title: Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.
abstract: Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.
authors.affiliation: Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands.
authors.forename: Jasper J
authors.initials: JJ
authors.lastname: Koehorst
authors.affiliation: Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands.
authors.forename: Jesse C J
authors.initials: JC
authors.lastname: van Dam
authors.affiliation: Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands.
authors.forename: Ruben G A
authors.initials: RG
authors.lastname: van Heck
authors.affiliation: Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands.
authors.forename: Edoardo
authors.initials: E
authors.lastname: Saccenti
authors.affiliation: Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands.|LifeGlimmer GmbH, Berlin, Germany.
authors.forename: Vitor A P Martins
authors.initials: VA
authors.lastname: Dos Santos
authors.affiliation: Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands.
authors.forename: Maria
authors.initials: M
authors.lastname: Suarez-Diez
authors.affiliation: Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, 6708 WE, The Netherlands.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Schaap
mesh_terms: D019295:Computational Biology / Q000379:methods; D004734:Energy Metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006801:Humans; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011549:Pseudomonas / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D057188:Workflow