Genomic characterization of the Yersinia genus

• Type of Material: Article
• Authors: Peter E. Chen, Naval Medical Research Center; Christopher Cook, Naval Medical Research Center; Andrew C. Stewart, Naval Medical Research Center; Niranjan Nagarajan, University of Maryland; Dan D. Sommer, University of Maryland; Mihai Pop, University of Maryland; Brendan Thomason, Naval Medical Research Center; Maureen P. Kiley Thomason, Naval Medical Research Center; Shannon Lentz, Naval Medical Research Center; Nichole Nolan, Naval Medical Research Center; Shanmuga Sozhamannan, Naval Medical Research Center; Alexander Sulakvelidze, University of Florida; Alfred Mateczun, Naval Medical Research Center; Lei Du, Life Sciences Inc.; Michael Zwick, Emory University; Timothy D Read, Emory University
• Language: English
• Date: 2010-01-04
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: ©2010 Chen et al.; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://genomebiology.com/2010/11/1/R1
• Title of Journal or Parent Work: Genome Biology
• ISSN: 1465-6906
• Volume: 11
• Issue: R1
• Start Page: 1
• End Page: 18
• Grant/Funding Information: This work was supported by grant TMTI0068_07_NM_T from the Joint Science and Technology Office for Chemical and Biological Defense (JSTO-CBD), Defense Threat Reduction Agency Initiative to TDR.
• Research Categories: Health Sciences, General; Biology, Genetics

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.