Phylogeny, Diversity and Molecular Diagnostics of Ralstonia solanacearum

Fegan, Mark; Taghavi, Seyed Mohsen; Sly, Lindsay I.; Hayward, Andrew

doi:10.1007/978-3-662-03592-4_4

Cited by 86 publications

(60 citation statements)

References 23 publications

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“…Trees resulting from PCR-RFLP analysis of the hrp gene region, AFLP and 16S rRNA sequencing showed the separation of R. solanacearum into two major groups, confirming and extending the conclusions of previous investigations using DNA-DNA hybridization (Palleroni & Doudoroff, 1971), and more recently of RFLP analyses (Cook et al, 1989(Cook et al, , 1991Cook & Sequeira, 1994), of PCR amplification with tRNA consensus (Seal et al, 1992), of 16S rRNA sequencing (Li et al, 1993 ;Taghavi et al, 1996), and of sequencing of the 16S-23S rRNA gene spacer region, the endoglucanase gene and the polygalacturonase gene (Fegan et al, 1998). The first division, named ' Americanum ' by Cook et al (1989), includes biovars 1, 2 and N2 ; and the second division named ' Asiaticum ' contains biovars 3, 4 and 5.…”

Section: Clustering Of the Pcr-rflp And Aflp Profilessupporting

confidence: 82%

“…strains : the ' Americanum ' division contains biovar 1, 2 and N2 strains whereas the ' Asiaticum ' division comprises biovars 3, 4 and 5 strains. Sequence analysis of the 16S rRNA gene (Li et al, 1993 ;Seal et al, 1993 ;Taghavi et al, 1996), the 16S-23S rRNA gene intergenic spacer region, the polygalacturonase gene and the endoglucanase gene (Fegan et al, 1998) have confirmed the two divisions and revealed a further subdivision including Indonesian isolates.…”

Section: Introductionmentioning

confidence: 98%

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Genetic diversity of Ralstonia solanacearum as assessed by PCR-RFLP of the hrp gene region, AFLP and 16S rRNA sequence analysis, and identification of an African subdivision The GenBank accession numbers for the sequences determined in this work are AF207891–AF207897.

et al. 2000

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The genetic diversity among strains in a worldwide collection of Ralstonia solanacearum, causal agent of bacterial wilt, was assessed by using three different molecular methods. PCR-RFLP analysis of the hrp gene region was extended from previous studies to include additional strains and showed that five amplicons were produced not only with all R. solanacearum strains but also with strains of the closely related bacteria Pseudomonas syzygii and the blood disease bacterium (BDB). However, the three bacterial taxa could be discriminated by specific restriction profiles. The PCR-RFLP clustering, which agreed with the biovar classification and the geographical origin of strains, was confirmed by AFLP. Moreover, AFLP permitted very fine discrimination between different isolates and was able to differentiate strains that were not distinguishable by PCR-RFLP. AFLP and PCR-RFLP analyses confirmed the results of previous investigations which split the species into two divisions, but revealed a further subdivision. This observation was further supported by 16S rRNA sequence data, which grouped biovar 1 strains originating from the southern part of Africa.

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Section: Clustering Of the Pcr-rflp And Aflp Profilessupporting

confidence: 82%

Section: Introductionmentioning

confidence: 98%

Genetic diversity of Ralstonia solanacearum as assessed by PCR-RFLP of the hrp gene region, AFLP and 16S rRNA sequence analysis, and identification of an African subdivision The GenBank accession numbers for the sequences determined in this work are AF207891–AF207897.

et al. 2000

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“…However, ClonalFrame genealogies reconstructed on different gene sets (total data set, housekeeping genes, genes exhibiting low or high r) placed ACH732 either basal to the genealogy or within phylotype IV (data not shown). Incongruence of the phylogenetic assignment of this strain was already reported: the first published egl-based classification placed it within phylotype I (Poussier et al, 2000a), whereas intergenic transcribed tracer-based classification (Fegan et al, 1998) and mutS-based classification considered it a single phylogenetic group . Comparative genomic hybridization results (Remenant et al, 2010) established that ACH732 contained an original gene content, although placed within phylotype IV (Supplementary Figure S6).…”

Section: Discussionmentioning

confidence: 87%

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

et al. 2011

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We used multilocus sequence analysis (MLSA) on a worldwide collection of the plant pathogenic Ralstonia solanacearum (Betaproteobacteria) to retrace its complex evolutionary history. Using genetic imprints left during R. solanacearum evolution, we were able to delineate distinct evolutionary complex displaying contrasting dynamics. Among the phylotypes already described (I, IIA, IIB, III, IV), eight groups of strains with distinct evolutionary patterns, named clades, were identified. From our recombination analysis, we identified 21 recombination events that occurred within and across these lineages. Although appearing the most divergent and ancestral phylotype, phylotype IV was inferred as a gene donor for the majority of the recombination events that we detected. Whereas this phylotype apparently fuelled the species diversity, ongoing diversification was mainly detected within phylotype I, IIA and III. These three groups presented a recent expanding population structure, a high level of homologous recombination and evidences of long-distance migrations. Factors such as adaptation to a specific host or intense trading of infected crops may have promoted this diversification. Whether R. solanacearum lineages will eventually evolve in distinct species remains an open question. The intensification of cropping and increase of geographical dispersion may favour situations of phylotype sympatry and promote higher exchange of key factors for host adaptation from their common genetic pool.

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“…The egl gene was amplified by PCR in a 25-μL reaction mixture containing 2.5 μL of 10× reaction buffer (supplied), 2 μL of dNTP mixture (200 μM/L each), 1 mM/L MgSO 4 , 800 nmol/L of each primer (endo-F: 5′-ATGCATGCCGCTGGTCGCCGC-3′; endo-R: 5′-GCGTTGCCCGGCACGAACACC-3′) 8 , 0.5 U of KOD-Plus DNA Polymerase (Toyobo Co., Osaka, Japan), and 1 μL of extracted DNA. Amplifications were performed in an automated thermocycler (model 9700, Applied Biosystems) with initial denaturation at 95°C for 5 min., followed by 35 cycles of denaturation at 94°C for 30 s, annealing at 65°C for 1 min., and then extension at 72°C for 1 min.…”

Section: Sequencing Of Egl and Muts Genesmentioning

confidence: 99%

“…Recently, sequence information on the R. solanacearum genome (e.g., rRNA, ITS, hrpB, egl, mutS, gyrB) has been rapidly accumulated, thereby becoming an efficient tool for the identification and discrimination of individual strains 2,8,23,24,30,31,32,40 . Phylogenetic analyses based on the sequence data of a specific gene (egl) have facilitated the division of worldwide strains into more than 50 groups (sequevars) 3,9,22,26,41,42,44 .…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Zingiberaceae Plant Isolates of Ralstonia solanacearum in the Asia-Pacific Region

Waki

Horita

Kurose

et al. 2013

JARQ

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The genetic diversity of Ralstonia solanacearum strains isolated from Zingiberaceae plants in the Asia-Pacific region was assessed by examining their biochemical properties, discriminating the phylogeny by polymerase chain reaction (PCR), and analyzing the egl and mutS gene sequences. These data were compared with those of reference strains covering the known diversity within the R. solanacearum species complex. Fifty-two of the Zingiberaceae plant isolates belong to either biovar 3 or biovar 4. Multiplex PCR analyses indicated that these strains belong to phylotype I. Phylogenetic analyses revealed that the investigated strains could be further divided into five or more groups and three major groups, based on the egl and mutS gene sequences, respectively. These groups were closely correlated with the host species and/or geographical origin. Our findings suggest that R. solanacearum strains affecting Zingiberaceae plants have multiple origins from within the Asia-Pacific region, and may have been disseminated with seed rhizomes.

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Phylogeny, Diversity and Molecular Diagnostics of Ralstonia solanacearum

Cited by 86 publications

References 23 publications

Genetic diversity of Ralstonia solanacearum as assessed by PCR-RFLP of the hrp gene region, AFLP and 16S rRNA sequence analysis, and identification of an African subdivision The GenBank accession numbers for the sequences determined in this work are AF207891–AF207897.

Genetic diversity of Ralstonia solanacearum as assessed by PCR-RFLP of the hrp gene region, AFLP and 16S rRNA sequence analysis, and identification of an African subdivision The GenBank accession numbers for the sequences determined in this work are AF207891–AF207897.

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

Genetic Diversity of Zingiberaceae Plant Isolates of Ralstonia solanacearum in the Asia-Pacific Region

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