Genome diversity among regional populations ofFrancisella tularensissubspeciestularensisandFrancisella tularensissubspeciesholarcticaisolated from the US

Samrakandi, Mustapha M.; Zhang, C; Zhang, M; Nietfeldt, Joseph; Kim, J; Iwen, Peter C.; Olson, Michael E.; Fey, Paul D.; Duhamel, G. E.; Hinrichs, Steven H.; Cirillo, Jeffrey D.; Benson, Andrew K.

doi:10.1111/j.1574-6968.2004.tb09672.x

Cited by 23 publications

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References 27 publications

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“…F. tularensis is divided into three subspecies (subsp. ): tularensis (type A); holarctica (type B); and mediasiatica [1,2]. Tularemia caused by type A strains occurs only in North America, whereas tularemia caused by type B strains occurs throughout the northern hemisphere.…”

Section: Introductionmentioning

confidence: 99%

Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay

et al. 2009

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BackgroundA low genetic diversity in Francisella tularensis has been documented. Current DNA based genotyping methods for typing F. tularensis offer a limited and varying degree of subspecies, clade and strain level discrimination power. Whole genome sequencing is the most accurate and reliable method to identify, type and determine phylogenetic relationships among strains of a species. However, lower cost typing schemes are necessary in order to enable typing of hundreds or even thousands of isolates.ResultsWe have generated a high-resolution phylogenetic tree from 40 Francisella isolates, including 13 F. tularensis subspecies holarctica (type B) strains, 26 F. tularensis subsp. tularensis (type A) strains and a single F. novicida strain. The tree was generated from global multi-strain single nucleotide polymorphism (SNP) data collected using a set of six Affymetrix GeneChip® resequencing arrays with the non-repetitive portion of LVS (type B) as the reference sequence complemented with unique sequences of SCHU S4 (type A). Global SNP based phylogenetic clustering was able to resolve all non-related strains. The phylogenetic tree was used to guide the selection of informative SNPs specific to major nodes in the tree for development of a genotyping assay for identification of F. tularensis subspecies and clades. We designed and validated an assay that uses these SNPs to accurately genotype 39 additional F. tularensis strains as type A (A1, A2, A1a or A1b) or type B (B1 or B2).ConclusionWhole-genome SNP based clustering was shown to accurately identify SNPs for differentiation of F. tularensis subspecies and clades, emphasizing the potential power and utility of this methodology for selecting SNPs for typing of F. tularensis to the strain level. Additionally, whole genome sequence based SNP information gained from a representative population of strains may be used to perform evolutionary or phylogenetic comparisons of strains, or selection of unique strains for whole-genome sequencing projects.

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Section: Introductionmentioning

confidence: 99%

Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay

et al. 2009

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Current awareness on comparative and functional genomics

2005

Comp Funct Genom

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Weed genomics: New tools to understand weed biology (Review). Trends Plant Sci 9: (8) 391. Baxevanis AD. 2003. Using genomic databases for sequence-based biological discovery (Review). Mol Med 9: (9-12) 185. Benning C. 2004. Genetic mutant screening by direct metabolite analysis (Review). Anal Biochem 332: (1) 1. Brouzes E, Farge E. 2004. Interplay of mechanical deformation and patterned gene expression in developing embryos. Curr Opin Genet Dev 14: (4) 367. Brunner AM, Nilsson O. 2004. Revisiting tree maturation and floral initiation in the poplar functional genomics era (Review). New Phytol 164: (1) 43.

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Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization

Taboada

Luebbert

Nash

2007

Comparative Genomics

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Genome sequencing has revealed the remarkable amount of genetic diversity that can be encountered in bacterial genomes. In particular, the comparison of genome sequences from closely related strains has uncovered significant differences in gene content, hinting at the dynamic nature of bacterial genomes. The study of these genome dynamics is crucial to leveraging genomic information because the genome sequence of a single bacterial strain may not accurately represent the genome of the species. The dynamic nature of bacterial genome content has required us to apply the concepts of comparative genomics (CG) at the species level. Although direct genome sequence comparisons are an ideal method of performing CG, one current constraint is the limited availability of multiple genome sequences from a given bacterial species. DNA microarray-based comparative genomic hybridization (MCGH), which can be used to determine the presence or absence of thousands of genes in a single hybridization experiment, provides a powerful alternative for determining genome content and has been successfully used to investigate the genome dynamics of a wide number of bacterial species. Although MCGH-based studies have already provided a new vista on bacterial genome diversity, original methods for MCGH have been limited by the absence of novel gene sequences included in the microarray. New applications of the MCGH platform not only promise to accelerate the pace of novel gene discovery but will also help provide an integrated microarray-based approach to the study of bacterial CG.

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Genome diversity among regional populations ofFrancisella tularensissubspeciestularensisandFrancisella tularensissubspeciesholarcticaisolated from the US

Cited by 23 publications

References 27 publications

Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay

Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay

Current awareness on comparative and functional genomics

Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization

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