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Journal of Bacteriology, August 2006, p. 5904-5914, Vol. 188, No. 16
0021-9193/06/$08.00+0     doi:10.1128/JB.00437-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Paired-End Sequence Mapping Detects Extensive Genomic Rearrangement and Translocation during Divergence of Francisella tularensis subsp. tularensis and Francisella tularensis subsp. holarctica Populations{dagger} ,{ddagger}

Michael P. Dempsey,1,2 Joseph Nietfeldt,3 Jacques Ravel,4 Steven Hinrichs,1 Robert Crawford,2 and Andrew K. Benson3*

Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198,1 Division of Microbiology, Armed Forces Institute of Pathology, Washington, D.C. 20306-6000,2 Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska 68583-0919,3 The Institute for Genome Research, Rockville, Maryland 208504

Received 29 March 2006/ Accepted 8 June 2006

Comparative genome hybridization of the Francisella tularensis subsp. tularensis and F. tularensis subsp. holarctica populations have shown that genome content is highly conserved, with relatively few genes in the F. tularensis subsp. tularensis genome being absent in other F. tularensis subspecies. To determine if organization of the genome differs between global populations of F. tularensis subsp. tularensis and F. tularensis subsp. holarctica, we have used paired-end sequence mapping (PESM) to identify regions of the genome where synteny is broken. The PESM approach compares the physical distances between paired-end sequencing reads of a library of a wild-type reference F. tularensis subsp. holarctica strain to the predicted lengths between the reads based on map coordinates of two different F. tularensis genome sequences. A total of 17 different continuous regions were identified in the F. tularensis subsp. holarctica genome (CRholarctica) which are noncontiguous in the F. tularensis subsp. tularensis genome. Six of the 17 different CRholarctica are positioned as adjacent pairs in the F. tularensis subsp. tularensis genome sequence but are translocated in F. tularensis subsp. holarctica, implying that their arrangements are ancestral in F. tularensis subsp. tularensis and derived in F. tularensis subsp. holarctica. PCR analysis of the CRholarctica in 88 additional F. tularensis subsp. tularensis and F. tularensis subsp. holarctica isolates showed that the arrangements of the CRholarctica are highly conserved, particularly in F. tularensis subsp. holarctica, consistent with the hypothesis that global populations of F. tularensis subsp. holarctica have recently experienced a periodic selection event or they have emerged from a recent clonal expansion. Two unique F. tularensis subsp. tularensis-like strains were also observed which likely are derived from evolutionary intermediates and may represent a new taxonomic unit.

* Corresponding author. Mailing address: Department of Food Science and Technology, University of Nebraska, 330 Food Industry Complex, Lincoln, NE 68583-0919. Phone: (402) 472-5637. Fax: (402) 472-1693. E-mail: abenson1{at}unl.edu.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} This paper is a contribution of the University of Nebraska Agricultural Research Division, Lincoln (journal series no. 15265).

Journal of Bacteriology, August 2006, p. 5904-5914, Vol. 188, No. 16
0021-9193/06/$08.00+0     doi:10.1128/JB.00437-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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