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Genomic characterization of the Yersinia genus

Peter E Chen1, Christopher Cook1, Andrew C Stewart1, Niranjan Nagarajan27, Dan D Sommer2, Mihai Pop2, Brendan Thomason1, Maureen P Kiley Thomason1, Shannon Lentz1, Nichole Nolan1, Shanmuga Sozhamannan1, Alexander Sulakvelidze3, Alfred Mateczun1, Lei Du4, Michael E Zwick15 and Timothy D Read156*

  • * Corresponding author: Timothy D Read tread@emory.edu

  • † Equal contributors

Author Affiliations

1 Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, USA

2 University of Maryland Institute for Advanced Computer Sciences, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA

3 Emerging Pathogens Institute and Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida 32610, USA

4 454 Life Sciences Inc., 15 Commercial Street, Branford, Connecticut 06405, USA

5 Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA

6 Division of Infectious Diseases, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA

7 Current address: Computational and Mathematical Biology, Genome Institute of Singapore, Singapore-127726

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Genome Biology 2010, 11:R1  doi:10.1186/gb-2010-11-1-r1

Published: 4 January 2010

Abstract

Background

New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) had been sequenced. However, there were no genomic data on the Yersinia species with more limited virulence potential, frequently found in soil and water environments.

Results

We used high-throughput sequencing-by-synthesis instruments to obtain 25- to 42-fold average redundancy, whole-genome shotgun data from the type strains of eight species: Y. aldovae, Y. bercovieri, Y. frederiksenii, Y. kristensenii, Y. intermedia, Y. mollaretii, Y. rohdei, and Y. ruckeri. The deepest branching species in the genus, Y. ruckeri, causative agent of red mouth disease in fish, has the smallest genome (3.7 Mb), although it shares the same core set of approximately 2,500 genes as the other members of the species, whose genomes range in size from 4.3 to 4.8 Mb. Yersinia genomes had a similar global partition of protein functions, as measured by the distribution of Cluster of Orthologous Groups families. Genome to genome variation in islands with genes encoding functions such as ureases, hydrogeneases and B-12 cofactor metabolite reactions may reflect adaptations to colonizing specific host habitats.

Conclusions

Rapid high-quality draft sequencing was used successfully to compare pathogenic and non-pathogenic members of the Yersinia genus. This work underscores the importance of the acquisition of horizontally transferred genes in the evolution of Y. pestis and points to virulence determinants that have been gained and lost on multiple occasions in the history of the genus.