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Journal of Bacteriology, April 2009, p. 2864-2870, Vol. 191, No. 8
0021-9193/09/$08.00+0 doi:10.1128/JB.01581-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella
,
Jeffrey T. Foster,1
Stephen M. Beckstrom-Sternberg,1,2
Talima Pearson,1
James S. Beckstrom-Sternberg,1
Patrick S. G. Chain,3,4,5
Francisco F. Roberto,6
Jonathan Hnath,7
Tom Brettin,8 and
Paul Keim1*
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011-4073,1 Translational Genomics Research Institute, Phoenix, Arizona 85004,2 Microbial Program, Joint Genome Institute, Walnut Creek, California 94598,3 Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550,4 Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824,5 Idaho National Laboratory, Idaho Falls, Idaho 83415,6 National Biodefense Analysis and Countermeasures Center, Frederick, Maryland 21703,7 Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 875458
Received 7 November 2008/ Accepted 23 January 2009
Brucellae are worldwide bacterial pathogens of livestock and wildlife, but phylogenetic reconstructions have been challenging due to limited genetic diversity. We assessed the taxonomic and evolutionary relationships of five Brucella species—Brucella abortus, B. melitensis, B. suis, B. canis, and B. ovis—using whole-genome comparisons. We developed a phylogeny using single nucleotide polymorphisms (SNPs) from 13 genomes and rooted the tree using the closely related soil bacterium and opportunistic human pathogen, Ochrobactrum anthropi. Whole-genome sequencing and a SNP-based approach provided the requisite level of genetic detail to resolve species in the highly conserved brucellae. Comparisons among the Brucella genomes revealed 20,154 orthologous SNPs that were shared in all genomes. Rooting with Ochrobactrum anthropi reveals that the B. ovis lineage is basal to the rest of the Brucella lineage. We found that B. suis is a highly divergent clade with extensive intraspecific genetic diversity. Furthermore, B. suis was determined to be paraphyletic in our analyses, only forming a monophyletic clade when the B. canis genome was included. Using a molecular clock with these data suggests that most Brucella species diverged from their common B. ovis ancestor in the past 86,000 to 296,000 years, which precedes the domestication of their livestock hosts. Detailed knowledge of the Brucella phylogeny will lead to an improved understanding of the ecology, evolutionary history, and host relationships for this genus and can be used for determining appropriate genotyping approaches for rapid detection and diagnostic assays for molecular epidemiological and clinical studies.
* Corresponding author. Mailing address: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073. Phone: (928) 523-1078. Fax: (928) 523-4015. E-mail: paul.keim{at}nau.edu
Published ahead of print on 6 February 2009.
Supplemental material for this article may be found at http://jb.asm.org/.
Journal of Bacteriology, April 2009, p. 2864-2870, Vol. 191, No. 8
0021-9193/09/$08.00+0 doi:10.1128/JB.01581-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»