Articles
IN SILICO ANALYSIS OF VARIABLE NUMBER OF TANDEM REPEATS IN ERWINIA AMYLOVORA GENOME
Article number
896_13
Pages
115 – 118
Language
English
Abstract
Erwinia amylovora exhibits limited diversity among isolates.
Molecular epidemiology of this bacterium is hindered by a lack of simple methods for high resolution exchangeable molecular typing.
A method comparing number of tandem repeats of specific sequences among isolates proved useful in differentiating among isolates of other monophyletic species such as Yersinia pestis. We report here of an in silico analysis of E. amylovora chromosome for the presence of variable number of tandem repeats (VNTS) that are a promising basis for a reliable, discriminatory method.
DNA repeats were identified in the genome of E. amylovora CFBP 1430 (Smits et al., 2010) using tandem repeat finder software available at http://minisatellites.u-psud.fr/GPMS (Denoeud and Vergnaud, 2004; Grissa et al., 2008). Results confirm the presence of VNTRs at a density slightly lower than in most of other plant pathogenic bacteria included in the study.
Comparing two available genome sequences of E. amylovora, CFBP 1430 and ATCC 49946, differences between VNTRs were found further indicating good potential of VNTR analysis as a basis of a novel genotyping method to study its diversity.
Molecular epidemiology of this bacterium is hindered by a lack of simple methods for high resolution exchangeable molecular typing.
A method comparing number of tandem repeats of specific sequences among isolates proved useful in differentiating among isolates of other monophyletic species such as Yersinia pestis. We report here of an in silico analysis of E. amylovora chromosome for the presence of variable number of tandem repeats (VNTS) that are a promising basis for a reliable, discriminatory method.
DNA repeats were identified in the genome of E. amylovora CFBP 1430 (Smits et al., 2010) using tandem repeat finder software available at http://minisatellites.u-psud.fr/GPMS (Denoeud and Vergnaud, 2004; Grissa et al., 2008). Results confirm the presence of VNTRs at a density slightly lower than in most of other plant pathogenic bacteria included in the study.
Comparing two available genome sequences of E. amylovora, CFBP 1430 and ATCC 49946, differences between VNTRs were found further indicating good potential of VNTR analysis as a basis of a novel genotyping method to study its diversity.
Publication
Authors
T. Dreo, M. Ravnikar, J.E. Frey, T.H.M. Smits, B. Duffy
Keywords
Erwinia amylovora, diversity, variable number of tandem repeats, MLVA
Online Articles (80)