Publications (17)49.11 Total impact
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Article: Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives.
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ABSTRACT: To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.PLoS ONE 01/2012; 7(5):e37003. · 4.09 Impact Factor -
Article: Development of an assay for rapid detection and quantification of Verticillium dahliae in soil.
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ABSTRACT: ABSTRACT Verticillium dahliae is responsible for Verticillium wilt on a wide range of hosts, including strawberry, on which low soil inoculum densities can cause significant crop loss. Determination of inoculum density is currently done by soil plating but this can take 6 to 8 weeks to complete and delay the grower's ability to make planting decisions. To provide a faster means for estimating pathogen populations in the soil, a multiplexed TaqMan real-time polymerase chain reaction (PCR) assay based on the ribosomal DNA (rDNA) intergenic spacer (IGS) was developed for V. dahliae. The assay was specific for V. dahliae and included an internal control for evaluation of inhibition due to the presence of PCR inhibitors in DNA extracted from soil samples. An excellent correlation was observed in regression analysis (R(2) = 0.96) between real-time PCR results and inoculum densities determined by soil plating in a range of field soils with pathogen densities as low as 1 to 2 microsclerotia/g of soil. Variation in copy number of the rDNA was also evaluated among isolates by SYBR Green real-time PCR amplification of the V. dahliae-specific amplicon compared with amplification of several single-copy genes and was estimated to range from ≈24 to 73 copies per haploid genome, which translated into possible differences in results among isolates of ≈1.8 cycle thresholds. Analysis of the variation in results of V. dahliae quantification among extractions of the same soil sample indicated that assaying four replicate DNA extractions for each field sample would provide accurate results. A TaqMan assay also was developed to help identify colonies of V. tricorpus on soil plates.Phytopathology 11/2011; 102(3):331-43. · 2.80 Impact Factor -
Article: Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi.
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ABSTRACT: Although Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments, and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination, the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species, seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates with A1 and A2 mating type. Three of the regions were primarily intergenic regions between trnG and rns, rns and nad3, and nad6 and cox1, while the remaining loci spanned cox2, nad9, rps10, and secY coding regions and some of the flanking spacer regions. In total, 45 mitochondrial haplotypes were identified (75% of the total isolates examined) with differences due to single-nucleotide polymorphisms (SNPs, totaling 152 bp) and length mutations (17 indels >2 bp representing a total of 910 bp in length). SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions, while both SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition or loss of unique sequences while others were due to variable numbers of subrepeats (in the trnG-rns region, there were 3 to 12 copies of a 24-bp subrepeat sequence that differentiated 17 haplotypes). Network analysis of the haplotypes identified eight primary clades, with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. The isolate grouping in the network corresponded to mating type and previously published isozyme classifications, with three exceptions: a haplotype representing an A1 mating type (H29) was placed well within the A2 mating type haplotype grouping, one haplotype (H26) had isolates with two isozyme classifications, and one isozyme group was represented on separate network clades, suggesting that recombination has occurred in the past. Among the 62 isolates examined, several examples were identified of isolates recovered from different geographic regions having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the data set to determine whether fewer loci could be sequenced to classify haplotypes indicated that the trnG-rns and rns-nad6 loci would classify 87% of the haplotypes identified in this study, while additional sequencing of the nad9 or secY loci would further differentiate the remaining six haplotypes. Based on conservation of gene order in Phytophthora spp., the trnG-rns locus should be useful for mitochondrial haplotype classification in other species, as should the cox2, nad9, rps10, and secY loci. However, the rns-nad3 and nad6-cox1 loci span regions that can have a different gene order in some Phytophthora spp.Phytopathology 11/2011; 102(2):229-39. · 2.80 Impact Factor -
Article: Mitochondrial haplotype analysis as a tool for differentiating isolates of Verticillium dahliae.
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ABSTRACT: The ability to monitor mitochondrial background in Verticillium dahliae may provide an additional tool for population studies and monitoring clonal populations. Published mitochondrial genome sequences of V. dahliae (DQ351941) were used to design primers for amplification of spacer regions for assessment of mitochondrial haplotype differences among isolates. Five regions were examined (5,229 bp, or 19% of the total genome size) for 30 isolates representing a range in vegetative compatibility group (VCG), host, and geographic origin. Observed differences among isolates were due to single nucleotide polymorphisms, different numbers of bases in specific homopolymeric regions, and copies of subrepeated sequences. When the differences observed for each locus were totaled there were 28 total groupings; when the results of each locus for individual isolates were combined there were 15 mitochondrial haplotypes. Some of the observed groupings correlated with VCG. For example, five VCG-1A and VCG-1B isolates from California, Spain, and Greece had identical haplotypes; however, this was not observed for VCG-2 or VCG-4 isolates. While some VCG-2 isolates also were identical and fell into a single haplotype, five haplotypes were found for this group (five other haplotypes were observed for other isolates that had not been characterized to VCG but grouped with VCG-2 isolates in the phylogenetic analysis). Likewise, five VCG-4 isolates fell into four mitochondrial haplotypes, one of which was identical to the largest VCG-2 grouping. A heterokaryon self-incompatible isolate that was reported in the literature to cluster with VCG-2 isolates by amplified fragment length polymorphism analysis was identical with VCG-1 isolates for four of the five loci, but was intermediate between VCG-1 and VCG-2 in the haplotype analysis. Phylogenetic analysis with these regions revealed the mitochondrial background of VCG-1 and VCG2-B to be monophyletic but VCG-2A and VCG-4 could not be separated. The results obtained indicate that there is variation in mitochondrial haplotypes and this type of analysis may be a useful for characterization of isolates. While data from all five regions was used for the haplotype separation in this study, depending on the VCG or the level of variability observed within a population it is possible to use fewer loci.Phytopathology 11/2010; 100(11):1231-9. · 2.80 Impact Factor -
Article: The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes.
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ABSTRACT: Sequences of selected marker loci have been widely used for the identification of specific pathogens and the development of sequence-based diagnostic methods. Although such approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own pitfalls. These include erroneous and incomplete data in reference databases, poor or oversimplified interpretation of search results, and problems associated with defining species boundaries. In this letter, we outline the potential benefits and drawbacks of using sequence data for identification and taxonomic deduction of plant-pathogenic fungi and oomycetes, using phytophthora as a primary example. We also discuss potential remedies for these pitfalls and address why coordinated community efforts are essential to make such remedies more efficient and robust.Phytopathology 08/2010; 100(8):732-7. · 2.80 Impact Factor -
Article: Standardizing the nomenclature for clonal lineages of the sudden oak death pathogen, Phytophthora ramorum.
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ABSTRACT: Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages. Here we propose a system for naming clonal lineages of P. ramorum based on a consensus established by the P. ramorum research community. Clonal lineages are named with a two letter identifier for the continent on which they were first found (e.g., NA = North America; EU = Europe) followed by a number indicating order of appearance. Clonal lineages known to date are designated NA1 (mating type: A2; distribution: North America; environment: forest and nurseries), NA2 (A2; North America; nurseries), and EU1 (predominantly A1, rarely A2; Europe and North America; nurseries and gardens). It is expected that novel lineages or new variants within the existing three clonal lineages could in time emerge.Phytopathology 08/2009; 99(7):792-5. · 2.80 Impact Factor -
Article: Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum.
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ABSTRACT: The mitochondrial genome of an isolate of Phytophthora ramorum from Europe (EU) was sequenced and compared to the previously published genome sequence of an isolate from California (NA). The EU mitochondrial genome had the identical gene order and encoded for the same suite of genes as the NA mitochondrial genome, but had 13 single nucleotide polymorphisms (SNPs) and at 39,494 bp was 180 bp longer. This length difference was due to an increase in the size of the spacer region between the nad5 and nad6 genes caused by a chimeric region containing duplication of the spacer sequence and additional sequences from the flanking genes. Recombination between the 1,150 bp-inverted repeats (IR) generated orientational isomers where the gene order was reversed between the IR. A total of seven primer pairs were developed for amplification of regions where the SNPs were located and two other regions where additional SNPs were encountered when a larger number of isolates were examined. Sequence data for a total of 5,743 bp for 40 isolates collected from a range of geographic areas was compared and 28 loci were found to be polymorphic. The combination of these polymorphisms revealed a total of 4 mitochondrial haplotypes; the traditional EU (haplotype I), the traditional NA (haplotype IIa), the third nuclear lineage of the pathogen recovered from a nursery in Washington State (haplotype III) and a new haplotype representing a subgroup of NA isolates from an Oregon forest (haplotype IIb). Phylogenetic analysis using the sequences generated from the haplotype analysis supported a high affinity for haplotypes IIa and IIb, both of which were distinct from haplotype I, with haplotype I basal to these and haplotype III representing the ancestral state.Current Genetics 08/2008; 54(1):23-34. · 2.56 Impact Factor -
Article: Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae.
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ABSTRACT: The sequences of the mitochondrial genomes of the oomycetes Phytophthora ramorum and P. sojae were determined during the course of complete nuclear genome sequencing (Tyler et al., Science, 313:1261,2006). Both mitochondrial genomes are circular mapping, with sizes of 39,314 bp for P. ramorum and 42,977 bp for P. sojae. Each contains a total of 37 recognizable protein-encoding genes, 26 or 25 tRNAs (P. ramorum and P. sojae, respectively) specifying 19 amino acids, six more open reading frames (ORFs) that are conserved, presumably due to functional constraint, across Phytophthora species (P. sojae, P. ramorum, and P. infestans), six ORFs that are unique for P. sojae and one that is unique for P. ramorum. Non-coding regions comprise about 11.5 and 18.4% of the genomes of P. ramorum and P. sojae, respectively. Relative to P. sojae, there is an inverted repeat of 1,150 bp in P. ramorum that includes an unassigned unique ORF, a tRNA gene, and adjacent non-coding sequences, but otherwise the gene order in both species is identical. Comparisons of these genomes with published sequences of the P. infestans mitochondrial genome reveals a number of similarities, but the gene order in P. infestans differed in two adjacent locations due to inversions and specific regions of the genomes exhibited greater divergence than others. For example, the breakpoints for the inversions observed in P. infestans corresponded to regions of high sequence divergence in comparisons between P. ramorum and P. sojae and the location of a hypervariable microsatellite sequence (eight repeats of 24 bp) in the P. sojae genome corresponds to a site of major length variation in P. infestans. Although the overwhelming majority of each genome is conserved (81-92%), there are a number of genes that evolve more rapidly than others. Some of these rapidly evolving genes appear specific to Phytophthora, arose recently, and future evaluation of their function and the effects of their loss could prove fruitful for understanding the phylogeny of these devastating plant pathogens.Current Genetics 06/2007; 51(5):285-96. · 2.56 Impact Factor -
Article: Real-Time Fluorescent Polymerase Chain Reaction Detection of Phytophthora ramorum and Phytophthora pseudosyringae Using Mitochondrial Gene Regions.
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ABSTRACT: ABSTRACT A real-time fluorescent polymerase chain reaction (PCR) detection method for the sudden oak death pathogen Phytophthora ramorum was developed based on mitochondrial DNA sequence with an ABI Prism 7700 (TaqMan) Sequence Detection System. Primers and probes were also developed for detecting P. pseudosyringae, a newly described species that causes symptoms similar to P. ramorum on certain hosts. The species-specific primer-probe systems were combined in a multiplex assay with a plant primer-probe system to allow plant DNA present in extracted samples to serve as a positive control in each reaction. The lower limit of detection of P. ramorum DNA was 1 fg of genomic DNA, lower than for many other described PCR procedures for detecting Phytophthora species. The assay was also used in a three-way multiplex format to simultaneously detect P. ramorum, P. pseudosyringae, and plant DNA in a single tube. P. ramorum was detected down to a 10(-5) dilution of extracted tissue of artificially infected rhododendron 'Cunningham's White', and the amount of pathogen DNA present in the infected tissue was estimated using a standard curve. The multiplex assay was also used to detect P. ramorum in infected California field samples from several hosts determined to contain the pathogen by other methods. The real-time PCR assay we describe is highly sensitive and specific, and has several advantages over conventional PCR assays used for P. ramorum detection to confirm positive P. ramorum finds in nurseries and elsewhere.Phytopathology 05/2006; 96(4):336-45. · 2.80 Impact Factor -
Article: Identification of phytophthora isolates to species level using restriction fragment length polymorphism analysis of a polymerase chain reaction-amplified region of mitochondrial DNA.
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ABSTRACT: ABSTRACT Polymerase chain reaction primers spanning the mitochondrially encoded coxI and II genes have been identified that were capable of amplifying target DNA from all 152 isolates of 31 species in the genus Phytophthora that were tested. Digestion of the amplicons with restriction enzymes generated species-specific restriction fragment length polymorphism banding profiles that were effective for isolate classification to a species level. Of the 24 species in which multiple isolates were examined, intraspecific polymorphisms were not observed for 16 species, while 5 species exhibited limited intraspecific polymorphism that could be explained by the addition/loss of a single restriction site. Intraspecific polymorphisms were observed for P. megakarya, P. megasperma, and P. syringae; however, these differences may be a reflection of the variation that exists in these species as reported in the literature. Although digestion with AluI alone could differentiate most species tested, single digests with a total of four restriction enzymes were used in this investigation to enhance the accuracy of the technique and minimize the effect of intraspecific variability on correct isolate identification. The use of the computer program BioNumerics simplified data analysis and identification of isolates. Successful template amplification was obtained with DNA recovered from hyphae using a boiling miniprep procedure, thereby reducing the time and materials needed for conducting this analysis.Phytopathology 10/2004; 94(9):983-91. · 2.80 Impact Factor -
Article: Molecular Detection of Phytophthora ramorum, the Causal Agent of Sudden Oak Death in California, and Two Additional Species Commonly Recovered from Diseased Plant Material.
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ABSTRACT: ABSTRACT Sudden oak death is a disease currently devastating forest ecosystems in several coastal areas of California. The pathogen causing this is Phy-tophthora ramorum, although species such as P. nemorosa and P. pseudo-syringae often are recovered from symptomatic plants as well. A molecular marker system was developed based on mitochondrial sequences of the cox I and II genes for detection of Phytophthora spp. in general, and P. ramorum, P. nemorosa, and P. pseudosyringae in particular. The first-round multiplex amplification contained two primer pairs, one for amplification of plant sequences to serve as an internal control to ensure that extracted DNA was of sufficient quality to allow for polymerase chain reaction (PCR) amplification and the other specific for amplification of sequences from Phytophthora spp. The plant primers amplified the desired amplicon size in the 29 plant species tested and did not interfere with amplification by the Phytophthora genus-specific primer pair. Using DNA from purified cultures, the Phytophthora genus-specific primer pair amplified a fragment diagnostic for the genus from all 45 Phytophthora spp. evaluated, although the efficiency of amplification was lower for P. lateralis and P. sojae than for the other species. The genus-specific primer pair did not amplify sequences from the 30 Pythium spp. tested or from 29 plant species, although occasional faint bands were observed for several additional plant species. With the exception of one plant species, the resulting amplicons were smaller than the Phytophthora genus-specific amplicon. The products of the first-round amplification were diluted and amplified with primer pairs nested within the genus-specific amplicon that were specific for either P. ramorum, P. nemorosa, or P. pseudo-syringae. These species-specific primers amplified the target sequence from all isolates of the pathogens under evaluation; for P. ramorum, this included 24 isolates from California, Germany, and the Netherlands. Using purified pathogen DNA, the limit of detection for P. ramorum using this marker system was approximately 2.0 fg of total DNA. However, when this DNA was spiked with DNA from healthy plant tissue extracted with a commercial miniprep procedure, the sensitivity of detection was reduced by 100- to 1,000-fold, depending on the plant species. This marker system was validated with DNA extracted from naturally infected plant samples collected from the field by comparing the sequence of the Phytophthora genus-specific amplicon, morphological identification of cultures recovered from the same lesions and, for P. ramorum, amplification with a previously published rDNA internal transcribed spacer species-specific primer pair. Results were compared and validated with three different brands of thermal cyclers in two different laboratories to provide information about how the described PCR assay performs under different laboratory conditions. The specificity of the Phytophthora genus-specific primers suggests that they will have utility for pathogen detection in other Phytophthora pathosystems.Phytopathology 07/2004; 94(6):621-31. · 2.80 Impact Factor -
Article: Phylogenetic relationships of Phytophthora ramorum, P. nemorosa, and P. pseudosyringae, three species recovered from areas in California with sudden oak death.
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ABSTRACT: Sudden oak death has been an emerging disease problem in coastal California and has caused significant losses in forest ecosystems in some regions of the state. The causal agent of this disease has been described as Phytophthora ramorum with two other less aggressive species, P. nemorosa and P. pseudosyringae, recovered from some symptomatic plants. The phylogenetic relationship of these species with other members of the genus was examined by sequence alignment of 667 bp of the mitochondrially-encoded cytochrome oxidase II gene and the nuclear encoded rDNA internal transcribed spacer region. P. ramorum was most closely related to P. hibernalis and P. lateralis in trees from both regions, although the specific relationship among species differed depending on the tree. In the cox II tree these species were on a single clade with P. lateralis basal to a group containing P. ramorum and P. hibernalis. On the maximum parsimony ITS tree P. ramorum was most closely affiliated with P. lateralis and in the same clade as P. hibernalis, but with maximum likelihood analysis P. ramorum was basal to a grouping of P. hibernalis and P. lateralis. While bootstrap support was strong for the grouping of these species together, it was not for determining the relationship among them. In contrast to the cox II tree, the clade containing these three species grouped with P. cryptogea, P. drechsleri, P. erythroseptica, and P. syringae in the ITS tree. Since the same isolates of these species were used for both the cox II and ITS sequence analysis, this difference in species grouping suggests either a differential rate of evolutionary divergence for these two regions, incorrect assumptions about alignment of ITS sequences, or different evolutionary histories of the regions under study. Analysis of combined cox II and ITS data sets gave trees where the relationships among these species were the same as for the ITS tree alone, although the results of the partition homogeneity test (P=0.072) suggest caution should be used in interpretation of this data. All analyses supported a close relationship between P. ilicis, P. nemorosa and P. pseudosyringae, although the analysis did not clarify the evolutionary relationships among these three species. Interestingly, these three species had a unique 6 bp deletion in the cox II gene just before the termination codon. While there was some similarity in phylogenetic grouping of these species and morphological characteristics, this was not consistent across all comparisons in the genus. Data would suggest that P. ramorum, P. nemorosa and P. pseudosyringae are phylogenetically distinct new species and not the result of interspecific hybridization.Mycological Research 01/2004; 107(Pt 12):1379-91. · 2.81 Impact Factor -
Article: Development of alternative strategies for management of soilborne pathogens currently controlled with methyl bromide.
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ABSTRACT: The current standard treatment for management of soilborne pests in some high-value crop production systems is preplant fumigation with mixtures of methyl bromide and chloropicrin. With the impending phase-out of methyl bromide, the agricultural industries that rely on soil fumigation face the need for development of alternative pest management strategies. To maintain farm productivity, immediate term research has focused on evaluation of alternative fumigants, modification of current crop production practices to accommodate their use, and improvement of application technologies to reduce the environmental effects of fumigant applications. Longer-term research goals have focused on developing a more integrated approach for pest management that incorporates the use of cultural practices to reduce pathogen pressure, host resistance to disease, and biological approaches for stimulating plant growth and control of root diseases.Annual Review of Phytopathology 02/2003; 41:325-50. · 9.88 Impact Factor -
Article: The internet-based fungal pathogen database: a proposed model.
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ABSTRACT: ABSTRACT A better understanding of the phenotypic and genetic diversity of significant agricultural pathogens and how their populations change in the field is critical for designing successful, long-term disease management strategies. Although efforts to determine the genetic diversity of plant pathogens have substantially increased in recent years, mainly due to the availability of various molecular tools, complementary efforts to archive and integrate the resulting data have been very limited. As a consequence, it is often difficult to compare the available data from various laboratories because the data have been generated by diverse tools, often preventing any direct comparisons, and are saved in a format that is unsuitable for comparative studies. The establishment of an internet-based database that cross-links the digitized genotypic and phenotypic information of individual pathogens at both the species and population levels may allow us to effectively address these problems by coordinating the generation of data and its subsequent archiving. We discuss the needs, benefits, and potential structure of such a database.Phytopathology 04/2002; 92(3):232-6. · 2.80 Impact Factor -
Article: Using sigmoidal curve-fitting in a real-time PCR detection assay to determine detection thresholds
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ABSTRACT: Phytophthora ramorum, the causal agent of sudden oak death (SOD) is a quarantine pathogen that has forced the implementation of extraordinary measures to track and contain the movement of infected nursery stock both within and outside of the three western states of California, Oregon and Washington. Federal guidelines in the United States for diagnostic testing of P. ramorum are in place to insure the sensitivity and reliability of detection tests. PCR assays are used to determine whether the Phytophthora sp. detected by the initial immunoassay screening is P. ramorum. Most of the time definitive results can be obtained from a single PCR reaction. However, there are times when the accuracy of the results can be called into question because of low pathogen titer, a situation that can result in false negatives given the limits of detection of the marker system. In addition, experimental samples often contain significant amounts of PCR inhibitors that can also give results outside the normal detection cutoffs. Therefore the need for re-testing the samples using the same or alternative methods of pathogen detection is manifest. To understand the effect of low DNA concentration, or the role of PCR inhibitors in the extracted DNA in the sensitivity of detection of P .ramorum, plant and pathogen specific markers were amplified in real time PCR experiments using TaqMan® chemistry. The kinetics of amplification of the PCR reactions were modeled using a four-parametric sigmoidal curve. Standard curves of pure P. ramorum DNA and plant host DNA, with standard amounts of P. ramorum DNA added, were created and used to establish a base for data analysis. Samples having low pathogen titer were amplified and the values of the sigmoid curve parameters described. Statistical analysis of data allowed the identification of samples falling outside the proposed 95 percent confidence interval. Curve modeling also provided experimental support for determining threshold values for assessing the presence of the pathogen.Oak Death Third Science Symposium. 04/2002; -
Article: Standardizing the Nomenclature for Clonal Lineages of the Sudden Oak Death Pathogen, Phytophthora ramorum.
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ABSTRACT: Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages. Here we propose a system for naming clonal lineages of P. ramorum based on a consensus established by the P. ramorum research community. Clonal lineages are named with a two letter identifier for the continent on which they were first found (e.g., NA = North America; EU = Europe) followed by a number indicating order of appearance. Clonal lineages known to date are designated NA1 (mating type: A2; distribution: North America; environment: forest and nurseries), NA2 (A2; North America; nurseries), and EU1 (predominantly A1, rarely A2; Europe and North America; nurseries and gardens). It is expected that novel lineages or new variants within the existing three clonal lineages could in time emerge. -
Article: Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes.
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ABSTRACT: The phylogenetic relationships of 51 isolates representing 27 species of Phytophthora were assessed by sequence alignment of 568 bp of the mitochondrially encoded cytochrome oxidase II gene. A total of 1299 bp of the cytochrome oxidase I gene also were examined for a subset of 13 species. The cox II gene trees constructed by a heuristic search, based on maximum parsimony for a bootstrap 50% majority-rule consensus tree, revealed 18 species grouping into seven clades and nine species unaffiliated with a specific clade. The phylogenetic relationships among species observed on cox II gene trees did not exhibit consistent similarities in groupings for morphology, pathogenicity, host range or temperature optima. The topology of cox I gene trees, constructed by a heuristic search based on maximum parsimony for a bootstrap 50% majority-rule consensus tree for 13 species of Phytophthora, revealed 10 species grouping into three clades and three species unaffiliated with a specific clade. The groupings in general agreed with what was observed in the cox II tree. Species relationships observed for the cox II gene tree were in agreement with those based on ITS regions, with several notable exceptions. Some of these differences were noted in species in which the same isolates were used for both ITS and cox II analysis, suggesting either a differential rate of evolutionary divergence for these two regions or incorrect assumptions about alignment of ITS sequences. Analysis of combined data sets of ITS and cox II sequences generated a tree that did not differ substantially from analysis of ITS data alone, however, the results of a partition homogeneity test suggest that combining data sets may not be valid.Mycologia 95(2):269-84. · 2.03 Impact Factor
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- Phytopathology (9)
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Institutions
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2012
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Franklin and Marshall College
Lancaster, PA, USA
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2003–2012
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United States Department of Agriculture
- Agricultural Research Service (ARS)
Fort Collins, CO, USA
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2011
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Agricultural Research Service
Washington, D. C., DC, USA
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