Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

Abstract

Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas Genome Database (http://www.pseudomonas.com) integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences. This aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies. The wide range of tools for comparing Pseudomonas annotations and sequences now includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions. Views link to genome-scale experimental data as well as comparative genomics analyses that incorporate robust genera-geared methods for predicting and clustering orthologs. These analyses can be exploited for identifying putative essential and core Pseudomonas genes or identifying large-scale evolutionary events. The Pseudomonas Genome Database aims to provide a continually updated, high quality source of genome annotations, specifically tailored for Pseudomonas researchers, but using an approach that may be implemented for other genera-level research communities.

Non-social adaptation defers a tragedy of the commons in Pseudomonas aeruginosa quorum sensing

“…We also sequenced the genome of the ancestral PAO1 wild-type strain for comparison. Genomes were assembled using the published PAO1 genome sequence as a reference (Stover et al, 2000;Winsor et al, 2011). In all, our analysis showed the HC harbored only three mutations when compared with the wild-type ancestor, including lasR.…”

“…The mutations were single-nucleotide polymorphisms in lasR (PA1430) and in PA2408, as well as an 18 base-pair truncation in psdR (PA4499). PA2408 encodes a probable adenosine triphosphate (ATP)-binding component of an ABC (ATP-binding cassette) transporter, and psdR encodes a transcriptional regulator (Kiely et al, 2008;Winsor et al, 2011) (Table 2). Targeted Sanger sequencing of all three loci in two additional HC and cheater isolates from day 12 of two independent in vitro evolution experiments revealed that mutations in lasR and psdR are ubiquitous in isolates displaying both phenotypes, but mutations in PA2408 are not (Supplementary Table S2).…”

“…Sequencing of the HC isolate produced 507 094 reads covering B187 Mb, whereas the ancestral PAO1 produced 501 270 reads covering B200 Mb. Raw 454 reads were assembled using the Roche 454 Newbler assembler (Roche Diagnostics, Basel, Switzerland) with the PAO1 genome as a reference (Stover et al, 2000;Margulies et al, 2005;Winsor et al, 2011). The HC assembly utilized an average map length of 370 bp and average sequence depth of 29.5, whereas the ancestral PAO1 assembly utilized an average map length of 401 bp and average sequence depth of 31.7.…”

Dispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles

“…The libraries were sequenced using the Illumina MiSeq V2 platform with a paired-end protocol and read lengths of 150 nt. The sequence reads were mapped onto the P. aeruginosa PAO1 reference genome, which is available for download from the Pseudomonas Genome Database (http://www.pseudomonas.com) 46 , using the 'RNA-Seq and expression analysis' application of the CLC genomics Workbench 6.0 (CLC Bio, Aarhus, Denmark). The following criteria were used to filter the unique sequence reads: maximum number of hits for a read of 1, minimum length fraction of 0.9, minimum similarity fraction of 0.8 and maximum number of two mismatches.…”

Homeostasis and Catabolism of Choline and Glycine Betaine: Lessons from Pseudomonas aeruginosa

“…While choline is ubiquitous in eukaryotes, the ability to synthesize choline or GB de novo from phosphatidylethanolamine or glycine is less prevalent in bacteria and evidence suggests that it is absent in the pseudomonads (42). While de novo choline synthesis has not been demonstrated in the pseudomonads, transporters for exogenous choline import are ubiquitous within this group based on analyses of current genome sequences (43). Import of choline and GB has been well studied in these and other bacteria, and I direct readers to relevant reviews on the topic (44)(45)(46).…”