Specific Detection of Xylella fastidiosa Pierce's Disease Strains

Banks, Donna; Albibi, R; Chen, Jianchi; Lamikanra, Olusola; Jarret, Robert L.; Smith, Barbara J.

doi:10.1007/s002849900423

Cited by 28 publications

(20 citation statements)

References 12 publications

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“…Insects, including the glassy-winged sharpshooter (5), are the vectors for transmitting these diseases. Xf can be differentiated into subspecies or pathovars depending on such criteria as plant host specificity and pathogenicity (2,(6)(7)(8)(9)(10)(11). We will refer throughout to the citrus, almond, and oleander strains as: Xf pv citrus (XFA), Xf pv almond (XFX), and Xf pv oleander (XFY).…”

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confidence: 99%

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

Bhattacharyya

Stilwagen

Ivanova

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

101

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Xylella fastidiosa (Xf ) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two ''gapped'' Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an ''in silico'' cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.

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mentioning

confidence: 99%

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

Bhattacharyya

Stilwagen

Ivanova

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

101

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“…The greater than 70% similarity indicated that X. fastidiosa was a single species (11); however, no meaningful phylogenetic relationships could be defined. Randomly amplified polymorphic DNA analysis (RAPD) led to a more comprehensive phylogenetic classification of a larger variety of X. fastidiosa plant-host pathovars distributed across its range, such as grapevine (western United States), mulberry and oak (eastern United States), and coffee (South America) (1,4,10,14,20,26). Similarity indices of the RAPDs indicated that bacteria isolated from the same plant-host species were more similar than bacteria from different hosts (20).…”

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confidence: 99%

A Multigene Phylogenetic Study of Clonal Diversity and Divergence in North American Strains of the Plant Pathogen Xylella fastidiosa

Schuenzel¹,

Scally²,

Stouthamer

et al. 2005

Appl Environ Microbiol

131

136

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Xylella fastidiosa is a pathogen that causes leaf scorch and related diseases in over 100 plant species, including Pierce's disease in grapevines (PD), phony peach disease (PP), plum leaf scald (PLS), and leaf scorch in almond (ALS), oak (OAK), and oleander (OLS). We used a high-resolution DNA sequence approach to investigate the evolutionary relationships, geographic variation, and divergence times among the X. fastidiosa isolates causing these diseases in North America. Using a large data set of 10 coding loci and 26 isolates, the phylogeny of X. fastidiosa defined three major clades. Two of these clades correspond to the recently identified X. fastidiosa subspecies piercei (PD and some ALS isolates) and X. fastidiosa subsp. multiplex (OAK, PP, PLS, and some ALS isolates). The third clade grouped all of the OLS isolates into a genetically distinct group, named X. fastidiosa subsp. sandyi. These well-differentiated clades indicate that, historically, X. fastidiosa has been a clonal organism. Based on their synonymous-site divergence (ϳ3%), these three clades probably originated more than 15,000 years ago, long before the introduction of the nonnative plants that characterize most infections. The sister clades of X. fastidiosa subsp. sandyi and X. fastidiosa subsp. piercei have synonymoussite evolutionary rates 2.9 times faster than X. fastidiosa subsp. multiplex, possibly due to generation time differences. Within X. fastidiosa subsp. multiplex, a low level (ϳ0.1%) of genetic differentiation indicates the recent divergence of ALS isolates from the PP, PLS, and OAK isolates due to host plant adaptation and/or allopatry. The low level of variation within the X. fastidiosa subsp. piercei and X. fastidiosa subsp. sandyi clades, despite their antiquity, suggests strong selection, possibly driven by host plant adaptation.Bacterial systematics is based on identifying species that reflect historical phenotypic clusters, while recognizing that clear species groups can be obscured by the action of genetic processes uncommon among eukaryotes that facilitate horizontal gene transfer from unrelated sources (11). Named bacterial species are often further subdivided by the recognition of distinct pathovars and strains that typically infect different hosts. This strain recognition has been facilitated by the availability of whole-genome DNA sequence data for the phylogenetic comparison of an increasing number of species. Within species, isolates can be compared across multiple loci, enabling strain diversity and genetic diversity to be quantified.Many species exhibit a high degree of genetic diversity among strains that infect the same host, and this pattern is typical of the gamma subdivision proteobacteria, e.g., Escherichia coli (17, 27), Vibrio cholerae (5), Pseudomonas stutzeri (36), Xanthomonas axonopodis pv. manihotis (30), and Xanthomonas fragariae (31). Xylella fastidiosa, another gamma subdivision proteobacterium, offers an opportunity to study genetic variability both between and within plant-host strains (pathovars...

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“…Due to the presence of economically important crops in this list, Xf has been the subject of increasing attention in recent years (Hartung et al 1994;Chen et al 1995;Pooler and Hartung 1995;Banks et al 1999), leading to the complete genomic sequencing of a strain (9a5c) associated with CVC in Brazil, which turned out to be the first plant bacterium to have its complete genome elucidated. This work also involved an extensive in silico evaluation of the bacterium's presumed proteome, allowing the formulation of a virtual metabolome that provided a comprehensive view of the major biochemical processes that occur in this microorganism (Simpson et al 2000).…”

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confidence: 99%

Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

Nunes¹,

Rosato²,

Muto³

et al. 2003

Genome Res.

104

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Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species

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Specific Detection of Xylella fastidiosa Pierce's Disease Strains

Cited by 28 publications

References 12 publications

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

A Multigene Phylogenetic Study of Clonal Diversity and Divergence in North American Strains of the Plant Pathogen Xylella fastidiosa

Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

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