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Rescooped by Rebecca McDougal from Phytophthora biology
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Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6  Phytophthora  Species | oomycetes | Scoop.it
Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular char

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Phytopathology Journal - 104(10):1052 - Abstract

Phytopathology Journal - 104(10):1052 - Abstract | oomycetes | Scoop.it

Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora spp. associated with different sources and stages in the nursery production cycle. Plants, potting media, used containers, water, greenhouse soil, and container yard substrates were systematically sampled from propagation to the field. From 674 Phytophthora isolates recovered, 28 different species or taxa were identified. The most commonly isolated species from plants were Phytophthora plurivora (33%), P. cinnamomi (26%), P. syringae (19%), and P. citrophthora (11%). From soil and gravel substrates, P. plurivora accounted for 25% of the isolates, with P. taxon Pgchlamydo, P. cryptogea, and P. cinnamomi accounting for 18, 17, and 15%, respectively. Five species (P. plurivora, P. syringae, P. taxon Pgchlamydo, P. gonapodyides, and P. cryptogea) were found in all nurseries. The greatest diversity of taxa occurred in irrigation water reservoirs (20 taxa), with the majority of isolates belonging to internal transcribed spacer clade 6, typically including aquatic opportunists. Nurseries differed in composition of Phytophthora communities across years, seasons, and source within the nursery. These findings suggest likely contamination hazards and target critical control points for management of Phytophthora disease using a systems approach.


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Bioinformatics Analysis Reveals Abundant Short Alpha-Helices as a Common Structural Feature of Oomycete RxLR Effector Proteins

Bioinformatics Analysis Reveals Abundant Short Alpha-Helices as a Common Structural Feature of Oomycete RxLR Effector Proteins | oomycetes | Scoop.it
“ RxLR effectors represent one of the largest and most diverse effector families in oomycete plant pathogens. These effectors have attracted enormous attention since they can be delivered inside the plant cell and manipulates host immunity. With the exceptions of a signal peptide and the following RxLR-dEER and C-terminal W/Y/L motifs identified from the sequences themselves, nearly no functional domains have been found. Recently, protein structures of several RxLRs were revealed to comprise alph”
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Recent Progress in RXLR Effector Research — Molecular Plant-Microbe Interactions

Recent Progress in RXLR Effector Research — Molecular Plant-Microbe Interactions | oomycetes | Scoop.it

Some of the most devastating oomycete pathogens deploy effector proteins, with the signature amino acid motif RXLR, that enter plant cells to promote virulence. Research on the function and evolution of RXLR effectors has been very active over the decade that has transpired since their discovery. Comparative genomics indicate that RXLR genes play a major role in virulence for Phytophthora and downy mildew species. Importantly, gene-for-gene resistance against these oomycete lineages is based on recognition of RXLR proteins. Comparative genomics have revealed several mechanisms through which this resistance can be broken, most notably involving epigenetic control of RXLR gene expression. Structural studies have revealed a core fold that is present in the majority of RXLR proteins, providing a foundation for detailed mechanistic understanding of virulence and avirulence functions. Finally, functional studies have demonstrated that suppression of host immunity is a major function for RXLR proteins. Host protein targets are being identified in a variety of plant cell compartments. Some targets comprise hubs that are also manipulated by bacteria and fungi, thereby revealing key points of vulnerability in the plant immune network.


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Towards a universal barcode of oomycetes – a comparison of the cox1 and cox2 loci - Choi - 2015 - Molecular Ecology Resources - Wiley Online Library

Towards a universal barcode of oomycetes – a comparison of the cox1 and cox2 loci - Choi - 2015 - Molecular Ecology Resources - Wiley Online Library | oomycetes | Scoop.it

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.


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PLOS Pathogens: An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus (2013)

PLOS Pathogens: An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus (2013) | oomycetes | Scoop.it

The potato late blight pathogen Phytophthora infestans secretes an array of effector proteins thought to act in its hosts by disarming defences and promoting pathogen colonisation. However, little is known about the host targets of these effectors and how they are manipulated by the pathogen. This work describes the identification of two putative membrane-associated NAC transcription factors (TF) as the host targets of the RxLR effector PITG_03192 (Pi03192). The effector interacts with NAC Targeted by Phytophthora (NTP) 1 and NTP2 at the endoplasmic reticulum (ER) membrane, where these proteins are localised. Transcripts of NTP1 and NTP2 rapidly accumulate following treatment with culture filtrate (CF) from in vitro grown P. infestans, which acts as a mixture of Phytophthora PAMPs and elicitors, but significantly decrease during P. infestans infection, indicating that pathogen activity may prevent their up-regulation. Silencing of NTP1 or NTP2 in the model host plant Nicotiana benthamiana increases susceptibility to P. infestans, whereas silencing of Pi03192 in P. infestans reduces pathogenicity. Transient expression of Pi03192 in planta restores pathogenicity of the Pi03192-silenced line. Moreover, colonisation by the Pi03192-silenced line is significantly enhanced on N. benthamiana plants in which either NTP1 or NTP2 have been silenced. StNTP1 and StNTP2 proteins are released from the ER membrane following treatment with P. infestans CF and accumulate in the nucleus, after which they are rapidly turned over by the 26S proteasome. In contrast, treatment with the defined PAMP flg22 fails to up-regulate NTP1 and NTP2, or promote re-localisation of their protein products to the nucleus, indicating that these events follow perception of a component of CF that appears to be independent of the FLS2/flg22 pathway. Importantly, Pi03192 prevents CF-triggered re-localisation of StNTP1 and StNTP2 from the ER into the nucleus, revealing a novel effector mode-of-action to promote disease progression.


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PlantVillage: Keeping Up With The Plant Destroyers (2014)

PlantVillage: Keeping Up With The Plant Destroyers (2014) | oomycetes | Scoop.it

Readers of PlantVillage who visited popular pages like the one on tomato late blight would have come across the term “oomycetes” and probably wondered what in the world is an oomycete? It’s the taxon of microbes that groups many plant pathogens such as Phytophthora, Pythium, and the downy mildews. These are destructive pathogens of plants. Phytophthora, which stems from Greek words meaning plant-destroyer, is a diverse group of plant pathogens with over 100 species known to science . It includes the infamous Irish potato famine pathogen Phytophthora infestans. When this pathogen reached Ireland in the 1840s, it triggered famine and mayhem with one million people dead and another million forced to leave the island. Today, the late blight disease caused by P. infestans threatens not only tomatoes and potatoes in your gardens but also commercial and subsistence farming worldwide. Matt Fisher, Sarah Gurr and their colleagues recently estimated that losses due to late blight add up to enough calories to feed hundreds of millions of people.

 

So what are these oomycetes that are so feared by gardeners and farmers alike? Traditionally oomycetes were thought to be fungi (yeasts, molds and mushrooms). They are not. Modern methods of evolutionary analyses, known as phylogenetics, have cemented the view that oomycetes are only distant relatives of the fungi. In fact, fungi are more closely related to you and I than they are to the oomycetes. Oomycete biologists like to quip “bats are not birds, dolphins are not fish, and oomycetes are not fungi.” In fact, oomycetes turned out to have unexpected marine cousins in brown algae (kelp) and diatoms in a grouping known as the heterokonts. Oomycetes form a very deep branch in the tree of life and may have evolved from marine parasitic microorganisms. Just a few months ago, while I was visiting Christine Strullu-Derrien and Paul Kenrick at the Natural History Museum in London, I had the amazing opportunity to hold a fossil oomycete that is 300 million year old. Already in those ancient times, oomycetes were successful colonizers of plants and may even have been parasitic.

 

But evolution is a complicated process. More often than widely assumed, it proceeded as a reticulate network rather than a straight line. One example is the transfer of genes from one organism to another. This process, known as horizontal or lateral gene transfer, has occurred frequently in bacteria but is not as well documented in more complex organisms like oomycetes and fungi. Nonetheless, Tom Richard and colleagues at Exeter University reported that oomycetes have at some point in their evolution acquired genes from fungi. Whether this took place hundreds million years ago or more recently is not yet resolved. But as Tom likes to say “oomycetes are 99% not fungi”. How this phenomenon has contributed to the evolution of oomycetes into destructive plant pathogens is an interesting research topic.

 

But why all the misery? Why are oomycetes the scourge of farmers worldwide? The truth is, although Phytophthora are astonishing plant killers that can wipe out crops in days, the secret of their success is their ability to rapidly adapt to resistant plant varieties. Just like the constantly morphing flu virus, the potato blight pathogen and its relatives continuously spawn new races adapted to the resistant varieties released by plant breeders and even occasionally to new host plants. Like Lewis Carroll’s fictional Red Queen, plant breeders and biotechnologists only hope is to strenuously run to keep in the same place. If only we could produce resistant varieties more often then perhaps we’ll have a chance to outrace the ever-evolving blight pathogen.

 

So while you lament your blighted potatoes and your dying tomatoes, take a moment to ponder over the awesome parasite that’s making your vegetable garden look so gloomy. That microbe has already colonized plants way before humans emerged on earth. And for hundreds of millions of years it has kept on changing, evolving, and adapting ensuring its uninterrupted survival on an astonishing array of plant species and varieties. When humans domesticated plants, it could not resist the offering and adopted the crops as its new hosts. Ultimately, it moved to new continents and farmlands causing misery and despair. But we haven’t given up. Plant pathologists are hard at work learning more about these parasites and applying new knowledge and technologies to build disease-resistant crops.


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Molecular Cellular Proteomics: Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans (2014)

Molecular Cellular Proteomics: Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans (2014) | oomycetes | Scoop.it

Oomycetes are filamentous organisms that cause notorious diseases, several of which have a high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focussed on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyse P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.


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Phytophthora spp. associated with forest soils in eastern and north-central U.S. oak ecosystems

Phytophthora spp. associated with forest soils in eastern and north-central U.S. oak ecosystems http://t.co/1Rzop2oK31
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California's iconic redwoods in danger from fire and infectious disease - US National Science Foundation (NSF)

California's iconic redwoods in danger from fire and infectious disease - US National Science Foundation (NSF) | oomycetes | Scoop.it

First it was sudden oak death, the oak disease caused by the plant pathogen Phytophthora ramorum that threatened California's extensive coastal forests.

 

Now these forests' stately trees are facing a new menace: the combined effects of sudden oak death and fire. And this time, the iconic redwoods are at risk.

 

Usually resistant to the effects of wildfires, California's coast redwoods are now burning as fast as other trees. Why?


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Mary Williams's curator insight, August 21, 2013 4:48 PM

Noooo - one of my favorite trees, I was born very close to a coastal redwood grove!

Rescooped by Rebecca McDougal from Phytophthora biology
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Phytopathology: Evolution, Diversity, and Taxonomy of the Peronosporaceae, with Focus on the Genus Peronospora (2016)

Phytopathology: Evolution, Diversity, and Taxonomy of the Peronosporaceae, with Focus on the Genus Peronospora (2016) | oomycetes | Scoop.it

Downy mildews are a notorious group of oomycete plant pathogens, causing high economic losses in various crops and ornamentals. The most species-rich genus of oomycetes is the genus Peronospora. This review provides a wide overview of these pathogens, ranging from macro- and micro-evolutionary patterns, their biodiversity and ecology to short overviews for the currently economically most important pathogens and potential emerging diseases. In this overview, the taxonomy of economically relevant species is also discussed, as the application of the correct names and species concepts is a prerequisite for effective quarantine regulations and phytosanitary measures.


Via Kamoun Lab @ TSL, Niklaus Grunwald
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Spatial and Temporal Analysis of Populations of the Sudden Oak Death Pathogen in Oregon Forests

Spatial and Temporal Analysis of Populations of the Sudden Oak Death Pathogen in Oregon Forests | oomycetes | Scoop.it

Sudden oak death caused by the oomycete Phytophthora ramorum was first discovered in California toward the end of the 20th century and subsequently emerged on tanoak forests in Oregon before its first detection in 2001 by aerial surveys. The Oregon Department of Forestry has since monitored the epidemic and sampled symptomatic tanoak trees from 2001 to the present. Populations sampled over this period were genotyped using microsatellites and studied to infer the population genetic history. To date, only the NA1 clonal lineage is established in this region, although three lineages exist on the North American west coast. The original introduction into the Joe Hall area eventually spread to several regions: mostly north but also east and southwest. A new introduction into Hunter Creek appears to correspond to a second introduction not clustering with the early introduction. Our data are best explained by both introductions originating from nursery populations in California or Oregon and resulting from two distinct introduction events. Continued vigilance and eradication of nursery populations of P. ramorum are important to avoid further emergence and potential introduction of other clonal lineages.


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bioRxiv: Successful asexual lineages of the Irish potato Famine pathogen are triploid (2015)

bioRxiv: Successful asexual lineages of the Irish potato Famine pathogen are triploid (2015) | oomycetes | Scoop.it

The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually and has a potential to adapt both abiotic and biotic environment. Although in many regions the A1 and A2 mating types coexist, the far majority of isolates belong to few clonal, asexual lineages. As other oomycetes, P. infestans is thought to be diploid during the vegetative phase of its life cycle, but it was observed that trisomy correlated with virulence and mating type locus and that polyploidy can occur in some isolates. It remains unknown about the frequency of polyploidy occurrence in nature and the relationship between ploidy level and sexuality. Here we discovered that the sexuality of P. infestans isolates correlates with ploidy by comparison of microsatellite fingerprinting, genome-wide polymorphism, DNA quantity, and chromosome numbers. The sexual progeny of P. infestans in nature are diploid, whereas the asexual lineages are mostly triploids, including successful clonal lineages US-1 and 13_A2. This study reveals polyploidization as an extra evolutionary risk to this notorious plant destroyer.


Via Kamoun Lab @ TSL, Niklaus Grunwald
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Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries — Plant Disease

Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries — Plant Disease | oomycetes | Scoop.it

The genus Phytophthora contains some of the most notorious plant pathogens affecting nursery crops. Given the recent emergence of the sudden oak death pathogen Phytophthora ramorum, particularly in association with Rhododendron spp., characterization of Phytophthora communities associated with this host in nursery environments is prudent. Many taxa may present symptoms similar to P. ramorum but we do not necessarily know their identity, frequency, and importance. Here, we present a survey of Phytophthora taxa observed from seven nurseries in the U.S. state of Oregon. Incidence and diversity of Phytophthora communities differed significantly among nurseries and among seasons within nursery. The taxa P. syringae and P. plurivora were widespread and detected at most of the nurseries sampled. Nine other taxa were also detected but were found either in a single nursery or were shared among only a few nurseries. Characterization of the Phytophthora communities present in nurseries is an important step toward understanding the ecology of these organisms as well as an aid to nursery managers in determining what risks may be present when symptomatic plants are observed. This study builds on an increasing literature, which characterizes Phytophthora community structure in nurseries.


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An Ephemeral Sexual Population of Phytophthora infestans in the Northeastern United States and Canada

Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50:50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified.


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New Phytologist: The Phytophthora parasitica RXLR effector Penetration-Specific Effector 1 favours Arabidopsis thaliana infection by interfering with auxin physiology (2013)

New Phytologist: The Phytophthora parasitica RXLR effector Penetration-Specific Effector 1 favours Arabidopsis thaliana infection by interfering with auxin physiology (2013) | oomycetes | Scoop.it

Pathogenic oomycetes have evolved RXLR effectors to thwart plant defense mechanisms and invade host tissues. We analysed the function of one of these effectors (Penetration-Specific Effector 1 (PSE1)) whose transcript is transiently accumulated during penetration of host roots by the oomycete Phytophthora parasitica.Expression of PSE1 protein in tobacco (Nicotiana tabacum and Nicotiana benthamiana) leaves and in Arabidopsis thaliana plants was used to assess the role of this effector in plant physiology and in interactions with pathogens. A pharmacological approach and marker lines were used to charcterize the A. thaliana phenotypes.Expression of PSE1 in A. thaliana led to developmental perturbations associated with low concentrations of auxin at the root apex. This modification of auxin content was associated with an altered distribution of the PIN4 and PIN7 auxin efflux carriers. The PSE1 protein facilitated plant infection: it suppressed plant cell death activated by Pseudomonas syringae avirulence gene AvrPto andPhytophthora cryptogea elicitin cryptogein in tobacco and exacerbated disease symptoms upon inoculation of transgenic A. thalianaplantlets with P. parasitica in an auxin-dependant manner.We propose that P. parasitica secretes the PSE1 protein during the penetration process to favour the infection by locally modulating the auxin content. These results support the hypothesis that effectors from plant pathogens may act on a limited set of targets, including hormones.


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Molecular Plant Pathology: The Top 10 oomycete pathogens in molecular plant pathology (2014)

Molecular Plant Pathology: The Top 10 oomycete pathogens in molecular plant pathology (2014) | oomycetes | Scoop.it

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens that threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. The article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

 

See also [link below]:

 

Top 10 plant-parasitic nematodes in molecular plant pathology
Top 10 plant viruses in molecular plant pathology
Top 10 plant pathogenic bacteria in molecular plant pathology
The Top 10 fungal pathogens in molecular plant pathology

 

http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1364-3703/homepage/free_poster.htm


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European Journal of Plant Pathology: Phylogeny and evolution of plant pathogenic oomycetes - a global overview (2014)

European Journal of Plant Pathology: Phylogeny and evolution of plant pathogenic oomycetes - a global overview (2014) | oomycetes | Scoop.it

Oomycetes have colonised all continents and oceans in a great variety of habitats and are arguably one of the most successful eukaryotic lineages. This is contrasted by the limited knowledge available for this group in various fields in comparison to other ubiquitous eukaryotes, such as unikont fungi, animals or plants. In this review an overview is given on the evolution and diversification of the oomycetes, with focus on the plant parasitic lineages and aspects of wild pathosystems.


Via Kamoun Lab @ TSL, David Studholme
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PLOS ONE: RNA-Seq Reveals Infection-Related Gen...

PLOS ONE: RNA-Seq Reveals Infection-Related Gen... | oomycetes | Scoop.it
Phytophthora capsici is a soilborne plant pathogen capable of infecting a wide range of plants, including many solanaceous crops. However, genetic resistance and fungicides often fail to manage P.
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