SNP synteny analysis of Staphylococcus aureus and Pseudomonas aeruginosa population genomics.
FEMS Microbiol Lett
; 363(19)2016 Oct 01.
Article
em En
| MEDLINE
| ID: mdl-27702754
ABSTRACT
Genomic sequence diversity of a bacterial species mainly results from the frequency distribution of single nucleotide polymorphisms (SNPs). Here we report on an SNP matrix-based binary algorithm to determine the intraclonal or interclonal genomic diversity by the number of shared sequential SNPs, the so-called SNP synteny or haplotype. All SNP positions and the frequency and length distribution of haplotypes are determined from pairwise alignment of completely sequenced genomes. This metric is invariant regarding the reference genome chosen. Information is obtained about the size of haplotypes, genomic gradients of recombination frequency, relatedness of strains and population composition of a taxon or clonal populations. The approach is illustrated with whole genome data sets of Staphylococcus aureus and Pseudomonas aeruginosa strains.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Idioma:
En
Revista:
FEMS Microbiol Lett
Ano de publicação:
2016
Tipo de documento:
Article
País de afiliação:
Alemanha