Literature DB >> 11526010

Differentiation of strains of Xylella fastidiosa by a variable number of tandem repeat analysis.

H D Coletta-Filho1, M A Takita, A A de Souza, C I Aguilar-Vildoso, M A Machado.   

Abstract

Short sequence repeats (SSRs) with a potential variable number of tandem repeat (VNTR) loci were identified in the genome of the citrus pathogen Xylella fastidiosa and used for typing studies. Although mono- and dinucleotide repeats were absent, we found several intermediate-length 7-, 8-, and 9-nucleotide repeats, which we examined for allelic polymorphisms using PCR. Five genuine VNTR loci were highly polymorphic within a set of 27 X. fastidiosa strains from different hosts. The highest average Nei's measure of genetic diversity (H) estimated for VNTR loci was 0.51, compared to 0.17 derived from randomly amplified polymorphic DNA (RAPD) analysis. For citrus X. fastidiosa strains, some specific VNTR loci had a H value of 0.83, while the maximum value given by specific RAPD loci was 0.12. Our approach using VNTR markers provides a high-resolution tool for epidemiological, genetic, and ecological analysis of citrus-specific X. fastidiosa strains.

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Year:  2001        PMID： 11526010      PMCID： PMC93134          DOI： 10.1128/AEM.67.9.4091-4095.2001

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  17 in total

Review 1.  Occurrence and structure-function relationship of pentameric short sequence repeats in microbial genomes.

Authors:  A van Belkum; W van Leeuwen; S Scherer; H Verbrugh
Journal:  Res Microbiol       Date:  1999 Nov-Dec       Impact factor: 3.992

2.  Tandem repeats finder: a program to analyze DNA sequences.

Authors:  G Benson
Journal:  Nucleic Acids Res       Date:  1999-01-15       Impact factor: 16.971

3.  Genetic diversity of Pierce's disease strains and other pathotypes of Xylella fastidiosa.

Authors:  M Hendson; A H Purcell; D Chen; C Smart; M Guilhabert; B Kirkpatrick
Journal:  Appl Environ Microbiol       Date:  2001-02       Impact factor: 4.792

4.  Diversity in a variable-number tandem repeat from Yersinia pestis.

Authors:  D M Adair; P L Worsham; K K Hill; A M Klevytska; P J Jackson; A M Friedlander; P Keim
Journal:  J Clin Microbiol       Date:  2000-04       Impact factor: 5.948

5.  Multicenter evaluation of arbitrarily primed PCR for typing of Staphylococcus aureus strains.

Authors:  A van Belkum; J Kluytmans; W van Leeuwen; R Bax; W Quint; E Peters; A Fluit; C Vandenbroucke-Grauls; A van den Brule; H Koeleman
Journal:  J Clin Microbiol       Date:  1995-06       Impact factor: 5.948

6.  Genetic diversity of Mycobacterium africanum clinical isolates based on IS6110-restriction fragment length polymorphism analysis, spoligotyping, and variable number of tandem DNA repeats.

Authors:  C Viana-Niero; C Gutierrez; C Sola; I Filliol; F Boulahbal; V Vincent; N Rastogi
Journal:  J Clin Microbiol       Date:  2001-01       Impact factor: 5.948

7.  Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility.

Authors:  K Kremer; D van Soolingen; R Frothingham; W H Haas; P W Hermans; C Martín; P Palittapongarnpim; B B Plikaytis; L W Riley; M A Yakrus; J M Musser; J D van Embden
Journal:  J Clin Microbiol       Date:  1999-08       Impact factor: 5.948

8.  The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis.

Authors:  A J Simpson; F C Reinach; P Arruda; F A Abreu; M Acencio; R Alvarenga; L M Alves; J E Araya; G S Baia; C S Baptista; M H Barros; E D Bonaccorsi; S Bordin; J M Bové; M R Briones; M R Bueno; A A Camargo; L E Camargo; D M Carraro; H Carrer; N B Colauto; C Colombo; F F Costa; M C Costa; C M Costa-Neto; L L Coutinho; M Cristofani; E Dias-Neto; C Docena; H El-Dorry; A P Facincani; A J Ferreira; V C Ferreira; J A Ferro; J S Fraga; S C França; M C Franco; M Frohme; L R Furlan; M Garnier; G H Goldman; M H Goldman; S L Gomes; A Gruber; P L Ho; J D Hoheisel; M L Junqueira; E L Kemper; J P Kitajima; J E Krieger; E E Kuramae; F Laigret; M R Lambais; L C Leite; E G Lemos; M V Lemos; S A Lopes; C R Lopes; J A Machado; M A Machado; A M Madeira; H M Madeira; C L Marino; M V Marques; E A Martins; E M Martins; A Y Matsukuma; C F Menck; E C Miracca; C Y Miyaki; C B Monteriro-Vitorello; D H Moon; M A Nagai; A L Nascimento; L E Netto; A Nhani; F G Nobrega; L R Nunes; M A Oliveira; M C de Oliveira; R C de Oliveira; D A Palmieri; A Paris; B R Peixoto; G A Pereira; H A Pereira; J B Pesquero; R B Quaggio; P G Roberto; V Rodrigues; A J de M Rosa; V E de Rosa; R G de Sá; R V Santelli; H E Sawasaki; A C da Silva; A M da Silva; F R da Silva; W A da Silva; J F da Silveira; M L Silvestri; W J Siqueira; A A de Souza; A P de Souza; M F Terenzi; D Truffi; S M Tsai; M H Tsuhako; H Vallada; M A Van Sluys; S Verjovski-Almeida; A L Vettore; M A Zago; M Zatz; J Meidanis; J C Setubal
Journal:  Nature       Date:  2000-07-13       Impact factor: 49.962

9.  Randomly amplified polymorphic DNA analysis of Xylella fastidiosa Pierce's disease and oak leaf scorch pathotypes.

Authors:  J Chen; O Lamikanra; C J Chang; D L Hopkins
Journal:  Appl Environ Microbiol       Date:  1995-05       Impact factor: 4.792

10.  Genetic relationships among strains of Xylella fastidiosa from RAPD-PCR data.

Authors:  M R Pooler; J S Hartung
Journal:  Curr Microbiol       Date:  1995-08       Impact factor: 2.188
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  39 in total

1.  New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae.

Authors:  L Poulin; P Grygiel; M Magne; L Gagnevin; L M Rodriguez-R; N Forero Serna; S Zhao; M El Rafii; S Dao; C Tekete; I Wonni; O Koita; O Pruvost; V Verdier; C Vernière; R Koebnik
Journal:  Appl Environ Microbiol       Date:  2014-11-14       Impact factor: 4.792

2.  Multiple-locus variable-number tandem repeat analysis of Dutch Bordetella pertussis strains reveals rapid genetic changes with clonal expansion during the late 1990s.

Authors:  Leo M Schouls; Han G J van der Heide; Luc Vauterin; Paul Vauterin; Frits R Mooi
Journal:  J Bacteriol       Date:  2004-08       Impact factor: 3.490

3.  In silico comparison of bacterial strains using mutual information.

Authors:  D Swati
Journal:  J Biosci       Date:  2007-09       Impact factor: 1.826

4.  Use of variable-number tandem repeats to examine genetic diversity of Neisseria meningitidis.

Authors:  Siamak P Yazdankhah; Bjørn-Arne Lindstedt; Dominique A Caugant
Journal:  J Clin Microbiol       Date:  2005-04       Impact factor: 5.948

5.  Differentiation of "Candidatus Liberibacter asiaticus" isolates by variable-number tandem-repeat analysis.

Authors:  Hiroshi Katoh; Siti Subandiyah; Kenta Tomimura; Mitsuru Okuda; Hong-Ji Su; Toru Iwanami
Journal:  Appl Environ Microbiol       Date:  2011-01-14       Impact factor: 4.792

6.  DNA fingerprinting of Salmonella enterica subsp. enterica serovar typhimurium with emphasis on phage type DT104 based on variable number of tandem repeat loci.

Authors:  Bjørn-Arne Lindstedt; Even Heir; Elisabet Gjernes; Georg Kapperud
Journal:  J Clin Microbiol       Date:  2003-04       Impact factor: 5.948

7.  Detection and diversity assessment of Xylella fastidiosa in field-collected plant and insect samples by using 16S rRNA and gyrB sequences.

Authors:  Jorge L M Rodrigues; M E Silva-Stenico; J E Gomes; J R S Lopes; S M Tsai
Journal:  Appl Environ Microbiol       Date:  2003-07       Impact factor: 4.792

8.  Hypervariations of a protease-encoding gene, PD0218 (pspB), in Xylella fastidiosa strains causing almond leaf scorch and Pierce's disease in California.

Authors:  J Chen; E Civerolo; K Tubajika; S Livingston; B Higbee
Journal:  Appl Environ Microbiol       Date:  2008-05-02       Impact factor: 4.792

9.  Evaluation of the genetic structure of Xylella fastidiosa populations from different Citrus sinensis varieties.

Authors:  Helvécio Della Coletta-Filho; Marcos Antonio Machado
Journal:  Appl Environ Microbiol       Date:  2002-08       Impact factor: 4.792

10.  Multiple-locus variable number tandem repeat analysis of Staphylococcus aureus: comparison with pulsed-field gel electrophoresis and spa-typing.

Authors:  Leo M Schouls; Emile C Spalburg; Martijn van Luit; Xander W Huijsdens; Gerlinde N Pluister; Marga G van Santen-Verheuvel; Han G J van der Heide; Hajo Grundmann; Max E O C Heck; Albert J de Neeling
Journal:  PLoS One       Date:  2009-04-03       Impact factor: 3.240
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