Testing of a whole genome PCR scanning approach to identify genomic variability in four different species of lactic acid bacteria

Ben Zakour N., Grimaldi C., Gautier M., Langella P., Azevedo V., Maguin E. and Le Loir Y. (2006) Testing of a whole genome PCR scanning approach to identify genomic variability in four different species of lactic acid bacteria. Research in Microbiology, 157 4: 386-394. doi:10.1016/j.resmic.2005.09.006


Author Ben Zakour N.
Grimaldi C.
Gautier M.
Langella P.
Azevedo V.
Maguin E.
Le Loir Y.
Title Testing of a whole genome PCR scanning approach to identify genomic variability in four different species of lactic acid bacteria
Journal name Research in Microbiology   Check publisher's open access policy
ISSN 0923-2508
Publication date 2006-01-01
Sub-type Article (original research)
DOI 10.1016/j.resmic.2005.09.006
Volume 157
Issue 4
Start page 386
End page 394
Total pages 9
Language eng
Subject 2402 Applied Microbiology and Biotechnology
2404 Microbiology
Abstract Genomes can be markedly heterogeneous in conspecific bacterial strains. Genome sequences can be used to analyze genome plasticity via a PCR2 (plasticity of chromosome revealed by PCR) approach. Small-sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and then applied to several other strains. Analysis of the resulting patterns can reveal genome plasticity. GenoFrag, a software package for the design of primers optimized for PCR2 [N. Ben Zakour, M. Gautier, R. Andonov, D. Lavenier, M.F. Cochet, P. Veber, A. Sorokin, Y. Le Loir, GenoFrag: Software to design primers optimized for whole genome scanning by long-range PCR amplification, Nucleic Acids Res. 32 (2004) 17-24] was developed for the analysis of bacterial genome plasticity by whole genome amplification in ∼10-kb-long fragments. By applying GenoFrag, we provide herewith evidence that genome plasticity can be analyzed in lactic acid bacteria using a PCR2 approach. The genome sequences of Lactococcus lactis IL1403, Lactobacillus plantarum WCFS1, Lactobacillus bulgaricus ATCC11842 and Bifidobacterium longum NCC2705 were used to design four sets of primers. Each set was evaluated in silico to check that it ensured optimum coverage of the bacterial chromosome. To validate the primers generated by GenoFrag, a subset of primers was successfully used in LR-PCR experiments on genomic DNA from four L. bulgaricus strains.
Keyword Food grade bacteria
Genome variability
Long-range PCR
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: Scopus Import - Archived
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 1 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 2 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Thu, 03 Apr 2014, 01:39:44 EST by Nouri Ben Zakour on behalf of Examinations