TITLE:
Application of High-Throughput Sequencing: Discovery of Informative SNPs to Subtype Bacillus anthracis
AUTHORS:
Guillaume Girault, Simon Thierry, Emeline Cherchame, Sylviane Derzelle
KEYWORDS:
SNPs, Bacillus anthracis, Genotyping, HRM, Phylogeny
JOURNAL NAME:
Advances in Bioscience and Biotechnology,
Vol.5 No.7,
June
27,
2014
ABSTRACT:
Single Nucleotide Polymorphisms (SNPs) are the most common and abundant
genetic variation found in the genome of any living species, from bacteria to
humans. In bacterial genotyping, these evolutionarily stable point mutations
represent important DNA markers that can be used to elucidate deep
phylogenetic relationships among worldwide strains, but also to discriminate
closely related strains. With the advent of next generation sequencing (NGS)
technologies, affordable solutions are now available to get access to the
complete genome sequence of an organism. Sequencing efforts of an increasing
number of strains provide an unprecedented opportunity to create comprehensive
species phylogenies. In this study, a comparative analysis of 161 genomes of Bacillus anthracis has being conducted
to discover new informative SNPs that further resolves B. anthracis SNP-based phylogenetic tree. Nine previously
unpublished SNPs that define major groups or sub-groups within the B. anthracis species were selected and
developed into SNP discriminative assays. We report here a cost-effective
high-resolution melting-based genotyping method for the screening of 27
canonical SNPs that includes these new diagnostic markers. The present assays
are useful to rapidly assign an isolate to one sub-lineages or sub-groups and
determine its phylogenetic placement on the B. anthracis substructure population.