Koehorst, J.J. (Jasper Jan) (2018): Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data. Version 1. 4TU.ResearchData. dataset. https://doi.org/10.4121/uuid:948c10fe-7ea5-47f3-bdb2-d5b0f908820b

Dataset

• Microbiology
• Genetics

database, genome annotation, protein domains, Pseudomonas, Semantic web

CC BY 4.0

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by J.J. (Jasper Jan) Koehorst

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.

• 2018-09-26 first online, published, posted

4TU.Centre for Research Data

media types: application/x-gzip, text/plain

• https://doi.org/10.1038/srep38699

Wageningen University & Research, Department of Agrotechnology and Food Sciences

• Martins dos Santos, V.A.P (Vitor)
• Saccenti, E (Edoardo)
• Schaap, P.J. (Peter)
• Suarez Diez, M. (Maria)
• van Dam, J.C.J (Jesse)
• van Heck, R.G.A (Ruben)