Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

Jasper J. Koehorst, Jesse C.J. van Dam, Ruben G.A. van Heck, Edoardo Saccenti, Vitor Martins dos Santos, Maria Suarez-Diez*, Peter J. Schaap

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

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.

Original languageEnglish
Article number38699
Number of pages13
JournalScientific Reports
Volume6
DOIs
Publication statusPublished - 2016

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    Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

    Koehorst, J. (Creator), van Dam, J. C. J. (Contributor), van Heck, R. G. A. (Contributor), Saccenti, E. (Contributor), Martins dos Santos, V. (Contributor), Suarez Diez, M. (Contributor) & Schaap, P. (Contributor), Wageningen University & Research, 25 Sep 2018

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