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McCann HC. Skirmish or war: the emergence of agricultural plant pathogens. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:147-152. [PMID: 32712539 DOI: 10.1016/j.pbi.2020.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological and evolutionary processes underlying the emergence of infectious disease is critically important in guiding prevention, management and breeding strategies. Novel pathogen lineages may arise within agricultural environments, wild hosts or from non-host associated disease reservoirs. Although the source of most disease outbreaks remains unknown, environmental and zoonotic origins are frequently identified in mammalian pathosystems and expanded sampling of plant pathosystems reveals important links with wild populations. This review describes key ecological and evolutionary processes underlying disease emergence, with particular emphasis on shifts from wild reservoirs to cultivated hosts and genetic mechanisms driving host adaption subsequent to emergence.
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Affiliation(s)
- Honour C McCann
- New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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Francisco CS, Ceresini PC, Almeida RPP, Coletta-Filho HD. Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards. PHYTOPATHOLOGY 2017; 107:395-402. [PMID: 27992307 DOI: 10.1094/phyto-08-16-0300-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Xylella fastidiosa, an economically important plant-pathogenic bacterium, infects both coffee and citrus trees in Brazil. Although X. fastidiosa in citrus is well studied, knowledge about the population structure of this bacterium infecting coffee remains unknown. Here, we studied the population structure of X. fastidiosa infecting coffee trees in São Paulo State, Brazil, in four regions where citrus is also widely cultivated. Genotyping of over 500 isolates from coffee plants using 14 genomic microsatellite markers indicated that populations were largely geographically isolated, as previously found with populations of X. fastidiosa infecting citrus. These results were supported by a clustering analysis, which indicated three major genetic groups among the four sampled regions. Overall, approximately 38% of isolates showed significant membership coefficients not related to their original geographical populations (i.e., migrants), characterizing a significant degree of genotype flow among populations. To determine whether admixture occurred between isolates infecting citrus and coffee plants, one site with citrus and coffee orchards adjacent to each other was selected; over 100 isolates were typed from each host plant. No signal of natural admixture between citrus- and coffee-infecting isolates was found; artificial cross-infection assays with representative isolates also yielded no successful cross infection. A comparison determined that X. fastidiosa populations from coffee have higher genetic diversity and allelic richness compared with citrus. The results showed that coffee and citrus X. fastidiosa populations are effectively isolated from each other and, although coffee populations are spatially structured, migration has an important role in shaping diversity.
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Affiliation(s)
- Carolina S Francisco
- First author: Universidade Estadual Paulista (UNESP), Campus de Jaboticabal, Graduate Program in Genetics and Plant Breeding, São Paulo, Brazil; first and fourth authors: Centro APTA Citros Sylvio Moreira, Cordeiropolis, São Paulo, Brazil; second author: UNESP, Campus de Ilha Solteira, São Paulo, Brazil; third author: Department of Environmental Science, Policy and Management, University of California, Berkeley
| | - Paulo C Ceresini
- First author: Universidade Estadual Paulista (UNESP), Campus de Jaboticabal, Graduate Program in Genetics and Plant Breeding, São Paulo, Brazil; first and fourth authors: Centro APTA Citros Sylvio Moreira, Cordeiropolis, São Paulo, Brazil; second author: UNESP, Campus de Ilha Solteira, São Paulo, Brazil; third author: Department of Environmental Science, Policy and Management, University of California, Berkeley
| | - Rodrigo P P Almeida
- First author: Universidade Estadual Paulista (UNESP), Campus de Jaboticabal, Graduate Program in Genetics and Plant Breeding, São Paulo, Brazil; first and fourth authors: Centro APTA Citros Sylvio Moreira, Cordeiropolis, São Paulo, Brazil; second author: UNESP, Campus de Ilha Solteira, São Paulo, Brazil; third author: Department of Environmental Science, Policy and Management, University of California, Berkeley
| | - Helvécio D Coletta-Filho
- First author: Universidade Estadual Paulista (UNESP), Campus de Jaboticabal, Graduate Program in Genetics and Plant Breeding, São Paulo, Brazil; first and fourth authors: Centro APTA Citros Sylvio Moreira, Cordeiropolis, São Paulo, Brazil; second author: UNESP, Campus de Ilha Solteira, São Paulo, Brazil; third author: Department of Environmental Science, Policy and Management, University of California, Berkeley
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Opportunistic fungal pathogen Candida glabrata circulates between humans and yellow-legged gulls. Sci Rep 2016; 6:36157. [PMID: 27782182 PMCID: PMC5080578 DOI: 10.1038/srep36157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022] Open
Abstract
The opportunistic pathogenic yeast Candida glabrata is a component of the mycobiota of both humans and yellow-legged gulls that is prone to develop fluconazole resistance. Whether gulls are a reservoir of the yeast and facilitate the dissemination of human C. glabrata strains remains an open question. In this study, MLVA genotyping highlighted the lack of genetic structure of 190 C. glabrata strains isolated from either patients in three hospitals or fecal samples collected from gull breeding colonies located in five distinct areas along the French Mediterranean littoral. Fluconazole-resistant isolates were evenly distributed between both gull and human populations. These findings demonstrate that gulls are a reservoir of this species and facilitate the diffusion of C. glabrata and indirect transmission to human or animal hosts via environmental contamination. This eco-epidemiological view, which can be applied to other vertebrate host species, broadens our perspective regarding the reservoirs and dissemination patterns of antifungal-resistant human pathogenic yeast.
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Lin H, Islam MS, Cabrera-La Rosa JC, Civerolo EL, Groves RL. Population Structure of Xylella fastidiosa Associated with Almond Leaf Scorch Disease in the San Joaquin Valley of California. PHYTOPATHOLOGY 2015; 105:825-32. [PMID: 25807309 DOI: 10.1094/phyto-09-14-0254-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Xylella fastidiosa causes disease in many commercial crops, including almond leaf scorch (ALS) disease in susceptible almond (Prunus dulcis). In this study, genetic diversity and population structure of X. fastidiosa associated with ALS disease were evaluated. Isolates obtained from two almond orchards in Fresno and Kern County in the San Joaquin Valley of California were analyzed for two successive years. Multilocus simple-sequence repeat (SSR) analysis revealed two major genetic clusters that were associated with two host cultivars, 'Sonora' and 'Nonpareil', respectively, regardless of the year of study or location of the orchard. These relationships suggest that host cultivar selection and adaptation are major driving forces shaping ALS X. fastidiosa population structure in the San Joaquin Valley. This finding will provide insight into understanding pathogen adaptation and host selection in the context of ALS disease dynamics.
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Affiliation(s)
- Hong Lin
- First, second, and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; second author: Department of Viticulture and Enology, University of California, Davis 95616; third author: Universidad Privada Antenor Orrego, Trujillo, Perú; and fifth author: Department of Entomology, University of Wisconsin, Madison 53706
| | - Md Sajedul Islam
- First, second, and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; second author: Department of Viticulture and Enology, University of California, Davis 95616; third author: Universidad Privada Antenor Orrego, Trujillo, Perú; and fifth author: Department of Entomology, University of Wisconsin, Madison 53706
| | - Juan C Cabrera-La Rosa
- First, second, and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; second author: Department of Viticulture and Enology, University of California, Davis 95616; third author: Universidad Privada Antenor Orrego, Trujillo, Perú; and fifth author: Department of Entomology, University of Wisconsin, Madison 53706
| | - Edwin L Civerolo
- First, second, and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; second author: Department of Viticulture and Enology, University of California, Davis 95616; third author: Universidad Privada Antenor Orrego, Trujillo, Perú; and fifth author: Department of Entomology, University of Wisconsin, Madison 53706
| | - Russell L Groves
- First, second, and fourth authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; second author: Department of Viticulture and Enology, University of California, Davis 95616; third author: Universidad Privada Antenor Orrego, Trujillo, Perú; and fifth author: Department of Entomology, University of Wisconsin, Madison 53706
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Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi. Trends Genet 2015; 31:201-7. [PMID: 25765920 DOI: 10.1016/j.tig.2015.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/22/2022]
Abstract
Population genomic studies have the potential to address many unresolved questions about microbial pathogens by facilitating the identification of genes underlying ecologically important traits, such as novel virulence factors and adaptations to humans or other host species. Additionally, this framework improves estimations of population demography and evolutionary history to accurately reconstruct recent epidemics and identify the molecular and environmental factors that resulted in the outbreak. The Lyme disease bacterium, Borrelia burgdorferi, exemplifies the power and promise of the application of population genomics to microbial pathogens. We discuss here the future of evolutionary studies in B. burgdorferi, focusing on the primary evolutionary forces of horizontal gene transfer, natural selection, and migration, as investigations transition from analyses of single genes to genomes.
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Tsui CKM, Farfan L, Roe AD, Rice AV, Cooke JEK, El-Kassaby YA, Hamelin RC. Population structure of mountain pine beetle symbiont Leptographium longiclavatum and the implication on the multipartite beetle-fungi relationships. PLoS One 2014; 9:e105455. [PMID: 25153489 PMCID: PMC4143264 DOI: 10.1371/journal.pone.0105455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/24/2014] [Indexed: 12/26/2022] Open
Abstract
Over 18 million ha of forests have been destroyed in the past decade in Canada by the mountain pine beetle (MPB) and its fungal symbionts. Understanding their population dynamics is critical to improving modeling of beetle epidemics and providing potential clues to predict population expansion. Leptographium longiclavatum and Grosmannia clavigera are fungal symbionts of MPB that aid the beetle to colonize and kill their pine hosts. We investigated the genetic structure and demographic expansion of L. longiclavatum in populations established within the historic distribution range and in the newly colonized regions. We identified three genetic clusters/populations that coincide with independent geographic locations. The genetic profiles of the recently established populations in northern British Columbia (BC) and Alberta suggest that they originated from central and southern BC. Approximate Bayesian Computation supports the scenario that this recent expansion represents an admixture of individuals originating from BC and the Rocky Mountains. Highly significant correlations were found among genetic distance matrices of L. longiclavatum, G. clavigera, and MPB. This highlights the concordance of demographic processes in these interacting organisms sharing a highly specialized niche and supports the hypothesis of long-term multipartite beetle-fungus co-evolutionary history and mutualistic relationships.
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Affiliation(s)
- Clement Kin-Ming Tsui
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lina Farfan
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amanda D. Roe
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Adrianne V. Rice
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Janice E. K. Cooke
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Natural Resources Canada, Canadian Forest Services, Laurentian Forestry Centre, Québec City, Québec, Canada
- * E-mail:
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Coletta-Filho HD, Francisco CS, Almeida RPP. Temporal and spatial scaling of the genetic structure of a vector-borne plant pathogen. PHYTOPATHOLOGY 2014; 104:120-5. [PMID: 24397266 DOI: 10.1094/phyto-06-13-0154-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ecology of plant pathogens of perennial crops is affected by the long-lived nature of their immobile hosts. In addition, changes to the genetic structure of pathogen populations may affect disease epidemiology and management practices; examples include local adaptation of more fit genotypes or introduction of novel genotypes from geographically distant areas via human movement of infected plant material or insect vectors. We studied the genetic structure of Xylella fastidiosa populations causing disease in sweet orange plants in Brazil at multiple scales using fast-evolving molecular markers (simple-sequence DNA repeats). Results show that populations of X. fastidiosa were regionally isolated, and that isolation was maintained for populations analyzed a decade apart from each other. However, despite such geographic isolation, local populations present in year 2000 were largely replaced by novel genotypes in 2009 but not as a result of migration. At a smaller spatial scale (individual trees), results suggest that isolates within plants originated from a shared common ancestor. In summary, new insights on the ecology of this economically important plant pathogen were obtained by sampling populations at different spatial scales and two different time points.
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Sisterson MS, Stenger DC. Roguing with replacement in perennial crops: conditions for successful disease management. PHYTOPATHOLOGY 2013; 103:117-128. [PMID: 23075167 DOI: 10.1094/phyto-05-12-0101-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Replacement of diseased plants with healthy plants is commonly used to manage spread of plant pathogens in perennial cropping systems. This strategy has two potential benefits. First, removing infected plants may slow pathogen spread by eliminating inoculum sources. Second, replacing infected plants with uninfected plants may offset yield losses due to disease. The extent to which these benefits are realized depends on multiple factors. In this study, sensitivity analyses of two spatially explicit simulation models were used to evaluate how assumptions concerning implementation of a plant replacement program and pathogen spread interact to affect disease suppression. In conjunction, effects of assumptions concerning yield loss associated with disease and rates of plant maturity on yields were simultaneously evaluated. The first model was used to evaluate effects of plant replacement on pathogen spread and yield on a single farm, consisting of a perennial crop monoculture. The second model evaluated effects of plant replacement on pathogen spread and yield in a 100 farm crop growing region, with all farms maintaining a monoculture of the same perennial crop. Results indicated that efficient replacement of infected plants combined with a high degree of compliance among farms effectively slowed pathogen spread, resulting in replacement of few plants and high yields. In contrast, inefficient replacement of infected plants or limited compliance among farms failed to slow pathogen spread, resulting in replacement of large numbers of plants (on farms practicing replacement) with little yield benefit. Replacement of infected plants always increased yields relative to simulations without plant replacement provided that infected plants produced no useable yield. However, if infected plants produced useable yields, inefficient removal of infected plants resulted in lower yields relative to simulations without plant replacement for perennial crops with long maturation periods in some cases.
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Affiliation(s)
- Mark S Sisterson
- United States Department of Agriculture- Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA.
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Zhao S, Poulin L, Rodriguez-R LM, Serna NF, Liu SY, Wonni I, Szurek B, Verdier V, Leach JE, He YQ, Feng JX, Koebnik R. Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola. PHYTOPATHOLOGY 2012; 102:948-56. [PMID: 22957820 DOI: 10.1094/phyto-04-12-0078-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Xanthomonas oryzae pv. oryzicola is an important bacterial pathogen responsible for outbreaks of bacterial leaf streak (BLS) on rice, mostly occurring in Asia and parts of Africa. To better monitor epidemics and assess population structures, efficient tools that allow the precise identification and diagnosis of pathogenic populations are needed. In this study, we explored variable numbers of tandem repeats (VNTR) as a fast, reliable, and cost-effective molecular typing tool. Screening of three X. oryzae pv. oryzicola genome sequences (Philippine strain BLS256, Chinese strain GX01, and Malian strain MAI10) predicted 28 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 28 loci were designed and applied to a panel of 20 X. oryzae pv. oryzicola strains originating from Asia and Africa. Sequencing of PCR amplicons revealed 25 robust and polymorphic VNTR loci that are shared among Asian and African X. oryzae pv. oryzicola strains. A dendrogram constructed from 25 VNTR loci indicated that most Asian strains are clearly discriminated from African strains. However, in agreement with previous reports, one strain from Mali is related to Asian strains, pointing to a possible introduction of Asian strains to the African continent. The new VNTR-based tool described here is useful for studies of population structures and epidemiological monitoring of X. oryzae pv. oryzicola.
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Affiliation(s)
- Shuai Zhao
- Institut de Recherche pour le Developpement, Montpellier, France
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Lindeberg M. Genome-enabled perspectives on the composition, evolution, and expression of virulence determinants in bacterial plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:111-132. [PMID: 22559066 DOI: 10.1146/annurev-phyto-081211-173022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genome sequence analyses of bacterial plant pathogens are revealing important insights into the molecular determinants of pathogenicity and, through transcript characterization, responses to environmental conditions, evidence for small RNAs, and validation of uncharacterized genes. Genome comparison sheds further light on the processes impacting pathogen evolution and differences in gene repertoire among isolates contributing to niche specialization. Information derived from pathogen genome analysis is providing tools for use in diagnosis and interference with host-pathogen interactions for the purpose of disease control. However, the existing information infrastructure fails to adequately integrate the increasing numbers of sequence data sets, bioinformatic analyses, and experimental characterization, as required for effective systems-level analysis. Enhanced standardization of data formats at the point of publication is proposed as a possible solution.
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Affiliation(s)
- Magdalen Lindeberg
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, USA.
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Islam MS, Glynn JM, Bai Y, Duan YP, Coletta-Filho HD, Kuruba G, Civerolo EL, Lin H. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide. BMC Microbiol 2012; 12:39. [PMID: 22433492 PMCID: PMC3368738 DOI: 10.1186/1471-2180-12-39] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 03/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. RESULTS A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. CONCLUSIONS Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources of the dominant 'Ca. L. asiaticus' in Florida were not clearly understood, the less-pervasive groups may have been introduced directly from Asia or via Brazil. Notably, the recent outbreak of HLB in Florida probably occurred through multiple introductions. Microsatellite markers developed in this study provide adequate discriminatory power for the identification and differentiation of closely-related isolates, as well as for genetic studies of 'Ca. L. asiaticus'.
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Affiliation(s)
- Md-Sajedul Islam
- USDA-ARS San Joaquin Valley Agricultural Research Science Center, Parlier, CA 93648, USA
| | - Jonathan M Glynn
- USDA-ARS San Joaquin Valley Agricultural Research Science Center, Parlier, CA 93648, USA
| | - Yang Bai
- Guangxi Citrus Research Institute, Gulin, Guangxi 530004, China
| | - Yong-Ping Duan
- USDA-ARS Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | | | - Gopal Kuruba
- Citrus Research Station, Andhra Pradesh Horticultural University, Tirupati 517502, Andhra Pradesh, India
| | - Edwin L Civerolo
- USDA-ARS San Joaquin Valley Agricultural Research Science Center, Parlier, CA 93648, USA
| | - Hong Lin
- USDA-ARS San Joaquin Valley Agricultural Research Science Center, Parlier, CA 93648, USA
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Parker JK, Havird JC, De La Fuente L. Differentiation of Xylella fastidiosa strains via multilocus sequence analysis of environmentally mediated genes (MLSA-E). Appl Environ Microbiol 2012; 78:1385-96. [PMID: 22194287 PMCID: PMC3294468 DOI: 10.1128/aem.06679-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/13/2011] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- Jennifer K. Parker
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Justin C. Havird
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
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