@article {4122, title = {Management of Phytophthora pod rot disease on cocoa farms in Ghana}, journal = {Crop Protection}, volume = {22}, year = {2003}, month = {4/2003}, pages = {469 - 477}, abstract = {

From 1991 to 1997, field observations on trials involving the use of metalaxyl and copper-based fungicides were made on farmers{\textquoteright} farms in four Phytophthora megakarya affected cocoa growing regions of Ghana to control Phytophthora pod rot disease. Data on farm management practices, cocoa and shade tree types and densities, plot sizes, yield, land tenure and labour arrangements for farm operations, disease incidence and profitability of disease control were collected. Lower disease incidence and higher yields were recorded on fungicide-treated plots than on the untreated plots. The profitability of fungicide application depended on the level of farm management, nature of land tenure and labour arrangements for farm operations. The challenges involved in conducting trials with active participation by farmers are discussed. The involvement of farmers in the development of disease control programmes is crucial for subsequent adoption of the technology.

}, issn = {02612194}, doi = {10.1016/S0261-2194(02)00193-X}, url = {http://www.sciencedirect.com/science/article/pii/S026121940200193X}, author = {AY Akrofi and AA Appiah and IY Opoku} } @article {Blair2008266, title = {A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences}, journal = {Fungal Genetics and Biology}, volume = {45}, number = {3}, year = {2008}, pages = {266 - 277}, keywords = {Molecular markers}, issn = {1087-1845}, doi = {DOI: 10.1016/j.fgb.2007.10.010}, url = {http://www.sciencedirect.com/science/article/B6WFV-4PYP77J-1/2/ebf8754b49bc2fd36ab9e34941eeed43}, author = {Jaime E. Blair and Michael D. Coffey and Sook-Young Park and David M. Geiser and Seogchan Kang} } @article {4653, title = {Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides-P. megasperma ITS Clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile}, journal = {Mycological Research}, volume = {107}, year = {2003}, month = {Jan-03-2003}, pages = {277 - 290}, abstract = {

Phytophthora isolates associated with Phytophthora major ITS Clade 6 were grouped into 11 phenotypic taxa. These comprised the described morphospecies P. gonapodyides, P. megasperma s. str. and P. humicola; four previously identified but so far undescribed taxa, informally designated here P. sp. O-group, P. sp. Apple-cherry, P. taxon Pgchlamydo, and P. taxon Walnut; and four previously unknown taxa, designated P. taxon Oaksoil, P. taxon Raspberry, P. taxon Forestsoil, and P. taxon Riversoil. With the exception of P. gonapodyides each phenotypic taxon represented an unique ITS lineage. Two isolates morphologically identical to P. gonapodyides comprised a separate lineage and probably represent another taxon, designated here P. taxon Salixsoil. P. humicola, P. sp. O-group, P. sp. Apple-cherry and P. taxon Walnut grouped together as subclade I. Within subclade II, P. taxon Oaksoil, P. taxon Raspberry, P. taxon Forestsoil, P. taxon Riversoil and P. taxon Pgchlamydo formed a cluster of closely related but phenotypically distinct lineages basal to P. gonapodyides and P. megasperma, P. taxon Salixsoil being the most basal member. The taxonomy, adaptation and breeding systems of Clade 6 taxa are discussed. They show a strong association with forests and riparian ecosystems, only a limited association with agriculture and an ability to tolerate high temperatures. Also, in contrast to most other Phytophthora clades, Clade 6 taxa are predominantly sterile or inbreeding in culture. Only one taxon, P. sp. O-group, appears classically A1/A2 heterothallic.

}, issn = {09537562}, doi = {10.1017/S095375620300738X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0953756208611788}, author = {Brasier, Clive M. and Cooke, David E.L. and Duncan, James M. and Hansen, Everett M.} } @article {Brasier2003277, title = {Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides-P. megasperma ITS Clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile}, journal = {Mycological Research}, volume = {107}, number = {3}, year = {2003}, pages = {277 - 290}, issn = {0953-7562}, doi = {DOI: 10.1017/S095375620300738X}, url = {http://www.sciencedirect.com/science/article/B7XMR-4RT04VN-6/2/68f2582c518f07f52e7a0db891ca14dd}, author = {Clive M. Brasier and David E.L. Cooke and James M. Duncan and Hansen, Everett M.} } @article {4472, title = {Metabarcoding and development of new Real-time specific assays reveal Phytophthora species diversity in Holm Oak forests in eastern Spain}, journal = {Plant Pathology}, volume = {66}, year = {2017}, month = {Jan-04-2016}, pages = {115{\textendash}123}, abstract = {

The evergreen holm oaks (Quercus ilex subsp. ilex and Q.\ ilex subsp. ballota) are the most representative tree species in the Iberian peninsula and the main tree species in oak-rangeland ecosystems (dehesas). Oak decline in western, central and southern parts of Spain has been associated with root rot caused by Phytophthora cinnamomi for decades. However, Phytophthora species such as P.\ quercina and P.\ psychrophila have recently been found associated with Quercus decline in eastern Spain where calcareous soils are predominant. Soil and root samples from two Quercus forests presenting decline symptoms in two different geographical areas in eastern Spain (Carrascar de la Font Roja and Vallivana) were analysed by amplicon pyrosequencing. Metabarcoding analysis showed Phytophthora species diversity, and revealed that an uncultured Phytophthora taxon, named provisionally Phytophthora taxon ballota, was the predominant species in both areas. In addition, a real-time PCR assay, based on the pyrosequencing results, was developed for the detection of this uncultured Phytophthora taxon, and also for the detection of P.\ quercina. TaqMan assays were tested on soil and root samples, and on Phytophthora pure cultures. The new assays showed high specificity and were consistent with metabarcoding results. A new real-time PCR protocol is proposed to evaluate the implication of different Phytophthora spp. in oak decline in eastern Spain.

}, doi = {10.1111/ppa.12541}, url = {http://doi.wiley.com/10.1111/ppa.12541}, author = {Catal{\`a}, S. and Berbegal, M. and P{\'e}rez-Sierra, A. and Abad-Campos, P.} } @article {4012, title = {Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species}, journal = {Phytopathology}, volume = {103}, year = {2013}, month = {01/2013}, pages = {43 - 54}, abstract = {

Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

}, issn = {0031-949X}, doi = {10.1094/PHYTO-04-12-0092-R}, author = {Chen, Wen and Djama, Zeinab Robleh and Michael D. Coffey and Martin, Frank N. and Bilodeau, Guillaume J. and Radmer, Lorien and Denton, Geoff and L{\'e}vesque, C. Andr{\'e}} } @article {Cooke200017, title = {A molecular phylogeny of Phytophthora and related Oomycetes}, journal = {Fungal Genetics and Biology}, volume = {30}, number = {1}, year = {2000}, pages = {17-32}, abstract = {

Phylogenetic relationships among 50 Phytophthora species and between Phytophthora and other oomycetes were examined on the basis of the ITS sequences of genomic rDNA. Phytophthora grouped with Pythium, Peronospora, and Halophytophthora, distant from genera in the Saprolegniales. Albugo was intermediate between these two groups. Unlike Pythium, Phytophthora was essentially monophyletic, all but three species forming a cluster of eight clades. Two clades contained only species with nonpapillate sporangia. The other six clades included either papillate and semipapillate, or semipapillate and nonpapillate types, transcending traditional morphological groupings, which are evidently not natural assemblages. Peronospora was related to P. megakarya and P. palmivora and appears to be derived from a Phytophthora that has both lost the ability to produce zoospores and become an obligate biotroph. Three other Phytophthoras located some distance from the main Phytophthora-Peronospora cluster probably represent one or more additional genera.

}, keywords = {evolution, internal transcribed spacers, ITS, Peronospora., Pythium, rDNA}, issn = {1087-1845}, doi = {DOI: 10.1006/fgbi.2000.1202}, url = {http://www.sciencedirect.com/science/article/B6WFV-45FC03G-1G/2/1cb8ec25d08dae3a16f56e74cd92e99e}, author = {Cooke, D. E. L. and A. Drenth and Duncan, J. M. and G. Wagels and C.M. Brasier} } @article {4690, title = {Migratory passerine birds in Britain carry Phytophthora ramorum inoculum on their feathers and {\textquotedblleft}feet{\textquotedblright} at low frequency}, journal = {Forest Pathology}, volume = {50}, year = {2020}, month = {Dec-09-2019}, pages = {e12569}, abstract = {

In this study, we investigated whether birds could be vectors facilitating long-distance spread of Phytophthora ramorum in Britain. Migratory bird species associated with the main sporangium-producing host plants and most likely to pick up P.\ ramorum spores were considered. Swabs were taken from the flank and {\textquotedblleft}feet{\textquotedblright} of 1,014 birds over a 12-month period (April 2011{\textendash}March 2012) in the west of Britain and subsequently analyzed for the presence of P.\ ramorum using nested PCR. Ten positive samples from 10 birds were identified: three in Cornwall, one in Devon, three in Gloucestershire, two in north Wales and one in Merseyside. Phytophthora ramorum was detected on samples from four species of thrushes (Redwing Turdus iliacus, Fieldfare T.\ pilaris, Blackbird T.\ merula and Song Thrush T.\ philomelos) and one species of warbler (Chiffchaff Phylloscopus collybita). All birds that tested positive were sampled in late autumn and winter (October{\textendash}February), when long-distance movements (over 100\ km) would have stopped. The low incidence of P.\ ramorum found using PCR suggests that the incidence of inoculum, whether viable or not, on birds was low. The apparently low incidence of inoculum on birds suggests migratory passerine birds can carry P.\ ramorum inoculum on their feathers and {\textquotedblleft}feet,{\textquotedblright} albeit at low frequency. The dates of positive samples indicate that birds would not have been moving long distances at the time but further work is needed to estimate the extent of their contribution to the spread of P.\ ramorum in Britain.

}, doi = {10.1111/efp.v50.110.1111/efp.12569}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/efp.12569}, author = {Dadam, Daria and Siasou, Eleni and Woodward, Stephen and Clark, Jacquie A.} } @article {4700, title = {Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum}, journal = {mBio}, volume = {10}, year = {2019}, month = {Mar-12-2019}, abstract = {

Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0\% of RxLR and 18.8\% of Crinkler effector genes compared with 0.9\% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR.

IMPORTANCE Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve. Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence.

}, doi = {10.1128/mBio.02452-18}, url = {https://mbio.asm.org/content/10/2/e02452-18}, author = {Dale, Angela L. and Feau, Nicolas and Everhart, Sydney E. and Dhillon, Braham and Wong, Barbara and Sheppard, Julie and Bilodeau, Guillaume J. and Brar, Avneet and Tabima, Javier F. and Shen, Danyu and Brasier, Clive M. and Tyler, Brett M. and Gr{\"u}nwald, Niklaus J. and Hamelin, Richard C.}, editor = {Taylor, John W.} } @proceedings {417, title = {{\textquoteleft}{\textquoteleft}Mal del cipr{\'e}s{\textquoteright}{\textquoteright} disease: analysis of the association between aerial symptoms and vitality of trees.}, year = {2009}, pages = {282{\textendash}3}, publisher = {USDA Forest Service, Pacific Southwest Research Station: Gen. Tech. Rep. PSW-GTR-221, 282{\textendash}3}, address = {Albany, CA, USA}, author = {Floria, MP and Greslebin, A. G.} } @article {4333, title = {Management of red needle cast, caused by Phytophthora pluvialis, a new disease of radiata pine in New Zealand}, journal = {New Zealand Plant Protection}, volume = {67}, year = {2014}, pages = {48{\textendash}53}, abstract = {

Ten years ago there were no known foliar diseases caused by Phytophthora on pine trees worldwide. Since then two significant Phytophthora diseases have emerged on radiata pine, one of which is only known in New Zealand. Red needle cast is a disease caused by the pathogen Phytophthora pluvialis, which is thought to have originated from northwestern USA. This paper reviews the challenges the New Zealand forestry industry faces when dealing with this disease and evaluates the management options, such as chemical control, biological control and breeding programmes, being investigated to minimise its effect on forest productivity. The distribution of the pathogen in New Zealand and research that shows bark, logs and wood are free of the pathogen, therefore unlikely to pose biosecurity threats through trade in these products, are also outlined.

}, issn = {1175-9003 (print), 1179-352X (online)}, url = {http://www.nzpps.org/nzpp_abstract.php?paper=670480}, author = {Ganley, R.J. and Williams, N.M. and Rolando, C.A. and Hood, I.A. and Dungey, H.S. and Beets, P.N. and Bulman, L.S.} } @inbook {greenup_managing_1998, title = {Managing Chamaecyparis lawsoniana (Port-Orford-Cedar) to control the root disease caused by Phytophthora lateralis in the Pacific Northwest, USA.}, booktitle = {Coastally restricted forests}, year = {1998}, pages = {93{\textendash}100}, publisher = {New York : Oxford University Press, 1998}, organization = {New York : Oxford University Press, 1998}, keywords = {Chamaecyparis lawsoniana, disease control, literature reviews, Pacific States, Phytophthora lateralis, plant diseases and disorders, plant pathogenic fungi}, isbn = {0195075676 (alk. paper)}, author = {M. Greenup} } @article {doi:10.1094/PDIS.2000.84.1.4, title = {Managing Port-Orford-Cedar and the Introduced Pathogen Phytophthora lateralis}, journal = {Plant Disease}, volume = {84}, number = {1}, year = {2000}, pages = {4-14}, doi = {10.1094/PDIS.2000.84.1.4}, url = {http://apsjournals.apsnet.org/doi/abs/10.1094/PDIS.2000.84.1.4}, author = {Hansen, Everett M. and Goheen, Donald J. and Jules, Erik S. and Ullian, Barbara} } @article {4604, title = {Morphological and genetic analyses of the invasive forest pathogen Phytophthora austrocedri reveal that two clonal lineages colonized Britain and Argentina from a common ancestral population}, journal = {Phytopathology}, volume = {107}, year = {2017}, month = {Jan-12-2017}, pages = {1532 - 1540}, abstract = {

Phytophthora austrocedri is causing widespread mortality of Austrocedrus chilensis in Argentina and Juniperus communis in Britain. The pathogen has also been isolated from J. horizontalis in Germany. Isolates from Britain, Argentina, and Germany are homothallic, with no clear differences in the dimensions of sporangia, oogonia, or oospores. Argentinian and German isolates grew faster than British isolates across a range of media and had a higher temperature tolerance, although most isolates, regardless of origin, grew best at 15{\textdegree}C and all isolates were killed at 25{\textdegree}C. Argentinian and British isolates caused lesions when inoculated onto both A. chilensis and J. communis; however, the Argentinian isolate caused longer lesions on A. chilensis than on J. communis and vice versa for the British isolate. Genetic analyses of nuclear and mitochondrial loci showed that all British isolates are identical. Argentinian isolates and the German isolate are also identical but differ from the British isolates. Single-nucleotide polymorphisms are shared between the British and Argentinian isolates. We concluded that British isolates and Argentinian isolates conform to two distinct clonal lineages of P. austrocedri founded from the same as-yet-unidentified source population. These lineages should be recognized and treated as separate risks by international plant health legislation.

}, issn = {0031-949X}, doi = {10.1094/PHYTO-03-17-0126-R}, url = {https://apsjournals.apsnet.org/doi/10.1094/PHYTO-03-17-0126-Rhttps://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-03-17-0126-R}, author = {Henricot, B{\'e}atrice and P{\'e}rez-Sierra, Ana and Armstrong, April C. and Sharp, Paul M. and Green, Sarah} } @article {MEC:MEC2864, title = {Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations}, journal = {Molecular Ecology}, volume = {15}, number = {6}, year = {2006}, pages = {1493{\textendash}1505}, publisher = {Blackwell Publishing Ltd}, abstract = {

Analysis of 12 polymorphic simple sequence repeats identified in the genome sequence of Phytophthora ramorum, causal agent of {\textquoteleft}sudden oak death{\textquoteright}, 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 analysis determined populations in US forests reproduce clonally and are likely descendants of a single introduced individual. The 151 isolates analysed clustered in three clades. US forest and European nursery isolates clustered into two distinct clades, while one isolate from a US nursery belonged to a third novel clade. The combined microsatellite, sequencing and morphological analyses suggest the three clades represent distinct evolutionary lineages. All three clades were identified in some US nurseries, emphasizing the role of commercial plant trade in the movement of this pathogen.

}, keywords = {exotic microbe, oomycete, population genetics, SSR, Sudden oak death}, issn = {1365-294X}, doi = {10.1111/j.1365-294X.2006.02864.x}, url = {http://dx.doi.org/10.1111/j.1365-294X.2006.02864.x}, author = {K. Ivors and Garbelotto, M. and Vries, I. D. E. and Ruyter-Spira, C. and Hekkert, B. TE. and Rosenzweig, N. and Bonants, P.} } @article {4657, title = {Multiple new Phytophthora species from ITS Clade 6 associated with natural ecosystems in Australia: evolutionary and ecological implications}, journal = {Persoonia - Molecular Phylogeny and Evolution of Fungi}, volume = {26}, year = {2011}, month = {Jun-06-2013}, pages = {13 - 39}, abstract = {

During surveys of dying vegetation in natural ecosystems and associated waterways in Australia many new taxa have been identified from Phytophthora ITS Clade 6. For representative isolates, the region spanning the internal transcribed spacer region of the ribosomal DNA, the nuclear gene encoding heat shock protein 90 and the mitochondrial cox 1 gene were PCR amplified and sequenced. Based on phylogenetic analysis and morphological and physiological comparison, four species and one informally designated taxon have been described; Phytophthora gibbosa, P. gregata, P. litoralis, P. thermophila and P. taxon paludosa. Phytophthora gibbosa, P. gregata and P. taxon paludosa form a new cluster and share a common ancestor; they are homothallic and generally associated with dying vegetation in swampy or water-logged areas. Phytophthora thermophila and P. litoralis are sister species to each other and more distantly to P. gonapodyides. Both new species are common in waterways and cause scat tered mortality within native vegetation. They are self-sterile and appear well adapted for survival in an aquatic environment and inundated soils, filling the niche occupied by P. gonapodyides and P. taxon salixsoil in the northern hemisphere. Currently the origin of these new taxa, their pathogenicity and their role in natural ecosystems are unknown. Following the precautionary principle, they should be regarded as a potential threat to native ecosystems and managed to minimise their further spread.

}, issn = {00315850}, doi = {10.3767/003158511X557577}, url = {http://www.ingentaconnect.com/content/nhn/pimj/2011/00000026/00000001/art00002}, author = {Jung, T. and Stukely, M.J.C. and Hardy, G.E.St.J. and White, D. and Paap, T. and Dunstan, W.A. and Burgess, T.I.} } @article {Jung:2011:0031-5850:13, title = {Multiple new Phytophthora species from ITS Clade 6 associated with natural ecosystems in Australia: evolutionary and ecological implications}, journal = {Persoonia - Molecular Phylogeny and Evolution of Fungi}, volume = {26}, number = {1}, year = {2011}, pages = {13-39}, abstract = {

During surveys of dying vegetation in natural ecosystems and associated waterways in Australia many new taxa have been identified from Phytophthora ITS Clade 6. For representative isolates, the region spanning the internal transcribed spacer region of the ribosomal DNA, the nuclear gene encoding heat shock protein 90 and the mitochondrial cox 1 gene were PCR amplified and sequenced. Based on phylogenetic analysis and morphological and physiological comparison, four species and one informally designated taxon have been described; Phytophthora gibbosa, P. gregata, P. litoralis, P. thermophila and P. taxon paludosa. Phytophthora gibbosa, P. gregata and P. taxon paludosa form a new cluster and share a common ancestor; they are homothallic and generally associated with dying vegetation in swampy or water-logged areas. Phytophthora thermophila and P. litoralis are sister species to each other and more distantly to P. gonapodyides. Both new species are common in waterways and cause scat tered mortality within native vegetation. They are self-sterile and appear well adapted for survival in an aquatic environment and inundated soils, filling the niche occupied by P. gonapodyides and P. taxon salixsoil in the northern hemisphere. Currently the origin of these new taxa, their pathogenicity and their role in natural ecosystems are unknown. Following the precautionary principle, they should be regarded as a potential threat to native ecosystems and managed to minimise their further spread.

}, doi = {doi:10.3767/003158511X557577}, url = {http://www.ingentaconnect.com/content/nhn/pimj/2011/00000026/00000001/art00002}, author = {T. Jung and Stukely, M. J. C. and Hardy, G.E.S.t.J. and White, D. and Paap, T. and Dunstan, W.A. and Burgess, T. I.} } @article {4486, title = {Multiplex detection and identification of Phytophthora spp.~using target-specific primer extension and Luminex xTAG technology}, journal = {Plant Pathology}, volume = {65}, year = {2016}, month = {Jan-08-2016}, pages = {1008 - 1021}, abstract = {

There are more than 100 species that belong to the fungus-like genus Phytophthora, many of which can cause severe damage to plants in both natural and agricultural ecosystems. The availability of techniques for detection and identification are crucial for monitoring and control of these pathogens. In recent years, new methods using molecular approaches have been developed. However, the majority of them are designed to detect single Phytophthora species. Techniques that are able to target multiple species in one sample would offer advantages, especially for the assessment of Phytophthora diversity in the environment. This paper describes a multiplex assay for simultaneous detection and identification of 26 members of Phytophthora down to species level and another 22 to clade or subclade level through target-specific primer extension (TSPE) and the Luminex xTAG array detection system. The assay starts with PCR amplification of two genomic regions, ITS and coxI, followed by a multiplex TSPE reaction with clade-, subclade- and species-specific probes. As a result, biotin-dCTP labelled products are generated and subsequently detected through hybridization with a set of anti-TAG coupled, colour-coded paramagnetic beads. The specificity of the method has been tested using DNA extracts from over 400 isolates representing 110 Phytophthora species and subspecies. The sensitivity and robustness have been determined by the use of DNA mixtures, dilution series and environmental samples. Thus the developed technique allows simultaneous identification of multiple Phytophthora species, particularly useful for the detection of these pathogens in environmental samples such as soil, water and plant tissue.

}, doi = {10.1111/ppa.2016.65.issue-610.1111/ppa.12481}, url = {http://doi.wiley.com/10.1111/ppa.2016.65.issue-6http://doi.wiley.com/10.1111/ppa.12481http://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111\%2Fppa.12481}, author = {Kostov, K. and Verstappen, E. C. P. and Bergervoet, J. H. W. and De Weerdt, M. and Schoen, C. D. and Slavov, S. and Bonants, P. J. M.} } @article {springerlink:10.1007/s10342-011-0503-7, title = {Modelling Phytophthora disease risk in Austrocedrus chilensis forests of Patagonia}, journal = {European Journal of Forest Research}, year = {2011}, note = {10.1007/s10342-011-0503-7}, pages = {1-15}, publisher = {Springer Berlin / Heidelberg}, abstract = {

Austrocedrus chilensis forests suffer from a disease caused by Phytophthora austrocedrae, which is found often in wet soils. We applied three widely used modelling techniques, with different data requirements, to model disease potential distribution under current environmental conditions: Mahalanobis distance, Maxent and Logistic regression. Each model was built using field data of health condition and landscape layers of environmental conditions (distance to streams, slope, aspect, elevation, mean annual precipitation and soil pH NaF). We compared model predictions by area under the receiver operating characteristic curve and Kappa statistics. A reasonable ability to predict observed disease distribution was found for each of the three modelling techniques. However, Maxent and Logistic regression presented the best predictive performance, with significant differences with respect to the Mahalanobis distance model. Our results suggested that if good absence data are available, Logistic regression should be used in order to better discriminate sites with high risk of disease. On the other hand, if absence data are not available or doubtful, Maxent could be a very good option. The three models predicted that around 50\% (49{\textendash}56\%) of the currently asymptomatic forests are located on sites at risk of disease according to abiotic factors. Most of these asymptomatic forests surround the current diseased patches, at distances lower than 100 m from diseased patches. Management considerations and the scope of future studies were discussed in this article.

}, issn = {1612-4669}, url = {http://dx.doi.org/10.1007/s10342-011-0503-7}, author = {La Manna, L. and Matteucci, S. and T. Kitzberger} } @article {4246, title = {The Microscopic Examination of Phytophthora cinnamomi in Plant Tissues Using Fluorescent In Situ Hybridization}, journal = {Journal of Phytopathology}, volume = {162}, year = {2014}, month = {12/2014}, pages = {747 - 757}, abstract = {

The microscopic examination of Phytophthora cinnamomi in plant tissues is often difficult as structures such as hyphae, chlamydospores and oospores are frequently indistinguishable from those of other fungi and oomycetes, with histological stains not enabling species differentiation. This lack of staining specificity makes the localization of P.\ cinnamomi hyphae and reproductive structures within plant tissues difficult, especially in woody tissues. This study demonstrates that with the use of a species-specific fluorescently labelled DNA probe, P.\ cinnamomi can be specifically detected and visualized directly using fluorescent in situ hybridization (FISH) without damage to plant or pathogen cell integrity or the need for subculturing. This approach provides a new application for FISH with potential use in the detailed study of plant{\textendash}pathogen interactions in plants.

}, doi = {10.1111/jph.2014.162.issue-11-1210.1111/jph.12257}, url = {http://doi.wiley.com/10.1111/jph.2014.162.issue-11-12http://doi.wiley.com/10.1111/jph.12257}, author = {Li, Andrew Y. and Crone, Michael and Adams, Peter J. and Fenwick, Stanley G. and Hardy, Giles E. S. J. and Williams, Nari} } @article {269, title = {Modelling the influence of winter frosts on the development of the stem canker of red oak, caused by Phytophthora cinnamomi.}, journal = {Annales des Sciences Forestiere}, volume = {53}, year = {1996}, pages = {369-382}, doi = {DOI: 10.1051/forest:19960219}, url = {http://dx.doi.org/10.1051/forest:19960219}, author = {Mar{\c c}ais, B. and Dupuis, F. and Desprez-Loustau, M.L.} } @article {1297, title = {Molecular detection of Phytophthora ramorum, the causal agent of sudden oak death in California, and two additional species commonly recovered from diseased plant material}, journal = {Phytopathology}, volume = {94}, year = {2004}, pages = {621-631}, 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 ≈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.

}, url = {http://dx.doi.org/10.1094/PHYTO.2004.94.6.621}, author = {Martin, Frank N. and Tooley, Paul W. and Cheryl Blomquist} } @article {Mfegue01092012, title = {Microsatellite markers for population studies of Phytophthora megakarya (Pythiaceae), a cacao pathogen in Africa}, journal = {American Journal of Botany}, volume = {99}, year = {2012}, pages = {e353-e356}, abstract = {

{\quotesinglbase}{\"A}{\textcent} Premise of the study: Phytophthora megakarya is the agent of black pod disease of cacao and is the main pathogen of this crop in Africa. Population genetic studies are required to investigate how this pathogen emerged. To this end, we developed 12 novel polymorphic microsatellite markers for P. megakarya.{\quotesinglbase}{\"A}{\textcent} Methods and Results: Microsatellite sequences were obtained by pyrosequencing of multiplex-enriched libraries. Candidate loci with di- or trinucleotide motifs were selected, and primer pairs were tested with nine P. megakarya isolates. The 12 most polymorphic and unambiguous loci were selected to develop three multiplex PCR pools. The total number of alleles varied from two to nine, depending on loci, and higher than expected heterozygosity was observed.{\quotesinglbase}{\"A}{\textcent} Conclusions: These markers were used for population genetic studies of P. megakarya in Cameroon and for comparison with reference strains from West Africa. This is the first time that microsatellite markers have been developed for P. megakarya.

}, doi = {10.3732/ajb.1200053}, url = {http://www.amjbot.org/content/early/2012/08/29/ajb.1200053.abstract}, author = {Mfegue, C. V. and Herail, C. and Adreit, H. and Mbenoun, M. and Techou, Z. and Ten Hoopen, M. and Tharreau, D. and Ducamp, M.} } @article {4635, title = {Multiple alien Phytophthora taxa discovered on diseased ornamental plants in Spain}, journal = {Plant Pathology}, volume = {58}, year = {2009}, month = {Jan-02-2009}, pages = {100 - 110}, abstract = {

The plant trade is unwittingly accelerating the worldwide spread of well-known and new or undescribed Phytophthora species and creating novel niches for emerging pathogens. The results of a survey carried out from 2001 to 2006 in garden centres and nurseries of the Balearic Islands and eastern Spain combined with the analysis of samples received from ornamental nurseries from northern Spain reflected the extent of this global issue at the local scale. A total of 125 Phytophthora isolates were obtained from 37 different host species and 17 putative species identified on morphological features and direct sequencing of the internal transcribed spacer and four mitochondrial and nuclear genes. Five species, P. ramorum, P. hedraiandra, P. {\textquoteleft}niederhauserii{\textquoteright}, P. {\textquoteleft}kelmania{\textquoteright} and P. {\textquoteleft}taxon Pgchlamydo{\textquoteright} were formally unknown to science prior to 2001. In addition, 37 new host/pathogen combinations were first records for Spain, highlighting the risk of non-coevolved organisms from different biogeographic origins coming into contact under managed environments. The problem generated by new or rare taxa of Phytophthora found in nurseries for which no prior information on natural habitat and ecology is available for pest risk analysis is discussed.

}, issn = {00320862}, doi = {10.1111/j.1365-3059.2008.01930.x}, url = {http://doi.wiley.com/10.1111/j.1365-3059.2008.01930.x}, author = {Moralejo, E. and P{\'e}rez-Sierra, A. M. and {\'A}lvarez, L. A. and Belbahri, L. and Lefort, F. and Descals, E.} } @article {PPA:PPA2638, title = {The morphology, behaviour and molecular phylogeny of Phytophthora taxon Salixsoil and its redesignation as Phytophthora lacustris sp. nov.}, journal = {Plant Pathology}, year = {2012}, month = {04/2013}, pages = {355{\textendash}369}, publisher = {Blackwell Publishing Ltd}, abstract = {

Since its first isolation from Salix roots in 1972, isolates of a sexually sterile Phytophthora species have been obtained frequently from wet or riparian habitats worldwide and have also been isolated from roots of Alnus and Prunus spp. Although originally assigned to Phytophthora gonapodyides on morphological grounds, it was recognized that these isolates, informally named P.\ taxon Salixsoil, might represent a separate lineage within ITS Clade 6. Based on phylogenetic analyses and comparisons of morphology, growth-temperature relationships and pathogenicity, this taxon is formally described here as Phytophthora lacustris sp. nov. Isolates of P.\ lacustris form a clearly resolved cluster in both ITS and mitochondrial cox1 phylogenies, basal to most other Clade 6 taxa. Phytophthora lacustris shares several unusual behavioural properties with other aquatic Clade 6 species, such as sexual sterility and tolerance of high temperatures, that have been suggested as adaptations to riparian conditions. It appears to be widespread in Europe and has also been detected in Australia, New Zealand and the USA. It was shown to be weakly or moderately aggressive on inoculation to Alnus, Prunus and Salix. The extent of P.\ lacustris{\textquoteright} activity as a saprotroph in plant debris in water and as an opportunistic pathogen in riparian habitats needs further investigation. Its pathogenic potential to cultivated fruit trees also deserves attention because P.\ lacustris has apparently been introduced into the nursery trade.

}, keywords = {Alnus, phylogeny, Phytophthora ITS Clade 6, Prunus, riparian habitat, tree pathogen}, issn = {1365-3059}, doi = {10.1111/j.1365-3059.2012.02638.x}, url = {http://dx.doi.org/10.1111/j.1365-3059.2012.02638.x}, author = {Nechwatal, J. and Bakonyi, J. and Cacciola, S. O. and Cooke, D. E. L. and T. Jung and Nagy, Z. {\'A}. and Vannini, {\'A}. and A.M. Vettraino and C.M. Brasier} } @article {4137, title = {Management of black pod disease of cocoa with reduced number of fungicide application and crop sanitation}, journal = {African Journal of Agricultural Research }, volume = {2}, year = {2007}, pages = {601{\textendash}604}, abstract = {

Black pod disease caused by Phytophthora megakarya is the most important fungal disease on cocoa in Ghana. The current recommended control method of combining sanitation practices with 6 - 8 fungicide applications in a year is considered unfriendly to the environment, too expensive and time consuming. Consequently, fungicide adoption rate by farmers is extremely low. Studies were therefore conducted to determine the effectiveness of combining 1 - 3 fungicide application in June and/or September/October with crop sanitation for the control of cocoa black pod disease caused by P. megakarya. Sanitation practices were common to all the treatments and the fungicide application(s) superimposed. A semi-systemic fungicide, Ridomil 72 plus (12\% metalaxyl + 60\% copper-1-oxide), was used as the test fungicide. Fungicide application combined with crop sanitation practices were effective in the management of the severe form of black pod disease caused by P. megakarya, resulting in 25\% to 48\% disease reduction and 10.9\% to 51.8\% yield increase. Combining the sanitation practices with three fungicide applications gave significantly better results, in terms of disease control and yields than either sanitation practices alone or combining them with one or two fungicide applications. However, the combination of sanitation practices and three fungicide applications was significantly less effective than the standard fungicide application of six times a year. All the fungicide applications and/or crop sanitation practices were profitable with a Benefit Cost Ratio (BCR) ranging from 1.8 - 2.1.

}, url = {http://www.academicjournals.org/article/article1380898856_Opoku\%20et\%20al.pdf}, author = {OpokuI, Y and Assuah, MK and Aneani, F} } @article {4662, title = {A microsatellite analysis identifies global pathways of movement of Phytophthora cinnamomi and the likely sources of wildland infestations in California and Mexico}, journal = {Phytopathology}, year = {2019}, month = {Jun-05-2019}, abstract = {

The genetic structure of a sample of isolates of the oomycete plant pathogen Phytophthora cinnamomi from natural and agricultural outbreaks, and the long-distance movement of individual genotypes, were studied using four microsatellite markers genotyped for 159 isolates of Californian, Mexican, and worldwide origin. Allelic profiles identified 75 multilocus genotypes; STRUCTURE analysis placed them in three groups characterized by different geographic and host ranges, different genic and genotypic diversity, and different reproductive modes. When relationships among genotypes were visualized on a minimum spanning network (MSN), genotypes belonging to the same STRUCTURE group were contiguous with rare exceptions. A putatively ancestral Group 1 has high genic diversity, includes all A1 mating type isolates and all Papuan isolates in the sample, was rarely isolated from natural settings in California and Mexico, and was positioned at the center of the MSN. Putatively younger Groups 2 and 3 had lower genic diversity, were both neighbors to Group 1 but formed two distinct peripherical sectors of the MSN, and were equally present in agricultural commodities and natural settings in Mexico and California. A few genotypes, especially in Group 2 and 3, were isolated multiple times in different locations and settings. The presence of identical genotypes from the same hosts in different continents indicates that long-distance human-mediated movement of P. cinnamomi has occurred. The presence of identical genotypes at high frequency in neighboring wildlands and agricultural settings suggests that specific commodities may have been the source of recent wild infestations caused by novel invasive genotypes.

}, issn = {0031-949X}, doi = {10.1094/PHYTO-03-19-0102-R}, url = {https://apsjournals.apsnet.org/doi/10.1094/PHYTO-03-19-0102-R}, author = {Serrano, Maria S and Osmundson, Todd and Almaraz-Sanchez, Alejandra and Croucher, Peter JP and Swiecki, Ted and Alvarado, Dionisio and Garbelotto, Matteo} } @proceedings {682, title = {Management of P. kernoviae and P. ramorum in southwest England.}, volume = {General Technical Report PSW-GTR-221}, year = {2009}, pages = {177-183}, publisher = {U.S. Department of Agriculture, Forest Service Pacific Southwest Research Station}, address = {Monterey, California}, author = {Webber,Joan}, editor = {Goheen, E. M. and Susan J. Frankel} } @article {518341320011001, title = {Molecular diagnosis of Phytophthora lateralis in trees, water, and foliage baits using multiplex polymerase chain reaction.}, journal = {Forest Pathology}, volume = {31}, number = {5}, year = {2001}, pages = {275 - 283}, abstract = {

A polymerase chain reaction (PCR)-based protocol for detection of Phytophthora lateralis in plant tissues and water is described. Base-pair (bp) deletions in both of the ribosomal DNA internal transcribed spacer (ITS) regions in P. lateralis were used to design complementary PCR primer sequences that amplify a 738 bp fragment only if P. lateralis DNA is present in the sample. Universal control primers based on conserved sequences of the nuclear ribosomal small subunit are included in a multiplexed reaction, providing an internal check on the procedure. The universal primers amplify an approximately 550 bp fragment that is common to plants, protists, and true fungi. The procedure reliably detects P. lateralis in cedar stem tissues and in roots. Positive reactions were obtained with as few as 200 P. lateralis zoospores in water. (English) [ABSTRACT FROM AUTHOR]

}, keywords = {PHYTOPHTHORA diseases, PLANT diseases, polymerase chain reaction}, issn = {14374781}, doi = {10.1046/j.1439-0329.2001.00251.x}, author = {Winton, L. M. and Hansen, E.M.} }