Use of 16S rDNA Sequences as Signature Characters to Identify Xylella fastidiosa

Chen, Jianchi; Banks, Donna; Jarret, Robert L.; Chang, C. J.; Smith, Barbara J.

doi:10.1007/s002849910006

Cited by 35 publications

(27 citation statements)

References 20 publications

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“…Results obtained by Chen et al (2000) showed that the strains of X. fastidiosa could be divided into two groups, one group for strains of grape and mulbery and the second group for strains of citrus, oak, grape, plum, and mulberry, based on sequencing of the 16S rDNA gene. In this work, it was possible to observe that citrus and coffee strains formed a separate group from the strains from the other hosts.…”

Section: Discussionmentioning

confidence: 99%

“…The detection and characterization of X. fastidiosa strains have been done through classic procedures based on cultivation (Hopkins, 1989) as well as using molecular procedures, such as protein profiling and homology of DNA (Chang and Schaad, 1992), RFLP (Restriction Fragment Length Polymorphism -Chen et al 1992), PCR (Polymerase Chain Reaction - Minsavage et al 1994), sequencing of the ITS DNA sequence (Ciapina, 2001), 16S rDNA (Chen et al 2000) and SNP (Single Nucleotide Polymorphism -Wickert, 2007). But despite their physiologic, microbiologic, pathogenic and molecular differences, all strains are characterized as single species.…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of Xylella fastidiosa genetic diversity by fAFPL markers

2008

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-The first phytopathogenic bacterium with its DNA entirely sequenced is being detected and isolated from different host plants in several geographic regions. Although it causes diseases in cultures of economic importance, such as citrus, coffee, and grapevine little is known about the genetic relationships among different strains. Actually, all strains are grouped as a single species, Xylella fastidiosa, despite colonizing different hosts, developing symptoms, and different physiological and microbiological observed conditions. The existence of genetic diversity among X. fastidiosa strains was detected by different methodological techniques, since cultural to molecular methods. However, little is know about the phylogenetic relationships developed by Brazilian strains obtained from coffee and citrus plants. In order to evaluate it, fAFLP markers were used to verify genetic diversity and phylogenetic relationships developed by Brazilian and strange strains. fAFLP is an efficient technique, with high reproducibility that is currently used for bacterial typing and classification. The obtained results showed that Brazilian strains present genetic diversity and that the strains from this study were grouped distinctly according host and geographical origin like citrus-coffee, temecula-grapevine-mulberry and plum-elm. Index terms: fAFLP, Xylella fastidiosa, genetic diversity, DNA fingerprinting. DIVERSIDADE GENÉTICA DE Xylella fastidiosa AVALIADA POR MARCADORES fAFLPRESUMO-A primeira bactéria fitopatogênica a ter seu genoma totalmente seqüenciado foi detectada e isolada em diferentes hospedeiros em diferentes regiões geográficas. Embora seja causadora de doenças em culturas economicamente importantes, como citros, cafeeiro e videira, pouco se conhece acerca das relações genéticas estabelecidas entre isolados da bactéria. Atualmente, todos os isolados são agrupados como uma única espécie, Xylella fastidiosa, apesar de colonizarem diferentes hospedeiros que desenvolvem sintomas diferenciados e possuir diferentes condições fisiológicas e microbiológicas. A existência de diversidade genética entre isolados da bactéria foi detectada da por métodos culturais e moleculares, embora pouco se conheça acerca das relações genéticas de isolados brasileiros obtidos de citros e cafeeiro. Este trabalho teve por objetivo verificar, através de marcadores moleculares fAFLP a existência de diversidade genética e as relações filogenéticas estabelecidas pelos isolados das bactérias brasileiras e estrangeiras. Estes marcadores foram selecionados por sua alta reproducibilidade e por ser de uso comum para tipagem e classificação bacteriana. Os resultados obtidos mostraram que os isolados brasileiros apresentam diversidade genética e que os isolados deste estudo agruparamse de acordo com o hospedeiro e origem geográfica, a saber, citros-cafeeiro, temécula-videira-amoreira e ameixeira-elmo. Termos para indexação: fAFLP, Xylella fastidiosa, diversidade genética, marcadores de DNA.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Evaluation of Xylella fastidiosa genetic diversity by fAFPL markers

2008

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“…Qin et al (30) proposed the following natural groups of strains: 1, citrus and coffee; 2, grapevine, almond, and ragweed; and 3, elm, oak, and plum. Chen et al (6) proposed three strain groups based on 16S ribosomal DNA sequences: 1, citrus and coffee; 2, grapevine and mulberry; and 3, elm, oak, peach, plum, and periwinkle. Based on our analysis of giCVC1, we propose three groups of strains: 1, citrus, coffee, and possibly other South American strains; 2, grapevine, mulberry, oleander, and some almond strains, all from North America; and 3, elm, oak, plum, periwinkle, and some almond strains, again all from North America.…”

Section: Resultsmentioning

confidence: 99%

“…Molecular analyses at the species level have revealed three distinct groups. The grapevine-infecting variants responsible for PD are found in one group, while the citrus-infecting variants responsible for CVC are found in another (6,7,16). Initial expectations, based on geographical distributions, host diversity, differential disease symptoms, and molecular analyses, were that organisms from the three groups would be sufficiently different to support taxonomic separation at the subspecies or pathovar level (17,19,24).…”

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confidence: 99%

Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa

Sluys¹,

Oliveira²,

et al. 2003

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Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X. fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grapegrowing region of California. Comparative analyses with a previously sequenced X. fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X. fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X. fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.Different microorganisms are able to survive in and to colonize plant water-conductive vessels (xylem). The result of this association is either beneficial or detrimental to the plant host.Of the latter, an example is the association of Xylella fastidiosa (38) with diverse plant hosts. X. fastidiosa is a fastidious, insecttransmitted, xylem-inhabiting bacterium known to cause several economically important diseases of both monocotyledonous and dicotyledonous plants (14,17,29). These diseases include Pierce's disease (PD) of grapevine and citrus variegated chlorosis (CVC), which have rather distinct symptoms and geographical distributions.PD, caused by certain strains of X. fastidiosa, is characterized by wilted, shriveled, raisin-like fruit and scorched leaves that detach, leaving bare petioles attached to the canes (37). The bark of affected canes may lignify or mature irregularly, leaving

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“…This has been achieved by isolation, serology (e.g., ELISA) and several PCR methods using primers designed for DNA fragments obtained by incubation of total Xf genomic DNA with restriction enzymes, random amplification (Minsavage et al, 1994;Pooler and Hartung, 1995), and conserved genes like 16S rRNA (Chen et al, 2000) and gyrB (Rodrigues et al, 2003).…”

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confidence: 99%

Genome-based PCR Primers for Specific and Sensitive Detection and Quantification of Xylella fastidiosa

et al. 2006

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Xylella fastidiosa is an important pathogen of many commercial crops. Detection of X. fastidiosa is difficult due to low concentrations of the bacteria in insects and asymptomatic plant tissue, and non-uniform distribution in infected plants. A dual purpose conventional PCR and quantitative PCR (TaqManä) system was developed for the generic detection of X. fastidiosa strains. Primers HL5 and HL6, designed to amplify a unique region common to the sequenced genomes of four Xylella strains, amplified a 221 bp fragment from strains associated with PierceÕs disease of grapes, almond leaf scorch, and oleander leaf scorch disease and from DNA from an Xf strain associated with citrus variegated chlorosis. Standard curves were obtained using concentrations of Xylella ranging from 5 to 10 5 cells per reaction in water and grape extracts and 10-10 5 cells in insect DNA. Regression curves were similar, with correlation coefficients of r 2 > 0.97. In quantitative PCR, C t values ranged between 20 and 36 cycles for 5-10 5 bacterial cells per reaction. No amplicons were obtained with several non-Xf bacterial strains tested including related plant pathogenic, grape endophytic bacteria and endosymbiotic bacteria isolated from glassy-winged sharpshooters. The method was evaluated for clinical diagnosis of Xf in grapes, almonds and insect vectors. The procedure described is reliable for detection of the pathogen with a high degree of sensitivity and specificity.

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Use of 16S rDNA Sequences as Signature Characters to Identify Xylella fastidiosa

Cited by 35 publications

References 20 publications

Evaluation of Xylella fastidiosa genetic diversity by fAFPL markers

Evaluation of Xylella fastidiosa genetic diversity by fAFPL markers

Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa

Genome-based PCR Primers for Specific and Sensitive Detection and Quantification of Xylella fastidiosa

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