Abstract
We used whole-genome analysis and subsequent characterization of geographically diverse strains using new genetic signatures to identify distinct subgroups within Francisella tularensis subsp. tularensis group A.I: A.I.3, A.I.8, and A.I.12. These subgroups exhibit complex phylogeographic patterns within North America. The widest distribution was observed for A.I.12, which suggests an adaptive advantage.
Highlights
Sequencing of the 13 F. tularensis genomes was performed using an Illumina GA IIx instrument (Illumina Inc., San Diego, CA, USA) (100-bp pair-end reads) at the Translational Genomics Research Institute (TGen; Flagstaff, Arizona, USA) and the sequences were assembled using Abyss v1.3.3 (1)
Sequence reads were re-mapped to their corresponding genome sequence using bowtie[2] v2.0.0 (2) and subsequent Single Nucleotide Polymorphism (SNP)-calling by samtool mpileup (3) and VarScan v2.3.2 (4) using default parameters except p-value=0.9
Using the SNP information, positions for nucleotides that were supported by
Summary
Sequencing of the 13 F. tularensis genomes was performed using an Illumina GA IIx instrument (Illumina Inc., San Diego, CA, USA) (100-bp pair-end reads) at the Translational Genomics Research Institute (TGen; Flagstaff, Arizona, USA) and the sequences were assembled using Abyss v1.3.3 (1). To ensure high-quality data, the genome sequences were filtered to minimize uncertain sequence positions in the phylogenetic analysis.
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