Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 541463
Title Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data
Author(s) Koehorst, J.J.; Dam, J.C.J. van; Heck, R.G.A. van; Saccenti, E.; Martins dos Santos, V.A.P.; Suarez Diez, M.; Schaap, P.J.
DOI https://doi.org/10.4121/uuid:948c10fe-7ea5-47f3-bdb2-d5b0f908820b
Department(s) Systems and Synthetic Biology
VLAG
Publication type Dataset
Publication year 2018
Keyword(s) database - genome annotation - protein domains - Pseudomonas - semantic web
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.
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