Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment

Waleron, Małgorzata; Waleron, Krzysztof; Podhajska, Anna J.; Łojkowska, Ewa

doi:10.1099/00221287-148-2-583

Cited by 129 publications

(112 citation statements)

References 43 publications

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“…The protocol for PCR amplification of the recA locus was based on the method described by Waleron et al (2002). Final concentrations in the PCR mixture were 2.5 mM MgCl 2 , 300 nM each primer, 0.2 mM dNTPs and 1 U Taq polymerase, made up in a final volume of 25 ml.…”

Section: Methodsmentioning

confidence: 99%

“…However, within Dickeya, sequences were reported only for D. chrysanthemi and D. paradisiaca. Our current study using the recA locus (Waleron et al, 2002) will be a first phylogenetic analysis to use an open reading frame to indicate relatedness between all species within the genus. To determine Dickeya population sequence diversity and subspecies clade structure, we sequenced the recA locus from 188 strains obtained from culture collections.…”

Section: Introductionmentioning

confidence: 99%

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Dickeya species relatedness and clade structure determined by comparison of recA sequences

Parkinson¹,

Stead²,

Bew³

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

101

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Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe. Isolation of this sequevar on multiple occasions from Dianthus and (more recently) potato demonstrates that this lineage has become established in these species. The D. dadantii clade comprised 11 sequevars, and the known host range of the species was extended from eight to 19 species. New hosts included several ornamental species and potato. The clade DUC-1 was made up exclusively of potato strains originating from Europe, which had identical sequences, whilst DUC-2 strains were isolated mostly from a variety of monocotyledonous species. A single strain from Aglaonema sp. made up DUC-3. A single sequevar constituted the D. dieffenbachiae clade. The phylogenetic method described will provide a simple means for identification to the species and intraspecies level, which will support efforts to control these pathogens based on monitoring and surveillance.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dickeya species relatedness and clade structure determined by comparison of recA sequences

Parkinson¹,

Stead²,

Bew³

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

101

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“…S4) (Waleron et al, 2002), dnaX (Sławiak et al, 2009), IGS sequences (Fessehaie et al, 2002), fusA, gapA, purA and rplB (van der Wolf et al, 2014). The PCR amplification reactions for MLST were carried out using the primers listed in Table S3, and sequencing of the housekeeping genes was done (Lejin) using the ABI Sanger sequencing system.…”

mentioning

confidence: 99%

Dickeya fangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia)

Tian

Zhao²,

Yuan

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

104

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Gram-stain-negative, pectinolytic bacteria were repeatedly isolated from pear trees displaying symptoms of bleeding canker in China. Three strains, JS5 T , LN1 and QZH3, had identical 16S rRNA gene sequences that shared 99 % similarity to the type strain of Dickeya dadantii. Phylogenetic analysis of strains JS5 T , LN1 and QZH3 with isolates representing all species of the genus Dickeya and related Pectobacterium species supported their affiliation to Dickeya. Multi-locus sequence typing employing concatenated sequences encoding recA, fusA, gapA, purA, rplB, dnaX and the intergenic spacer illustrated a phylogeny which placed strains JS5 T , LN1 and QZH3 as a distinct clade, separate from all other species of the genus Dickeya. Average nucleotide identity values obtained in comparison with all species of the genus Dickeya supported the distinctiveness of strain JS5 T within the genus Dickeya. Additionally, all three strains were phenotypically distinguished from other species of the genus Dickeya by failing to hydrolyse casein, and by producing acids from (À)-D-arabinose, (+)melibiose, (+)raffinose, mannitol and myo-inositol, but not from 5-keto-D-gluconate or b-gentiobiose. The name Dickeya fangzhongdai sp. nov. is proposed to accommodate these strains; the type strain is JS5 T

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“…Internal transcribed spacer region between 16S and 23S ribosomal subunit (Maes et al1996b;Song et al, 2004) rpoB β subunit of RNA polymerase (Hocquellet et al, 1999) groEL Heat-shock protein (Yushan et al, 2010) gyrB β subunit of DNA gyrase (Mondal et al, 2012) recA Recombinase A protein (Eisen, 1995;Waleron et al, 2002;Young and Park, 2007) atpD ATP synthesis β chain (Young and Park, 2007) dnaK Heat shock protein 70, molecular chaperone DnaK (Young et al, 2008) rpoD Sigma -70 factor of RNA polymerase (Young et al, 2008) fyuA transmembrane protein, TonB-dependent receptor (Young et al, 2008) efP Eleongation factor P protein (Bui et al, 2010) glnA Glutamine synthetase I (Takle et al, 2007) in all bacteria at high copy number per genome with highly conserved regions, allowing for very sensitive detection (Mondal et al, 2004). Since the specificity of DNA-based techniques only relies on primer and probe sequences, such assays are also easy to develop and can be transposed into virtually every pathosystem.…”

Section: Genementioning

confidence: 99%

Advancements in the diagnosis of bacterial plant pathogens: An overview

Mondal¹

2013

Biotechnol. Mol. Biol. Rev.

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The timely detection and appropriate identification of causal agents associated with disease of crop plants or seeds are considered to be the most important issue in formulating the management strategies for plant diseases. This is particularly important for plant diseases of a bacterial nature, where disease-free planting materials is the only effective way to restrict the disease. The detection of bacterial pathogens still largely depends on cultural, morphological and biochemical properties. The protocol requires skilled taxonomical expertise and is also time and labor intensive. Moreover, it cannot discriminate between closely related strains of same bacterial pathogens. With the advent of polymerase chain reaction (PCR), nucleic acid based techniques have made the diagnostic procedures for plant pathogens, including bacteria, easier than the conventional approaches. The wide acceptability of nucleic acid based techniques is due to them being more sensitive, more accurate, more specific, and much faster than conventional techniques. The serology-based diagnoses are very often preferred over nucleo-based techniques as they are more user-friendly and less cumbersome, besides being sensitive, accurate, specific, and much faster than conventional techniques. This review critically analyzes the recent developments and scope of various nucleic acid-and serology-based techniques for the diagnosis of bacterial plant pathogens.

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Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment

Cited by 129 publications

References 43 publications

Dickeya species relatedness and clade structure determined by comparison of recA sequences

Dickeya species relatedness and clade structure determined by comparison of recA sequences

Dickeya fangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia)

Advancements in the diagnosis of bacterial plant pathogens: An overview

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