [39]. Therefore, identification of these accessory genomic elements in _P. aeruginosa_ has a major impact on the study of the evolution, adaptation, and infectious potential of this organism [35]. The general architecture of the _P.