Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
|---|
| landscape epidemiology and control of pathogens with cryptic and long-distance dispersal: sudden oak death in northern californian forests. | exotic pathogens and pests threaten ecosystem service, biodiversity, and crop security globally. if an invasive agent can disperse asymptomatically over long distances, multiple spatial and temporal scales interplay, making identification of effective strategies to regulate, monitor, and control disease extremely difficult. the management of outbreaks is also challenged by limited data on the actual area infested and the dynamics of spatial spread, due to financial, technological, or social cons ... | 2012 | 22241973 |
| genome-wide identification of laccase gene family in three phytophthora species. | phytophthora spp. is a primary pathogen in oomycete, causing economically and environmentally devastating epidemics of plants. laccases have been found in all domains of life but have not been reported in oomycte. in this paper, laccase genes of phytophthora spp. were identified in three genomes (phytophthora capsici, phytophthora sojae and phytophthora ramorum). 18 laccase genes were identified in total, including four in p. capsici genome, six in p. sojae genome and eight in p. ramorum genome. ... | 2012 | 23283515 |
| identification of new polymorphic microsatellite markers in the na1 and na2 lineages of phytophthora ramorum. | phytophthora ramorum is a recently introduced pathogen in europe and north america consisting of three clonal lineages. due to the very limited intra-lineage genetic variation, only a few polymorphic markers are available for use in studies involving the epidemiology and evolution of p. ramorum. a total of 159 primer pairs for candidate polymorphic ssr loci were tested with universal labeling. four polymorphic microsatellite loci were identified within the na1 lineage and one within the na2 line ... | 2011 | 21642345 |
| forest species diversity reduces disease risk in a generalist plant pathogen invasion. | empirical evidence suggests that biodiversity loss can increase disease transmission, yet our understanding of the 'diversity-disease hypothesis' for generalist pathogens in natural ecosystems is limited. we used a landscape epidemiological approach to examine two scenarios regarding diversity effects on the emerging plant pathogen phytophthora ramorum across a broad, heterogeneous ecoregion: (1) an amplification effect exists where disease risk is greater in areas with higher plant diversity du ... | 2011 | 21884563 |
| the inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in phytophthora. | pathogens belonging to the oomycota, a group of heterokont, fungal-like organisms, are amongst the most notorious pathogens in agriculture. in particular, the obligate biotrophic downy mildews and the hemibiotrophic members of the genus phytophthora are responsible for a huge variety of destructive diseases, including sudden oak death caused by p. ramorum, potato late blight caused by p. infestans, cucurbit downy mildew caused by pseudoperonospora cubensis, and grape downy mildew caused by plasm ... | 2011 | 22679601 |
| predicting the economic costs and property value losses attributed to sudden oak death damage in california (2010-2020). | phytophthora ramorum, cause of sudden oak death, is a quarantined, non-native, invasive forest pathogen resulting in substantial mortality in coastal live oak (quercus agrifolia) and several other related tree species on the pacific coast of the united states. we estimate the discounted cost of oak treatment, removal, and replacement on developed land in california communities using simulations of p. ramorum spread and infection risk over the next decade (2010-2020). an estimated 734 thousand oa ... | 2011 | 21224033 |
| forest type influences transmission of phytophthora ramorum in california oak woodlands. | the transmission ecology of phytophthora ramorum from bay laurel (umbellularia californica) leaves was compared between mixed-evergreen and redwood forest types throughout winter and summer disease cycles in central, coastal california. in a preliminary multisite study, we found that abscission rates of infected leaves were higher at mixed-evergreen sites. in addition, final infection counts were slightly higher at mixed-evergreen sites or not significantly different than at redwood sites, in pa ... | 2011 | 21391827 |
| interacting disturbances: wildfire severity affected by stage of forest disease invasion. | sudden oak death (sod) is an emerging forest disease causing extensive tree mortality in coastal california forests. recent california wildfires provided an opportunity to test a major assumption underlying discussions of sod and land management: sod mortality will increase fire severity. we examined prefire fuels from host species in a forest monitoring plot network in big sur, california (usa), to understand the interactions between disease-caused mortality and wildfire severity during the 200 ... | 2011 | 21563563 |
| networks in plant epidemiology: from genes to landscapes, countries, and continents. | there is increasing use of networks in ecology and epidemiology, but still relatively little application in phytopathology. networks are sets of elements (nodes) connected in various ways by links (edges). network analysis aims to understand system dynamics and outcomes in relation to network characteristics. many existing natural, social, and technological networks have been shown to have small-world (local connectivity with short-cuts) and scale-free (presence of super-connected nodes) propert ... | 2011 | 21062110 |
| aberrant genome size and instability of phytophthora ramorum oospore progenies. | the functionality of the sexual cycle in the heterothallic pathogen phytophthora ramorum, causal agent of sudden oak death, has recently been demonstrated. sexual reproduction could create genotypic variation and increase the pathogen's ability to adapt to other host plants or changing environments. genetic characterization using co-dominant microsatellite markers and flow cytometry of single-oospore progeny of crosses between a european a1 isolate and north american or european a2 isolates reve ... | 2011 | 21272658 |
| genetic characterization of phytophthora nicotianae by the analysis of polymorphic regions of the mitochondrial dna. | a new method based on the analysis of mitochondrial intergenic regions characterized by intraspecific variation in dna sequences was developed and applied to the study of the plant pathogen phytophthora nicotianae. two regions flanked by genes trny and rns and trnw and cox2 were identified by comparing the whole mitochondrial genomes of phytophthora infestans, phytophthora ramorum, and phytophthora sojae and amplified using primers designed from the flanking conserved genes. these regions were s ... | 2011 | 21530925 |
| phytophthora ramorum in canada: evidence for migration within north america and from europe. | phytophthora ramorum, the cause of sudden oak death on oak and ramorum blight on woody ornamentals, has been reported in ornamental nurseries on the west coast of north america from british columbia to california. long-distance migration of p. ramorum has occurred via the nursery trade, and shipments of host plants are known to have crossed the u.s.-canadian border. we investigated the genotypic diversity of p. ramorum in canadian nurseries and compared the canadian population with u.s. and euro ... | 2011 | 20879846 |
| learning from history, predicting the future: the uk dutch elm disease outbreak in relation to contemporary tree disease threats. | expanding international trade and increased transportation are heavily implicated in the growing threat posed by invasive pathogens to biodiversity and landscapes. with trees and woodland in the uk now facing threats from a number of disease systems, this paper looks to historical experience with the dutch elm disease (ded) epidemic of the 1970s to see what can be learned about an outbreak and attempts to prevent, manage and control it. the paper draws on an interdisciplinary investigation into ... | 2011 | 21624917 |
| a test system to quantify inoculum in runoff from phytophthora ramorum-infected plant roots. | foliar hosts of phytophthora ramorum are often susceptible to root infection, but the epidemiological significance of such infections is unknown. a standardized test system was developed to quantify inoculum in runoff from root-infected viburnum tinus 'spring bouquet' or rhododendron 'cunningham's white' cuttings. cuttings of both species gave off a maximum amount of inoculum 1 to 3 weeks after inoculation. the greatest amount of inoculum was recovered from viburnum roots that were 48 to 70 days ... | 2011 | 21830955 |
| Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. | Horizontal gene transfer (HGT) can radically alter the genomes of microorganisms, providing the capacity to adapt to new lifestyles, environments, and hosts. However, the extent of HGT between eukaryotes is unclear. Using whole-genome, gene-by-gene phylogenetic analysis we demonstrate an extensive pattern of cross-kingdom HGT between fungi and oomycetes. Comparative genomics, including the de novo genome sequence of Hyphochytrium catenoides, a free-living sister of the oomycetes, shows that thes ... | 2011 | 21878562 |
| myosin diversity in the diatom phaeodactylum tricornutum. | this report describes the domain architecture of ten myosins cloned from the pennate diatom phaeodactylum tricornutum. several of the p. tricornutum myosins show similarity to myosins from the centric diatom thalassiosira pseudonana as well as to one myosin from the oomycete phytophthora ramorum. the p. tricornutum myosins, ranging in size from 126 kda to over 250 kda, all possess the canonical head, neck and tail domains common to most myosins, though variations in each of these domains is evid ... | 2010 | 20217677 |
| incidence of endornaviruses in phytophthora taxon douglasfir and phytophthora ramorum. | in this investigation, we show that four phytophthora taxon douglasfir isolates from the usa, irrespective of their geographical location or host plant, and 20% of a representative cohort of phytophthora ramorum isolates contain endornavirus dsrnas. three endornavirus-specific rt-pcr amplicons were generated by rt-pcr using dsrna isolated from the four phytophthora taxon douglasfir isolates and one representative phytophthora ramorum isolate as template with oligonucleotide primers designed from ... | 2010 | 19915969 |
| balancing detection and eradication for control of epidemics: sudden oak death in mixed-species stands. | culling of infected individuals is a widely used measure for the control of several plant and animal pathogens but culling first requires detection of often cryptically-infected hosts. in this paper, we address the problem of how to allocate resources between detection and culling when the budget for disease management is limited. the results are generic but we motivate the problem for the control of a botanical epidemic in a natural ecosystem: sudden oak death in mixed evergreen forests in coas ... | 2010 | 20856850 |
| optimization of control strategies for epidemics in heterogeneous populations with symmetric and asymmetric transmission. | there is growing interest in incorporating economic factors into epidemiological models in order to identify optimal strategies for disease control when resources are limited. in this paper we consider how to optimize the control of a pathogen that is capable of infecting multiple hosts with different rates of transmission within and between species. our objective is to find control strategies that maximize the discounted number of healthy individuals. we consider two classes of host-pathogen sy ... | 2010 | 19900466 |
| analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of phytophthora infestans. | phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. it exhibits high evolutionary potential and rapidly adapts to host plants. the p. infestans genome experienced a repeat-driven expansion relative to the genomes of phytophthora sojae and phytophthora ramorum and shows a discontinuous distribution of gene density. effector genes, such as members of the rxlr and crinkler (crn) families, localize to expanded, repeat-rich and gene-sparse regions ... | 2010 | 21080964 |
| apparent competition in canopy trees determined by pathogen transmission rather than susceptibility. | epidemiological theory predicts that asymmetric transmission, susceptibility, and mortality within a community will drive pathogen and disease dynamics. these epidemiological asymmetries can result in apparent competition, where a highly infectious host reduces the abundance of less infectious or more susceptible members in a community via a shared pathogen. we show that the exotic pathogen phytophthora ramorum and resulting disease, sudden oak death, cause apparent competition among canopy tree ... | 2010 | 20391996 |
| rapid detection of phytophthora ramorum and p. kernoviae by two-minute dna extraction followed by isothermal amplification and amplicon detection by generic lateral flow device. | abstract a method for nucleic-acid-based detection of pathogens in plant material has been developed which comprises a simple and rapid method for extracting dna on the nitrocellulose membranes of lateral-flow devices, loop-mediated isothermal amplification (lamp) of target dna using labeled primers, and detection of the generically labeled amplification products by a sandwich immunoassay in a lateral-flow-device format. each of these steps can be performed without specialist equipment and is su ... | 2010 | 20055648 |
| clonal expansion of the belgian phytophthora ramorum populations based on new microsatellite markers. | co-existence of both mating types a1 and a2 within the eu1 lineage of phytophthora ramorum has only been observed in belgium, which begs the question whether sexual reproduction is occurring. a collection of 411 belgian p. ramorum isolates was established during a 7-year survey. our main objectives were genetic characterization of this population to test for sexual reproduction, determination of population structure, evolution and spread, and evaluation of the effectiveness and impact of control ... | 2010 | 20002581 |
| oospores progenies from phytophthora ramorum. | oospores of phytophthora ramorum were produced from intraspecific pairings between a european a1 and european or american a2 strains. their viability was evaluated through colouration with tetrazolium bromide. the distribution of oospores in the different classes of colouration was similar to that found in other phytophthora species (homothallic and heterothallic): most of the oospores stained purple, which corresponds to spores in dormancy. in order to produce single-oospore cultures, a method ... | 2010 | 20943147 |
| lessons learned from a decade of sudden oak death in california: evaluating local management. | sudden oak death has been impacting california's coastal forests for more than a decade. in that time, and in the absence of a centrally organized and coordinated set of mandatory management actions for this disease in california's wildlands and open spaces, many local communities have initiated their own management programs. we present five case studies to explore how local-level management has attempted to control this disease. from these case studies, we glean three lessons: connections count ... | 2010 | 20559634 |
| a five-minute dna extraction method for expedited detection of phytophthora ramorum following prescreening using phytophthora spp. lateral flow devices. | in a direct comparison with established methods for phytophthora ramorum detection (isolation followed by morphological identification, or conventional dna extraction followed by taqman real-time pcr) a rapid, simplified detection method in which membranes of lateral flow devices (lfds) are added directly to taqman real-time pcr reactions was used to test 202 plant samples collected by plant health inspectors in the field. p. ramorum prevalence within the 202 samples was approximately 40% accord ... | 2010 | 20171248 |
| effects of an invasive forest pathogen on abundance of ticks and their vertebrate hosts in a california lyme disease focus. | invasive species, including pathogens, can have important effects on local ecosystems, including indirect consequences on native species. this study focuses on the effects of an invasive plant pathogen on a vertebrate community and ixodes pacificus, the vector of the lyme disease pathogen (borrelia burgdorferi) in california. phytophthora ramorum, the causative agent of sudden oak death, is a non-native pathogen killing trees in california and oregon. we conducted a multi-year study using a grad ... | 2010 | 20941513 |
| aflps detect low genetic diversity for phytophthora nemorosa and p. pseudosyringae in the us and europe. | in california and oregon, two recently described oomycete forest pathogens, phytophthora nemorosa and p. pseudosyringae, overlap in their host and geographic ranges with the virulent p. ramorum, causal agent of "sudden oak death." epidemiological observations, namely broader geographic distribution and lack of landscape-level mortality, led to the hypothesis they are native to this region, whereas multiple lines of evidence indicate p. ramorum is exotic to north america. we used aflp analysis to ... | 2009 | 19061958 |
| ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen phytophthora ramorum. | the genus phytophthora includes some of the most destructive plant pathogens affecting agricultural and native ecosystems and is responsible for a number of recent emerging and re-emerging infectious diseases of plants. sudden oak death, caused by the exotic pathogen p. ramorum, has caused extensive mortality of oaks and tanoaks in northern california, and has brought economic losses to us and european nurseries as well due to its infection of common ornamental plants. in its known range, p. ram ... | 2009 | 19222751 |
| proteins related to green algal striated fiber assemblin are present in stramenopiles and alveolates. | in green algae, striated fiber assemblin (sfa) is the major protein of the striated microtubule-associated fibers that are structural elements in the flagellar basal apparatus. using basic local alignment search tool (blast) searches of recently established databases, sfa-like sequences were detected in the genomes not only of green algal species but also of a range of other protists. these included species in two alveolate subgroups, the ciliates (tetrahymena thermophila, paramecium tetraurelia ... | 2009 | 19333716 |
| inventory and comparative evolution of the abc superfamily in the genomes of phytophthora ramorum and phytophthora sojae. | automated and manual annotation of the atp binding cassette (abc) superfamily in the phytophthora ramorum and p. sojae genomes has identified 135 and 136 members, respectively, indicating that this family is comparable in size to the arabidopsis thaliana and rice genomes, and significantly larger than that of two fungal pathogens, fusarium graminearum and magnaporthe grisea. the high level of synteny between these oomycete genomes extends to the abc superfamily, where 108 orthologues were identi ... | 2009 | 19407922 |
| influence of the medium-solidifying agent, the nutrient, and the genotype on the production of gametangia by phytophthora ramorum in vitro. | the effect of different parameters, including the type of nutrients, the quality of the gelling agent, and the genotype of the strain, were evaluated in the production of gametangia by phytophthora ramorum in vitro. by comparing different agar sources on a carrot-based medium, a delay or a failure in the production of oospores was observed in pairings carried out on media supplemented with technical agar. in contrast, oospores were produced on other agar types, the production on media supplement ... | 2009 | 18848885 |
| population genetic analysis infers migration pathways of phytophthora ramorum in us nurseries. | recently introduced, exotic plant pathogens may exhibit low genetic diversity and be limited to clonal reproduction. however, rapidly mutating molecular markers such as microsatellites can reveal genetic variation within these populations and be used to model putative migration patterns. phytophthora ramorum is the exotic pathogen, discovered in the late 1990s, that is responsible for sudden oak death in california forests and ramorum blight of common ornamentals. the nursery trade has moved thi ... | 2009 | 19774068 |
| phytophthora ramorum does not cause physiologically significant systemic injury to california bay laurel, its primary reservoir host. | california bay laurel trees (umbellularia californica) play a crucial role in the reproduction and survival of phytophthora ramorum in coastal california forests by supporting sporulation during the rainy season and by providing a means for the pathogen to survive the dry, mediterranean summer. while bay laurel is thus critical to the epidemiology of sudden oak death and other p. ramorum diseases in california, the relatively minor symptoms observed on this reservoir host suggest that it may not ... | 2009 | 19821735 |
| evaluation of molecular markers for phytophthora ramorum detection and identification: testing for specificity using a standardized library of isolates. | given the importance of phytophthora ramorum from a regulatory standpoint, it is imperative that molecular markers for pathogen detection are fully tested to evaluate their specificity in detection of the pathogen. in an effort to evaluate 11 reported diagnostic techniques, we assembled a standardized dna library using accessions from the world phytophthora genetic resource collection for 315 isolates representing 60 described phytophthora spp. as well as 11 taxonomically unclassified isolates. ... | 2009 | 19271981 |
| migration patterns of the emerging plant pathogen phytophthora ramorum on the west coast of the united states of america. | phytophthora ramorum (oomycetes) is the causal agent of sudden oak death and ramorum blight on trees, shrubs, and woody ornamentals in the forests of coastal california and southwestern oregon and in nurseries of california, oregon, and washington. in this study, we investigated the genetic structure of p. ramorum on the west coast of the united states, focusing particularly on population differentiation potentially indicative of gene flow. in total, 576 isolates recovered from 2001 to 2005 were ... | 2009 | 19453234 |
| genetic diversity, structure, and demographic change in tanoak, lithocarpus densiflorus (fagaceae), the most susceptible species to sudden oak death in california. | knowledge of population genetic structure of tanoak (lithocarpus densiflorus) is of interest to pathologists seeking natural variation in resistance to sudden oak death disease, to resource managers who need indications of conservation priorities in this species now threatened by the introduced pathogen (phytophthora ramorum), and to biologists with interests in demographic processes that have shaped plant populations. we investigated population genetic structure using nuclear and chloroplast dn ... | 2009 | 21622338 |
| genetic epidemiology of the sudden oak death pathogen phytophthora ramorum in california. | a total of 669 isolates of phytophthora ramorum, the pathogen responsible for sudden oak death, were collected from 34 californian forests and from the ornamental plant-trade. seven microsatellite markers revealed 82 multilocus genotypes (mgs) of which only three were abundant (>10%). iteratively collapsing based upon minimum phi(st), yielded five meta-samples and five singleton populations. populations in the same meta-sample were geographically contiguous, with one exception, possibly explaine ... | 2009 | 19840268 |
| green fluorescent protein (gfp) as a reporter gene for the plant pathogenic oomycete phytophthora ramorum. | transgenic phytophthora ramorum strains that produce green fluorescent protein (gfp) constitutively were obtained after stable dna integration using a polyethylene glycol and caclâ‚‚-based transformation protocol. green fluorescent protein production was studied in developing colonies and in different propagules of the pathogen to evaluate its use in molecular and physiological studies. about 12% of the gfp transformants produced gfp to a level detectable by a confocal laser scanning microscope. g ... | 2009 | 19457053 |
| standardizing the nomenclature for clonal lineages of the sudden oak death pathogen, phytophthora ramorum. | 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 c ... | 2009 | 19522576 |
| survival, dispersal, and potential soil-mediated suppression of phytophthora ramorum in a california redwood-tanoak forest. | because the role of soil inoculum of phytophthora ramorum in the sudden oak death disease cycle is not well understood, this work addresses survival, chlamydospore production, pathogen suppression, and splash dispersal of the pathogen in infested forest soils. colonized rhododendron and bay laurel leaf disks were placed in mesh sachets before transfer to the field in january 2005 and 2006. sachets were placed under tanoak, bay laurel, and redwood at three vertical locations: leaf litter surface, ... | 2009 | 19351257 |
| are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? | how photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. the history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. in this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a ph ... | 2009 | 19843329 |
| disease spread in small-size directed networks: epidemic threshold, correlation between links to and from nodes, and clustering. | network epidemiology has mainly focused on large-scale complex networks. it is unclear whether findings of these investigations also apply to networks of small size. this knowledge gap is of relevance for many biological applications, including meta-communities, plant-pollinator interactions and the spread of the oomycete pathogen phytophthora ramorum in networks of plant nurseries. moreover, many small-size biological networks are inherently asymmetrical and thus cannot be realistically modelle ... | 2009 | 19545575 |
| effect of temperature and moisture period on infection of rhododendron 'cunningham's white' by phytophthora ramorum. | we investigated the temperature and moisture conditions that allow phytophthora ramorum to infect rhododendron 'cunningham's white'. most experiments were performed with a single p. ramorum isolate from the na1 clonal lineage. for whole plants incubated in dew chambers at 10 to 31 degrees c, the greatest proportion of diseased leaves, 77.5%, occurred at the optimum temperature of 20.5 degrees c. disease occurred over the entire range of temperatures tested, although amounts of disease were minor ... | 2009 | 19671006 |
| cross-species global proteomics reveals conserved and unique processes in phytophthora sojae and phytophthora ramorum. | phytophthora ramorum and phytophthora sojae are destructive plant pathogens. p. sojae has a narrow host range, whereas p. ramorum has a wide host range. a global proteomics comparison of the vegetative (mycelium) and infective (germinating cyst) life stages of p. sojae and p. ramorum was conducted to identify candidate proteins involved in host range, early infection, and vegetative growth. sixty-two candidates for early infection, 26 candidates for vegetative growth, and numerous proteins that ... | 2008 | 18316789 |
| mitochondrial haplotype determination in the oomycete plant pathogen phytophthora ramorum. | 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 an ... | 2008 | 18488228 |
| survival of phytophthora ramorum hyphae after exposure to temperature extremes and various humidities. | we examined the effect of short-term exposure to high and low temperatures and a range of relative humidity (rh) on survival of phytophthora ramorum hyphae. spore-free hyphal colonies were grown on dialysis squares atop v8 medium. colonies were transferred to water agar plates positioned at 27.5-50 c on a thermal gradient plate and incubated 2.5-480 min. for low temperature trials colonies were transferred to vials of distilled water and incubated in a water bath at -5 to -25 c for 1-24 h. in th ... | 2008 | 18592898 |
| influence of land-cover change on the spread of an invasive forest pathogen. | human-caused changes in land use and land cover have dramatically altered ecosystems worldwide and may facilitate the spread of infectious diseases. to address this issue, we examined the influence of land-cover changes between 1942 and 2000 on the establishment of an invasive pathogen, phytophthora ramorum, which causes the forest disease known as sudden oak death. we assessed effects of land-cover change, forest structure, and understory microclimate on measures of inoculum load and disease pr ... | 2008 | 18372563 |
| reconstruction of the sudden oak death epidemic in california through microsatellite analysis of the pathogen phytophthora ramorum. | the genetic structure of the clonally reproducing sudden oak death (sod) pathogen in california was investigated using seven variable microsatellites. a total of 35 multilocus genotypes were identified among 292 samples representative of populations from 14 forest sites and of the nursery trade. amova indicated significant genetic variability both within (44.34%) and among populations (55.66%). spatial autocorrelation analyses indicated that moran's index of similarity reached a minimum of 0.1 a ... | 2008 | 18444982 |
| early detection of emerging forest disease using dispersal estimation and ecological niche modeling. | distinguishing the manner in which dispersal limitation and niche requirements control the spread of invasive pathogens is important for prediction and early detection of disease outbreaks. here, we use niche modeling augmented by dispersal estimation to examine the degree to which local habitat conditions vs. force of infection predict invasion of phytophthora ramorum, the causal agent of the emerging infectious tree disease sudden oak death. we sampled 890 field plots for the presence of p. ra ... | 2008 | 18488603 |
| evidence for the role of synchronicity between host phenology and pathogen activity in the distribution of sudden oak death canker disease. | variations in synchronicity between colonization rate by the pathogen and host phenology may account for unexplained spatial distribution of canker disease. the hypothesis that synchronous pathogenicity and host development are necessary for incidence of sudden oak death disease was tested by correlating seasonal variations in host cambial phenology and response to inoculation with phytophthora ramorum. response to infection was estimated by inoculating branch cuttings from coast live oak (querc ... | 2008 | 19086294 |
| phytophthora ramorum: a pathogen with a remarkably wide host range causing sudden oak death on oaks and ramorum blight on woody ornamentals. | phytophthora ramorum is an oomycete plant pathogen classified in the kingdom stramenopila. p. ramorum is the causal agent of sudden oak death on coast live oak and tanoak as well as ramorum blight on woody ornamental and forest understorey plants. it causes stem cankers on trees, and leaf blight or stem dieback on ornamentals and understorey forest species. this pathogen is managed in the usa and europe by eradication where feasible, by containment elsewhere and by quarantine in many parts of th ... | 2008 | 19019002 |
| sources of inoculum for phytophthora ramorum in a redwood forest. | abstract sources of inoculum were investigated for dominant hosts of phytophthora ramorum in a redwood forest. infected trunks, twigs, and/or leaves of bay laurel (umbellularia californica), tanoak (lithocarpus densiflorus), and redwood (sequoia sempervirens) were tested in the laboratory for sporangia production. sporangia occurred on all plant tissues with the highest percentage on bay laurel leaves and tanoak twigs. to further compare these two species, field measurements of inoculum producti ... | 2008 | 18943203 |
| forest health conditions in north america. | some of the greatest forest health impacts in north america are caused by invasive forest insects and pathogens (e.g., emerald ash borer and sudden oak death in the us), by severe outbreaks of native pests (e.g., mountain pine beetle in canada), and fires exacerbated by changing climate. ozone and n and s pollutants continue to impact the health of forests in several regions of north america. long-term monitoring of forest health indicators has facilitated the assessment of forest health and sus ... | 2008 | 18479794 |
| evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate phytophthora virulence factor. | lateral gene transfer (lgt) can facilitate the acquisition of new functions in recipient lineages, which may enable them to colonize new environments. several recent publications have shown that gene transfer between prokaryotes and eukaryotes occurs with appreciable frequency. here we present a study of interdomain gene transfer of cutinases -- well documented virulence factors in fungi -- between eukaryotic plant pathogens phytophthora species and prokaryotic bacterial lineages. two putative c ... | 2008 | 18024004 |
| susceptibility to phytophthora ramorum in a key infectious host: landscape variation in host genotype, host phenotype, and environmental factors. | sudden oak death is an emerging forest disease caused by the invasive pathogen phytophthora ramorum. genetic and environmental factors affecting susceptibility to p. ramorum in the key inoculum-producing host tree umbellularia californica (bay laurel) were examined across a heterogeneous landscape in california, usa. laboratory susceptibility trials were conducted on detached leaves and assessed field disease levels for 97 host trees from 12 225-m(2) plots. genotype and phenotype characteristics ... | 2008 | 18069961 |
| isolation and identification of rhizoxin analogs from pseudomonas fluorescens pf-5 by using a genomic mining strategy. | the products synthesized from a hybrid polyketide synthase/nonribosomal peptide synthetase gene cluster in the genome of pseudomonas fluorescens pf-5 were identified using a genomics-guided strategy involving insertional mutagenesis and subsequent metabolite profiling. five analogs of rhizoxin, a 16-member macrolide with antifungal, phytotoxic, and antitumor activities, were produced by pf-5, but not by a mutant with an insertion in the gene cluster. the five rhizoxin analogs, one of which had n ... | 2008 | 18344330 |
| a phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease. | there is emerging evidence that the proteolytic machinery of plants plays important roles in defense against pathogens. the oomycete pathogen phytophthora infestans, the agent of the devastating late blight disease of tomato (lycopersicon esculentum) and potato (solanum tuberosum), has evolved an arsenal of protease inhibitors to overcome the action of host proteases. previously, we described a family of 14 kazal-like extracellular serine protease inhibitors from p. infestans. among these, epi1 ... | 2007 | 17085509 |
| phytophthora siskiyouensis, a new species from soil, water, myrtlewood (umbellularia californica) and tanoak (lithocarpus densiflorus) in southwestern oregon. | an unknown phytophthora species was recovered in southwestern oregon from rhododendron and tanoak leaf baits used for monitoring streams and soils for the presence of phytophthora ramorum, from a blighted shoot of myrtlewood and from tanoak bark cankers. isolates of this species yielded its-dna sequences that differed substantially from other phytophthora sequences in genbank. morphological features also differed from available descriptions of known phytophthora species. based on the combination ... | 2007 | 18268898 |
| rapid inventory of the ant assemblage in a temperate hardwood forest: species composition and assessment of sampling methods. | ants are key indicators of ecological change, but few studies have investigated how ant assemblages respond to dramatic changes in vegetation structure in temperate forests. pests and pathogens are causing widespread loss of dominant canopy tree species; ant species composition and abundance may be very sensitive to such losses. before the experimental removal of red oak trees to simulate effects of sudden oak death and examine the long-term impact of oak loss at the black rock forest (cornwall, ... | 2007 | 17716467 |
| a kingdom-specific protein domain hmm library for improved annotation of fungal genomes. | pfam is a general-purpose database of protein domain alignments and profile hidden markov models (hmms), which is very popular for the annotation of sequence data produced by genome sequencing projects. pfam provides models that are often very general in terms of the taxa that they cover and it has previously been suggested that such general models may lack some of the specificity or selectivity that would be provided by kingdom-specific models. | 2007 | 17425790 |
| photosynthetic declines in phytophthora ramorum-infected plants develop prior to water stress and in response to exogenous application of elicitins. | abstract phytophthora ramorum, causal agent of sudden oak death, is responsible for widespread oak mortality in california and oregon, and has the potential to infect 100 or more species. symptoms range from stem girdling and shoot blight to leaf spotting. in this study, we examined the physiological impacts of p. ramorum infection on rhododendron macrophyllum. in stem-inoculated plants, photosynthetic capacity (v(cmax)) significantly declined by approximately 21% 3 weeks after inoculation in vi ... | 2007 | 18943934 |
| detection, distribution, sporulation, and survival of phytophthora ramorum in a california redwood-tanoak forest soil. | abstract recovery of phytophthora ramorum from soils throughout sudden oak death-affected regions of california illustrates that soil may serve as an inoculum reservoir, but the role of soil inoculum in the disease cycle is unknown. this study addresses the efficacy of soil baiting, seasonal pathogen distribution under several epidemiologically important host species, summer survival and chlamydospore production in soil, and the impact of soil drying on pathogen survival. the efficacy of rhodode ... | 2007 | 18943696 |
| diagnostic values and utility of immunological, morphological, and molecular methods for in planta detection of phytophthora ramorum. | abstract in this study, six methods for the detection of phytophthora ramorum in planta were compared using naturally infested rhododendron plant material. the methods included two immunological methods, one an enzyme-linked immunosorbent assay (elisa) and the other using a lateral flow format (lfd). three molecular tests based on the polymerase chain reaction (pcr) using taqman chemistry also were assessed, including two assays designed for specific detection of p. ramorum and one designed for ... | 2007 | 18944177 |
| tracking the sudden oak death pathogen. | invasive species are, by definition, unwelcome and pathogenic ones, especially so. tracing the origins and spread of phytophthora ramorum, the devastating 'sudden oak death' pathogen, in the forests and nurseries of oregon has revealed differences between forest and nursery pathogen populations that suggest discrete sources of primary inoculum initiate each type of outbreak. new information on the ecology and evolution of this pathogen is presented that helps gauge the effectiveness of quarantin ... | 2007 | 17850541 |
| molecular detection of phytophthora ramorum by real-time polymerase chain reaction using taqman, sybr green, and molecular beacons. | abstract sudden oak death, caused by phytophthora ramorum, is a severe disease that affects many species of trees and shrubs. this pathogen is spreading rapidly and quarantine measures are currently in place to prevent dissemination to areas that were previously free of the pathogen. molecular assays that rapidly detect and identify p. ramorum frequently fail to reliably distinguish between p. ramorum and closely related species. to overcome this problem and to provide additional assays to incre ... | 2007 | 18943583 |
| correlation of isozyme profiles with genomic sequences of phytophthora ramorum and its p. sojae orthologues. | a correct interpretation of isozyme patterns can be seriously hampered by the lack of supporting genetic data. the availability of the complete genome sequence of phytophthora ramorum, enabled us to correlate isozyme profiles with the gene models predicted for these enzymes. thirty-nine p. ramorum strains were characterised employing isozyme analysis on malate dehydrogenase (mdh), nadp-dependent malic enzyme (mdhp), 6-phosphogluconate dehydrogenase (pgd), glucosephosphate isomerase (gpi) and lac ... | 2007 | 17968548 |
| phytophthora ramorum colonizes tanoak xylem and is associated with reduced stem water transport. | abstract isolation, detection with diagnostic polymerase chain reaction (pcr), and microscopy demonstrated the presence of phytophthora ramorum in the sapwood of mature, naturally infected tanoak (lithocarpus densiflorus) trees. the pathogen was strongly associated with discolored sapwood (p < 0.001), and was recovered or detected from 83% of discolored sapwood tissue samples. hyphae were abundant in the xylem vessels, ray parenchyma, and fiber tracheids. chlamydospores were observed in the vess ... | 2007 | 18943716 |
| mitochondrial genome sequences and comparative genomics of phytophthora ramorum and p. sojae. | 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 (o ... | 2007 | 17310332 |
| faster, simpler, more-specific methods for improved molecular detection of phytophthora ramorum in the field. | phytophthora ramorum is the causal agent of sudden oak death. the pathogen also affects a wide range of tree, shrub, and herbaceous species in natural and landscaped environments as well as plants in the nursery industry. a taqman real-time pcr method for the detection of this pathogen in the field has been described previously; this paper describes the development of a number of assays based on this method which have various advantages for use in the field. a scorpion real-time pcr assay that i ... | 2007 | 17449689 |
| an exploratory study of the nutritional composition of tanoak (lithocarpus densiflorus) acorns after potassium phosphonate treatment. | native american pomo communities who live in the northern coastal range of california and consume acorns from tanoak trees as part of traditional diets are facing the potential loss of many culturally important trees to sudden oak death. pomo and other native american communities are reluctant to use the protective fungicide, potassium phosphonate, on trees used for acorn collection without information on how the treatment affects acorn properties. in this study, select macronutrients and polyph ... | 2007 | 17559226 |
| population dynamics of the sudden oak death pathogen phytophthora ramorum in oregon from 2001 to 2004. | phytophthora ramorum (oomycetes) is an emerging plant pathogen in forests in southwestern oregon (curry county). moreover, since 2003 it has been repeatedly isolated from plants in oregon nurseries. in this study, we analysed the genetic diversity of the p. ramorum population in oregon from 2001 to 2004 by using microsatellites. a total of 323 isolates (272 from the infested forest; 51 from nurseries) were screened at 10 loci. the overall p. ramorum population in oregon is characterized by low g ... | 2007 | 17614910 |
| adaptive evolution has targeted the c-terminal domain of the rxlr effectors of plant pathogenic oomycetes. | oomycete plant pathogens deliver effector proteins inside host cells to modulate plant defense circuitry and to enable parasitic colonization. these effectors are defined by a conserved motif, termed rxlr (for arg, any amino acid, leu, arg), that is located downstream of the signal peptide and that has been implicated in host translocation. because the phenotypes of rxlr effectors extend to plant cells, their genes are expected to be the direct target of the evolutionary forces that drive the an ... | 2007 | 17675403 |
| phenolic chemistry of coast live oak response to phytophthora ramorum infection. | since the mid 1990s, phytophthora ramorum has been responsible for the widespread mortality of tanoaks, as well as several oak species throughout california and oregon forests. however, not all trees die, even in areas with high disease pressure, suggesting that some trees may be resistant to the pathogen. in this study, the chemical basis of host resistance was investigated. three field experiments were carried out in california between december 2004 and september 2005. the levels of nine pheno ... | 2007 | 17713820 |
| antimicrobial activity of extractable conifer heartwood compounds toward phytophthora ramorum. | ethyl acetate extracts from heartwood of seven western conifer trees and individual volatile compounds in the extracts were tested for antimicrobial activity against phytophthora ramorum. extracts from incense and western redcedar exhibited the strongest activity, followed by yellow-cedar, western juniper, and port-orford-cedar with moderate activity, and no activity for douglas-fir and redwood extracts. chemical composition of the extracts varied both qualitatively and quantitatively among the ... | 2007 | 17929093 |
| genomic polymorphism of isolates of phytophthora ramorum from polish ornamental nurseries compared with other european and north american isolates. | we undertook an analysis of the genomic relationships between 15 isolates of phytophthora ramorum werres, de cock et man in't veld, obtained from symptomatic plants growing in polish ornamental nurseries, and 2 representatives of the european population and 3 of the north american population. dendrograms were generated by upgma based on 786 amplification products obtained in issr-pcr reactions. the representatives of the european population and 13 of the "polish" isolates formed a common cluster ... | 2007 | 17998602 |
| taqman chemistry for phytophthora ramorum detection and quantification, with a comparison of diagnostic methods. | abstract the choice of detection method for phytopathogens can be critically important in determining the success or failure of pest regulation systems. we present an assay for phytophthora ramorum that uses 5' fluorogenic exonuclease (taqman) chemistry to detect and quantify the pathogen from diseased tissue, and include a universal primer and probe set for an internal positive control. this method is sensitive, detecting as little as 15 fg of target dna when used in a nested design or 50 fg wh ... | 2006 | 18943749 |
| real-time fluorescent polymerase chain reaction detection of phytophthora ramorum and phytophthora pseudosyringae using mitochondrial gene regions. | 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 prime ... | 2006 | 18943415 |
| stromata, sporangiomata and chlamydosori of phytophthora ramorum on inoculated mediterranean woody plants. | three types of multihyphal structures, stromata, sporangiomata and chlamydosori, are described for the plant pathogen phytophthora ramorum. their morphology, morphogenesis and position on the host organ were observed by dissecting, compound and scanning electron microscopy. stromata were consistently formed one to two weeks after zoospore inoculation of detached leaves and fruits of an assortment of mediterranean sclerophyll shrubs. stroma initials appeared subcuticularly or subepidermally and d ... | 2006 | 17059884 |
| development of a one-step real-time polymerase chain reaction assay for diagnosis of phytophthora ramorum. | abstract phytophthora ramorum is a recently described pathogen causing bleeding cankers, dieback, and leaf blight on trees and shrubs in parts of europe and north america, where the disease is commonly known as sudden oak death. this article describes the development of a single-round real-time polymerase chain reaction (pcr) assay based on taqman chemistry, designed within the internal transcribed spacer 1 region of the nuclear ribosomal (nr)rna gene for detection of p. ramorum in plant materia ... | 2006 | 18944053 |
| ancient origin of elicitin gene clusters in phytophthora genomes. | the genus phytophthora belongs to the oomycetes in the eukaryotic stramenopile lineage and is comprised of over 65 species that are all destructive plant pathogens on a wide range of dicotyledons. phytophthora produces elicitins (elis), a group of extracellular elicitor proteins that cause a hypersensitive response in tobacco. database mining revealed several new classes of elicitin-like (ell) sequences with diverse elicitin domains in phytophthora infestans, phytophthora sojae, phytophthora bra ... | 2006 | 16237208 |
| activation of zoosporogenesis-specific genes in phytophthora infestans involves a 7-nucleotide promoter motif and cold-induced membrane rigidity. | infections of plants by the oomycete phytophthora infestans typically result from zoospores, which develop from sporangia at cold temperatures. to help understand the relevant cold-induced signaling pathway, factors regulating the transcription of the zoosporogenesis-specific nif (nuclear lim-interactor-interacting factor) gene family were examined. sequences required for inducing pinifc3 were identified by analyzing truncated and mutated promoters using the beta-glucuronidase reporter in stable ... | 2006 | 16607021 |
| composting is an effective treatment option for sanitization of phytophthora ramorum-infected plant material. | to determine the effects of heat and composting treatments on the viability of the plant pathogen phytophthora ramorum grown on both artificial and various natural substrates. | 2006 | 16968293 |
| growth and sporulation of phytophthora ramorum in vitro in response to temperature and light. | phytophthora ramorum, recently found in the us, is causing concern for hardwood forests and the nursery industry. in an effort to identify some of the environmental limitations to growth and sporulation we undertook a laboratory study of four us and three european (eu) isolates. on v8 media, isolates grew when incubated at 2-28 c and produced chlamydospores at 8-28 c. sporangia were produced at all temperatures tested: 10-30 c for us isolates and 6-26 c for eu isolates. optimal temperatures were ... | 2006 | 17040065 |
| demography and recruitment limitations of three oak species in california. | we review published studies on the demography and recruitment of california oak trees and focus on the widespread dominant species of the foothill woodlands, quercus douglasii, q. lobata, and q. agrifolia, to ascertain the nature and strength of evidence for a decline in populations of these species. the vast majority of studies have been of short duration (less than three years), focused on the acorn and seedling life stages, and conducted at few locations within each species geographic range. ... | 2006 | 16776062 |
| multiple, non-allelic, intein-coding sequences in eukaryotic rna polymerase genes. | inteins are self-splicing protein elements. they are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. they are encoded as in-frame insertions within the genes for the host proteins. inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these a ... | 2006 | 17069655 |
| microsatellite markers identify three lineages of phytophthora ramorum in us nurseries, yet single lineages in us forest and european nursery populations. | analysis of 12 polymorphic simple sequence repeats identified in the genome sequence of phytophthora ramorum, causal agent of 'sudden oak death', revealed genotypic diversity to be significantly higher in nurseries (91% of total) than in forests (18% of total). our analysis identified only two closely related genotypes in us forests, while the genetic structure of populations from european nurseries was of intermediate complexity, including multiple, closely related genotypes. multilocus analysi ... | 2006 | 16629806 |
| computational and comparative analyses of 150 full-length cdna sequences from the oomycete plant pathogen phytophthora infestans. | phytophthora infestans is a devastating phytopathogenic oomycete that causes late blight on tomato and potato. recent genome sequencing efforts of p. infestans and other phytophthora species are generating vast amounts of sequence data providing opportunities to unlock the complex nature of pathogenesis. however, accurate annotation of phytophthora genomes will be a significant challenge. most of the information about gene structure in these species was gathered from a handful of genes resulting ... | 2006 | 16380277 |
| phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. | draft genome sequences have been determined for the soybean pathogen phytophthora sojae and the sudden oak death pathogen phytophthora ramorum. oömycetes such as these phytophthora species share the kingdom stramenopila with photosynthetic algae such as diatoms, and the presence of many phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. comparison of the two species' genomes reveals a rapid expansion and diversification of many protein fami ... | 2006 | 16946064 |
| novel phosphatidylinositol phosphate kinases with a g-protein coupled receptor signature are shared by dictyostelium and phytophthora. | g-protein coupled receptors (gpcr) and phosphatidylinositol phosphate kinases (pipk) are important key switches in signal transduction pathways. a novel class of proteins was identified in the genomes of two unrelated organisms that harbor both a gpcr and a pipk domain. dictyostelium discoideum contains one gpcr-pipk, which is crucial in cell-density sensing, and the genomes of phytophthora sojae and phytophthora ramorum each encode twelve gpcr-pipks. intriguingly, these are currently the only s ... | 2006 | 16876997 |
| gene duplication event in family 12 glycosyl hydrolase from phytophthora spp. | a total of 18 paralogs of xyloglucan-specific endoglucanases (egls) from the glycosyl hydrolase family 12 were identified and characterized in phytophthora sojae and phytophthora ramorum. these genes encode predicted extracellular enzymes, with sizes ranging from 189 to 435 amino acid residues, that would be capable of hydrolyzing the xyloglucan component of the host cell wall. in two cases, four and six functional copies of these genes were found in tight succession within a region of 5 and 18 ... | 2006 | 16784880 |
| the malarial host-targeting signal is conserved in the irish potato famine pathogen. | animal and plant eukaryotic pathogens, such as the human malaria parasite plasmodium falciparum and the potato late blight agent phytophthora infestans, are widely divergent eukaryotic microbes. yet they both produce secretory virulence and pathogenic proteins that alter host cell functions. in p. falciparum, export of parasite proteins to the host erythrocyte is mediated by leader sequences shown to contain a host-targeting (ht) motif centered on an rxlx (e, d, or q) core: this motif appears to ... | 2006 | 16733545 |
| vmd: a community annotation database for oomycetes and microbial genomes. | the vbi microbial database (vmd) is a database system designed to host a range of microbial genome sequences. at present, the database contains genome sequence and annotation data of two plant pathogens phytophthora sojae and phytophthora ramorum. with the completion of the draft genome sequences of these pathogens in collaboration with the doe joint genome institute (jgi), we have created this resource to make the sequences publicly available. the genome sequences (95 mb for p.sojae and 65 mb f ... | 2006 | 16381891 |
| phytophthora foliorum sp. nov., a new species causing leaf blight of azalea. | a previously unknown phytophthora was recovered more than 60 times from evergreen hybrid azalea leaves collected during surveys for the sudden oak death pathogen phytophthora ramorum in california and tennessee. the novel phytophthora was discovered when genomic dna from this species cross-reacted with the its-based diagnostic pcr primers used to screen plants for the presence of p. ramorum. this species had caducous, semi-papillate sporangia, was homothallic with both paragynous and amphigynous ... | 2006 | 17070028 |
| expressed peptide tags: an additional layer of data for genome annotation. | while genome sequencing is becoming ever more routine, genome annotation remains a challenging process. identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. here, we present a method to assist the annotation process through the use of proteomic data and bioinformatics. mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein d ... | 2006 | 17081056 |
| phytophthora genomics: the plant destroyers' genome decoded. | the year 2004 was an exciting one for the phytophthora research community. the united states department of energy joint genome institute (jgi) completed the draft genome sequence of two phytophthora species, phytophthora sojae and phytophthora ramorum. in august of that year over 50 people gathered at jgi in walnut creek, california, for an annotation jamboree and searched for the secrets and surprises that the two genomes have in petto. this culminated in a paper in science in september of this ... | 2006 | 17153913 |
| the repertoire of transfer rna genes is tuned to codon usage bias in the genomes of phytophthora sojae and phytophthora ramorum. | in all, 238 and 155 transfer (t)rna genes were predicted from the genomes of phytophthora sojae and p. ramorum, respectively. after omitting pseudogenes and undetermined types of trna genes, there remained 208 p. sojae trna genes and 140 p. ramorum trna genes. there were 45 types of trna genes, with distinct anticodons, in each species. fourteen common anticodon types of trnas are missing altogether from the genome in the two species; however, these appear to be compensated by wobbling of other ... | 2006 | 17153916 |
| extensive variation in nuclear mitochondrial dna content between the genomes of phytophthora sojae and phytophthora ramorum. | fragments of mitochondrial dna (mtdna) transferred to the nuclear genome are called nuclear mitochondrial dnas (numts). we report here a comparison of numt content between genomes from two species of the same genus. analysis of the genomes of phytophthora sojae and p. ramorum revealed large differences in the numt content of the two genomes: 16.27 x 10(-3) and 2.28 x 10(-3)% of each genome, respectively. substantial differences also exist between the two species in the sizes of the numts found i ... | 2006 | 17153917 |
| identification of cell wall-associated proteins from phytophthora ramorum. | the oomycete genus phytophthora comprises a large group of fungal-like plant pathogens. two phytophthora genomes recently have been sequenced; one of them is the genome of phytophthora ramorum, the causal agent of sudden oak death. during plant infection, extracellular proteins, either soluble secreted proteins or proteins associated with the cell wall, play important roles in the interaction with host plants. cell walls of p. ramorum contain 1 to 1.5% proteins, the remainder almost exclusively ... | 2006 | 17153919 |
| detection and quantification of phytophthora ramorum, p. kernoviae, p. citricola and p. quercina in symptomatic leaves by multiplex real-time pcr. | summary new species of phytophthora such as phytophthora ramorum, p. kernoviae and p. quercina together with p. citricola are plant pathogens which impact on forest health, natural ecosystem stability and international trade. a real-time multiplex pcr approach based on taqman pcr was developed to simultaneously identify and detect these four phytophthora species. specific primers and probes labelled with fam (p. ramorum), yakima yellow (p. kernoviae), rox (p. citricola) and cy5 (p. quercina) wer ... | 2006 | 20507453 |