Br.013 group . Interestingly, at this regional scale, canSNPs and MLVA exhibited considerable congruence in identifying genetic groups. Specifically, canSNPs identified six subclades and MLVA identified five, albeit with slightly different but not phylogenetically inconsistent membership due to the
nature of the two different marker types. SNPs discovered from whole selleckchem genome sequences selleck chemicals will typically provide greater discrimination than MLVA, as seen in subclades B.Br.030/031, B.Br.031/032 and B.Br.Georgia (Table 2), and can even be used to identify specific strains . However, discovering these rare SNPs requires whole genome sequencing whereas MLVA can identify nearly the same number of genetic groups by simply surveying a few highly polymorphic portions of the genome. At this regional scale, homoplasy does not appear to be much of a factor in obscuring phylogenetic signal for identifying
genetic groups using MLVA, although the relationships among those groups are less resolved as isolates from adjacent groups share MLVA genotypes. Together, SNPs and MLVA provide complementary approaches, by first accurately placing isolates in a phylogeny using SNPs and then discriminating among isolates within SNP-determined subclades using MLVA. This step-wise PI3K Inhibitor Library ic50 approach has been termed Progressive Hierarchical Resolving Assays using Nucleic Acids (PHRANA) . Conclusions We describe a new subpopulation in the B.Br.013 group
from Georgia that is genetically and geographically distinct from the other B.Br.013 group subpopulations found in Europe. Members of this
age are endemic to parts of Eastern Europe and Western BCKDHB Asia, though the complete geographic range remains unknown. The basal positioning of the Georgian lineage and its restricted geographic distribution illustrates the need for studies on additional Asian and East European isolates to gain a better understanding of the clonal expansion of F. tularensis subsp. holarctica. Methods Whole Genome Sequencing We sequenced a single Georgian isolate (F0673), representing the most common MLVA profile type of F. tularensis subsp. holarctica found in the country of Georgia (Chanturia, unpubl. data), using Illumina’s Genome Analyzer II (San Diego, CA). DNA from F0673 was prepared using a standard chloroform extraction protocol . Library preparation for this isolate involved sonication of 5 μg genomic DNA to an average fragment size of 350 bp, followed by sample preparation and cluster generation protocols for paired-end reads from Illumina. The library was quantified using SYBR-based qPCR and primers modified from the adaptor sequence. The library was then run in two lanes of the flow cell to increase overall coverage. Read lengths were ca. 40 bp, with a final yield of 32 Gb of sequence for the entire run. Image analysis for base calling and alignments followed the methods of Craig and colleagues .