Profile

Career

1992 -	Professor of Molecular Ecology	Department of Biology, University of York
1979 - 1992	Research group leader	John Innes Institute, Norwich
1978 - 1979	SRC Postdoctoral Fellow	School of Biology, University of Sussex
1975 - 1978	NIH Postdoctoral Fellow	Department of Ecology and Evolution, State University of New York at Stony Brook
1975	PhD	University of Cambridge (Natural Sciences - Genetics)
1972	BA	University of Cambridge (Natural Sciences - Genetics)

Research

Overview

Population genetics, molecular phylogeny and comparative genomics of rhizobia and other bacteria. Molecular ecology and diversity of mycorrhizal fungi. Bioinformatics and environmental genomics. Biologically-inspired computing.

Discoveries

Bacterial accessory genomes are assembled from a pool that is distinct from the core genome The main symbionts of Mimosa species are betaproteobacteria in the genus Burkholderia. The Glomus nuclear genome has multiple coexisting gene versions but the mitochondrion does not.

Current projects

• Population genomics of bacteria (Funding body: NERC)
• PLAZZMID: Evolutionary algorithms from bacterial and bee genomes (with Prof S Stepney and Mr T Clarke) (Funding body: EPSRC)
• Evolution and function of bacterial stomatins (Funding body: BBSRC)
• The evolution of bacterial genome composition (Funding body: NERC)
• Is there a third component in bacterial genomes? (Funding body: BBSRC)
• Genetic diversity of arbuscular mycorrhizal fungi (Funding body: Pakistan HEC)

Research group(s)

Status	Name	Project
Postdoctoral fellow	Ed Clark	PLAZZMID (with S Stepney and T Clarke)
Postdoctoral fellow	Simon Hickinbotham	PLAZZMID (with S Stepney and T Clarke)
Postdoctoral fellow	Elisa Giuntini	Population genomics of bacteria
Research Student	Nayoung Kim	The accessory genes in bacterial genomes
Research Student	Ganesh Lad	Adaptive diversity within an bacterial population
Research Student	Jasper Green	Evolution and function of bacterial stomatins
Research Student	Peter Harrison	Is there a third component in bacterial genomes?
Research Student	Jaikoo Lee	Molecular diversity of mycorrhizal fungi
Research Student	Muhammad Shakeel	Molecular diversity of mycorrhizal fungi
Research Student	Ryan Lower	The evolution of bacterial genome composition
Visiting Student	Terd Disayathanoowat	Bacterial diversity in bees
Visiting Student	Sang Watanarojanaporn	Diversity of mycorrhizal fungi in crops
Visiting Studet	Amanat Ali	Enzymes in rhizobia

Available PhD research projects

Comparative genomics and the evolution of bacteria (for 2012 - 13)

The number of completed bacterial genome sequences is increasing rapidly, and provides a rich data resource for computer-based studies aimed at understanding the composition and evolution of bacterial genomes. We also have extensive genome survey sequence data of our own on multiple isolates of rhizobia which require further analysis to elucidate the genetic structure of bacterial populations. The project will develop new tools and approaches for comparing and analysing genomes. A masters degree in bioinformatics would ideal preparation, and certainly a background in genetics and some aptitude for computer programming is important. In addition to computer-based studies, there is a possibility of some laboratory work collecting new data on genomic diversity. Our research group includes both lab- and computer-based people.

Recent relevant papers:

Lozano L, et al. (2010) Appl. Environ. Microbiol.76, 6504-6513.  [evolution of insertion sequences]
Tian CF, et al. (2010) FEMS Microbiology Ecology 73, 563-576. [multilocus population structure with recombination]
Harrison PW,  et al. (2010) Trends in Microbiology 18, 141-148. [comprehensive bioinformatic analysis supporting the ‘chromid’ concept]
Bontemps C, et al. (2010) Molecular Ecology 19, 44-52. [diverse species, little recombination]
Bailly X, et al. (2011) ISME Journal 10.1038/ismej.2011.55. [population genomics by next-gen sequencing]

Publications

Selected publications

Young JPW, Crossman L, Johnston A, et al. (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biology 7: R34

Vandenkoornhuyse P, Mahé S, Ineson P, Staddon P, Ostle N, Cliquet J-B, Francez A-J, Fitter AH and Young JPW (2007) Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA Proc Nat Acad Sci USA 104: 16970–1697

Lee J, Young JPW (2009) The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus. New Phytologist 183: 200-211

External activities

Memberships

• International Subcommittee on the Taxonomy of Rhizobium and Agrobacterium
• Steering Committee of the Glomus Genome Consortium

Editorial duties

• Editorial Board: BMC Ecology
• Editorial Board: ISME Journal
• Editorial Board: Comparative and Functional Genomics
• Editor-in-Chief: Genes