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Email Address: Peter E Chen: peter.chen@med.navy.mil; Christopher Cook: christopher.cook@med.navy.mil; Andrew C Stewart: andrew.stewart@med.navy.mil; Niranjan Nagarajan: ninagarajann@gis.a-star.edu.sg; Dan D Sommer: dsommer@umiacs.umd.edu; Mihai Pop: mpop@umiacs.umd.edu; Brendan Thomason: bthomason@afmic.detrick.army.mil; Maureen P Kiley Thomason: kileyma@mail.nih.gov; Shannon Lentz: scourtney12@gmail.com; Nichole Nolan: nichole.nolan@med.navy.mil; Shanmuga Sozhamannan: shanmuga.sozhamannan@med.navy.mil; Alexander Sulakvelidze: asulakvelidze@ufl.edu; Alfred Mateczun: alfred.mateczun@med.navy.mil; Lei Du: lei.du@roche.com; Michael E Zwick: mzwick@emory.edu; Timothy D Read: tread@emory.edu

TDR, MEZ, LD, and SS were involved in study design. AS, and AM were involved in materials. LD, MPKT, SL, and NNo were involved in 454 sequencing. SS, MPKT, and CC were involved in additional experiments.

PEC, TDR, CC, MEZ, ACS, NN, MP, BT, and DDS were involved in data analysis. TDR, MP, and NN wrote the paper.

We would like to thank Ayra Akmal, Kim Bishop-Lilly, Mike Cariaso, Brian Osborne, Bill Klimke, Tim Welch, Jennifer Tsai, Cheryl Timms Strauss and members of the 454 Service Center for their help and advice in completing this manuscript.

The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the US Department of the Navy, US Department of Defense, or the US Government. Some of the authors are employees of the US Government, and this work was prepared as part of their official duties. Title 17 USC §105 provides that 'Copyright protection under this title is not available for any work of the United States Government.' Title 17 USC §101 defines a US Government work as a work prepared by a military service member or employee of the US Government as part of that person's official duties.

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Research Funding:

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.

Genomic characterization of the Yersinia genus

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Journal Title:

Genome Biology

Volume:

Volume 11, Number R1

Publisher:

, Pages 1-18

Type of Work:

Article | Final Publisher PDF

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.

Copyright information:

©2010 Chen et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution 2.0 Generic License ( http://creativecommons.org/licenses/by/2.0/), which permits making multiple copies, distribution of derivative works, distribution, public display, and publicly performance, provided the original work is properly cited. This license requires credit be given to copyright holder and/or author, copyright and license notices be kept intact.

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