Phylogenetic Relationships of <i>Xylella fastidiosa</i> Strains Isolated from Landscape Ornamentals in Southern California

Hernández-Martínez, Rufina; Cerda, Karla A. de la; Costa, H. S.; Cooksey, Donald A.; Wong, F. P.

doi:10.1094/phyto-97-7-0857

Cited by 56 publications

(43 citation statements)

References 43 publications

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“…pauca (2,87) and X. fastidiosa subsp. multiplex (33,74,91) isolates but has been particularly limited among X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp.…”

Section: Discussionmentioning

confidence: 99%

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Differentiation of Xylella fastidiosa Strains via Multilocus Sequence Analysis of Environmentally Mediated Genes (MLSA-E)

Parker

Havird

Fuente

2012

Appl Environ Microbiol

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Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigate X. fastidiosa relationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identified a priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54 X. fastidiosa isolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with known X. fastidiosa subspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity. dN/dS ratios of environmentally mediated genes, though <1 due to high sequence similarity, are significantly greater than housekeeping gene dN/dS ratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such as X. fastidiosa isolates. Discovering the genetic relationships between X. fastidiosa isolates will provide new insights into the epidemiology of populations of X. fastidiosa, allowing improved disease management in economically important crops.X ylella fastidiosa is a Gram-negative plant-pathogenic bacterium that is adapted to live inside the xylem vessels of plant hosts and the foregut of leafhopper insect vectors (8). Biofilm formed inside the xylem vessels is believed to play a key role in disease development by obstructing water passage from the root to aerial parts of the plant (8). The bacterium infects several economically important agricultural crops, including grape, citrus, almond, and peach, as well as a variety of landscape trees and plants (38). Despite this broad host range, isolates of X. fastidiosa from different plant hosts are genetically very similar. Comparative genomic analyses between the most divergent X. fastidiosa complete genome strains (the Pierce's disease of grapevine type strain Temecula and the citrus variegated chlorosis type strain 9a5c) have shown that 98% of their genes are shared, and the average amino acid identity is 96% (85). Taxonomic analyses have grouped X. fastidiosa strains into several su...

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“…pauca (2,87) and X. fastidiosa subsp. multiplex (33,74,91) isolates but has been particularly limited among X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp.…”

Section: Discussionmentioning

confidence: 99%

“…fastidiosa and X. fastidiosa subsp. sandyi isolates (33,74,76,91), with the exception of X. fastidiosa subsp. fastidiosa isolates from Costa Rica (61).…”

Section: Discussionmentioning

confidence: 99%

Differentiation of Xylella fastidiosa Strains via Multilocus Sequence Analysis of Environmentally Mediated Genes (MLSA-E)

Parker

Havird

Fuente

2012

Appl Environ Microbiol

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“…X. fastidiosa subsp. multiplex has been isolated from a range of species, but most notably from native and non-native trees, including almond, elm, oak, olive, peach, pecan, plum, redbud, sweetgum, and sycamore (20,21,(23)(24)(25). Unlike subsp.…”

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confidence: 99%

Recent Evolutionary Radiation and Host Plant Specialization in the Xylella fastidiosa Subspecies Native to the United States

Nunney

Vickerman

Bromley

et al. 2013

Appl Environ Microbiol

112

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The bacterial pathogen, Xylella fastidiosa, infects many plant species in the Americas, making it a good model for investigating the genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates of the native U.S. subsp. multiplex that were largely unaffected by intersubspecific homologous recombination (IHR) and to investigate how their evolutionary history influences plant host specialization. We identified 110 "non-IHR" isolates, 2 minimally recombinant "intermediate" ones (including the subspecific type), and 31 with extensive IHR. The non-IHR and intermediate isolates defined 23 sequence types (STs) which we used to identify 22 plant hosts (73% trees) characteristic of the subspecies. Except for almond, subsp. multiplex showed no host overlap with the introduced subspecies (subspecies fastidiosa and sandyi). MLST sequences revealed that subsp. multiplex underwent recent radiation (<25% of subspecies age) which included only limited intrasubspecific recombination (/ ‫؍‬ 0.02); only one isolated lineage (ST50 from ash) was older. A total of 20 of the STs grouped into three loose phylogenetic clusters distinguished by nonoverlapping hosts (excepting purple leaf plum): "almond," "peach," and "oak" types. These host differences were not geographical, since all three types also occurred in California. ST designation was a good indicator of host specialization. ST09, widespread in the southeastern United States, only infected oak species, and all peach isolates were ST10 (from California, Florida, and Georgia). Only ST23 had a broad host range. Hosts of related genotypes were sometimes related, but often host groupings crossed plant family or even order, suggesting that phylogenetically plastic features of hosts affect bacterial pathogenicity.T he genetic typing of bacterial isolates is an increasingly important tool for understanding the epidemiology of pathogenic bacteria. It permits us to track biogeographical patterns, host specificity, and the evolutionary changes occurring within taxa. To achieve these goals, one of the most useful and widely used typing methodologies is multilocus sequence typing (MLST), introduced in 1998 (1, 2). The spread of this methodology has been rapid in the study of human bacterial pathogens; however, MLST schemes are equally important in the study of plant pathogens (3), and schemes for plant bacteria are beginning to become established, e.g., Pseudomonas syringae (4), Xylella fastidiosa (5, 6), fruit tree phytoplasmas (7), Ralstonia solanacearum (8), Xanthomonas spp. (9), and Acidovorax citrulli (10).The genetic typing of plant pathogens provides a critical first step in answering the important question of what genetic factors determine host specificity. Genome comparison among species and pathovars of Xanthomonas suggest specificity is determined by a complex set of genetic differences involving both gene content and gene sequence (11). Of these two kinds of difference, content and sequence, gene content differences are more easily studied, since it...

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“…First, the cause may be the acquisition of asymptomatic nursery tree material infected with X. fastidiosa from the central region and subsequent introduction onto the northwestern region for establishment of new coffee plantations. Another explanation is that these two geographical populations shared migrants from a common inoculum reservoir selective to host-specific X. fastidiosa genotypes, and that did not occur in other regions (Hernandez-Martinez et al 2007;Purcell and Saunders 1999;Randall et al 2009). Finally, it is plausible that the high levels of X. fastidiosa migration detected between central and northwestern São Paulo State populations may be a consequence of migrants exchanged with a third population not sampled in our study.…”

Section: Discussionmentioning

confidence: 99%

Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards

et al. 2017

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Phylogenetic Relationships of Xylella fastidiosa Strains Isolated from Landscape Ornamentals in Southern California

Cited by 56 publications

References 43 publications

Differentiation of Xylella fastidiosa Strains via Multilocus Sequence Analysis of Environmentally Mediated Genes (MLSA-E)

Differentiation of Xylella fastidiosa Strains via Multilocus Sequence Analysis of Environmentally Mediated Genes (MLSA-E)

Recent Evolutionary Radiation and Host Plant Specialization in the Xylella fastidiosa Subspecies Native to the United States

Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards

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