plant pathology
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Rescooped by Rebecca McDougal from Plants and Microbes
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Molecular Plant Pathology: Are lichens potential natural reservoirs for plant pathogens? (2016)

Molecular Plant Pathology: Are lichens potential natural reservoirs for plant pathogens? (2016) | plant pathology | Scoop.it

Most ecological studies on plant-pathogenic bacteria have focused, perhaps understandably, on the agricultural environment. Interest is increasing, however, in the occurrence of plantpathogenic bacteria in habitats outside of agriculture. The seminal work by Morris et al. (2008), for instance, has shown that Pseudomonas syringae occupies a wide range of niches linked with the water cycle, including alpine lakes, streams and snow. Moreover, it is becoming clear that traits that are linked to adaptation to biotic and abiotic stress in the non-agricultural environment can have a secondary function as virulence factors in plants (Morris et al., 2009). Indeed, adaptation to non-host environments has been suggested to have played a non-trivial role in the evolution of P. syringae phytopathogenicity and


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Molecular Plant Pathology: Plant hormones: A fungal point of view (2016)

Molecular Plant Pathology: Plant hormones: A fungal point of view (2016) | plant pathology | Scoop.it

Most classical plant hormones are also produced by pathogenic and symbiotic fungi. The way these molecules favor the invasion of plant tissues and the development of fungi inside plant tissues is still largely unknown. In this review, we examine the different roles of such hormone production by pathogenic fungi. Converging evidence suggest that these fungal-derived molecules have potentially two modes of action: (i) they may perturb plant processes, either positively or negatively, to favor invasion and nutrient uptake and (ii) they may also act as signals for the fungi themselves to engage appropriate developmental and physiological processes adapted to their environment. Indirect evidences suggest that abscisic acid, gibberellic acid and ethylene produced by fungi participate to pathogenicity. There is now evidence that auxin and cytokinins could be positive regulators required for virulence. Further research should establish whether or not fungal-derived hormones act like other fungal effectors. This article is protected by copyright. All rights reserved.


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Plant Physiology and Biochemistry: Reactive Oxygen Species, essential molecules, during plant-pathogen interactions (2016)

Plant Physiology and Biochemistry: Reactive Oxygen Species, essential molecules, during plant-pathogen interactions (2016) | plant pathology | Scoop.it

• Description on the best characterized enzymatic systems as NAD(P)H oxidase and apoplastic peroxidases and oxidases involving in the Reactive Oxygen Species (ROS) generation.


• ROS as essential molecule during plant-pathogen interactions.


• We described how the plant perceive the pathogen invasion and trigger resistance response using ROS as signal molecule.


Reactive oxygen species (ROS) are continually generated as a consequence of the normal metabolism in aerobic organisms. Accumulation and release of ROS into cell take place in response to a wide variety of adverse environmental conditions including salt, temperature, cold stresses and pathogen attack, among others. In plants, peroxidases class III, NADPH oxidase (NOX) locates in cell wall and plasma membrane, respectively, may be mainly enzymatic systems involving ROS generation. It is well documented that ROS play a dual role into cells, acting as important signal transduction molecules and as toxic molecules with strong oxidant power, however some aspects related to its function during plant-pathogen interactions remain unclear. This review focuses on the principal enzymatic systems involving ROS generation addressing the role of ROS as signal molecules during plant-pathogen interactions. We described how the chloroplasts, mitochondria and peroxisomes perceive the external stimuli as pathogen invasion, and trigger resistance response using ROS as signal molecule.


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Rakesh Yashroy's curator insight, February 29, 9:13 PM

Host-pathogen interface is a very important realm of health and disease @ https://en.wikipedia.org/wiki/Host-pathogen_interface

Rescooped by Rebecca McDougal from fungi bacteria publications
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi | plant pathology | Scoop.it

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.

Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353


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New insight into a complex plant-fungal pathogen interaction : Nature Genetics : Nature Publishing Group

New insight into a complex plant-fungal pathogen interaction : Nature Genetics : Nature Publishing Group | plant pathology | Scoop.it
“ The coevolution of plants and microbes has shaped plant mechanisms that detect and repel pathogens. A newly identified plant gene confers partial resistance to a fungal pathogen not by preventing initial infection but by limiting its spread through the plant.”
Via Niklaus Grunwald
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Eric Larson's curator insight, December 29, 2015 7:36 AM

Interesting insight.

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Functional overlap of the Arabidopsis leaf and root microbiota : Nature : Nature Publishing Group

Functional overlap of the Arabidopsis leaf and root microbiota : Nature : Nature Publishing Group | plant pathology | Scoop.it

Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsisleaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiota. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf- and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization. While this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche.


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eLIFE: Active invasion of bacteria into living fungal cells

eLIFE: Active invasion of bacteria into living fungal cells | plant pathology | Scoop.it

The rice seedling blight fungus Rhizopus microsporus and its endosymbiont Burkholderia rhizoxinica form an unusual, highly specific alliance to produce the highly potent antimitotic phytotoxin rhizoxin. Yet, it has remained a riddle how bacteria invade into the fungal cells. Genome mining for potential symbiosis factors and functional analyses revealed that a type 2 secretion system (T2SS) of the bacterial endosymbiont is required for the formation of the endosymbiosis. Comparative proteome analyses show that the T2SS releases chitinolytic enzymes (chitinase, chitosanase) and chitin-binding proteins. The genes responsible for chitinolytic proteins and T2SS components are highly expressed during infection. Through targeted gene knock-outs, sporulation assays and microscopic investigations we found that chitinase is essential for bacteria to enter hyphae. Unprecedented snapshots of the traceless bacterial intrusion were obtained using cryo-electron microscopy. Beyond unveiling the pivotal role of chitinolytic enzymes in the active invasion of a fungus by bacteria, these findings grant unprecedented insight into the fungal cell wall penetration and symbiosis formation.


Via Stéphane Hacquard, Francis Martin
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Transcription Activator-like Effectors: A Toolkit for Synthetic Biology - ACS Synth. Biol.

Transcription Activator-like Effectors: A Toolkit for Synthetic Biology - ACS Synth. Biol. | plant pathology | Scoop.it

(via T. Lahaye, thx)

Moore et al, 2014

Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species. TALEs assist infections by binding to specific DNA sequences and activating the expression of host genes. Recent results show that TALE proteins consist of a central repeat domain, which determines the DNA targeting specificity and can be rapidly synthesized de novo. Considering the highly modular nature of TALEs, their versatility, and the ease of constructing these proteins, this technology can have important implications for synthetic biology applications. Here, we review developments in the area with a particular focus on modifications for custom and controllable gene regulation.


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dromius's curator insight, March 13, 2014 4:30 AM

Table 2 gives an overview over assembly methods and their required time effort.

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Strategies of attack and defence in woody plant–Phytophthora interactions

Strategies of attack and defence in woody plant–Phytophthora interactions | plant pathology | Scoop.it

This review comprises both well-known and recently described Phytophthora species and concentrates on Phytophthora–woody plant interactions. First, comprehensive data on infection strategies are presented which were the basis for three models that explain invasion and spread of Phytophthora pathogens in different woody host plants. The first model describes infection of roots, the second concentrates on invasion of the trunk, and the last one summarizes infection and invasion of host plants via leaves. On the basis of morphological, physiological, biochemical and molecular data, scenarios are suggested which explain the sequences of reactions that occur in susceptible and tolerant plants following infections of roots or of stem bark. Particular emphasis is paid to the significance ofPhytophthora elicitins for such host–pathogen interactions. The overall goal is to shed light on the sequences of pathogenesis to better understand how Phytophthora pathogens harm their host plants.


Via Alejandro Rojas, David Studholme, Richard Hamelin
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Nari Williams's curator insight, July 8, 2014 5:39 PM

Great paper and a must read for all of us working in Phytophthora-tree interactions.

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The cryptic sexual strategies of human fungal pathogens : Nature Reviews

The cryptic sexual strategies of human fungal pathogens : Nature Reviews | plant pathology | Scoop.it

Sexual reproduction is a pervasive attribute of eukaryotic species and is now recognized to occur in many clinically important human fungal pathogens. These fungi use sexual or parasexual strategies for various purposes that can have an impact on pathogenesis, such as the formation of drug-resistant isolates, the generation of strains with increased virulence or the modulation of interactions with host cells. In this Review, we examine the mechanisms regulating fungal sex and the consequences of these programmes for human disease.


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Rescooped by Rebecca McDougal from Plant Breeding and Genomics News
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Transcriptome profiling of Gossypium barbadense inoculated with Verticillium dahliae provides a resource for cotton improvement

Background: Verticillium wilt, caused by the fungal pathogen Verticillium dahliae, is the most severe disease in cotton (Gossypium spp.), causing great lint losses worldwide. Disease management could be achieved in the field if genetically improved, resistant plants were used. However, the interaction between V. dahliae and cotton is a complicated process, and its molecular mechanism remains obscure. To understand better the defense response to this pathogen as a means for obtaining more tolerant cultivars, we monitored the transcriptome profiles of roots from resistant plants of G. barbadense cv. Pima90-53 that were challenged with V. dahliae. Results: In all, 46,192 high-quality expressed sequence tags (ESTs) were generated from a full-length cDNA library of G. barbadense. They were clustered and assembled into 23126 unigenes that comprised 2661 contigs and 20465 singletons. Those unigenes were assigned Gene Ontology terms and mapped to 289 KEGG pathways. A total of 3027 unigenes were found to be homologous to known defense-related genes in other plants. They were assigned to the functional classification of plant--pathogen interactions, including disease defenses and signal transduction. The branch of "SA[rightwards arrow]NPR1[rightwards arrow]TGA[rightwards arrow]PR-1[rightwards arrow]Disease resistance" was first discovered in the interaction of cotton--V. dahliae, indicating that this wilt process includes both biotrophic and necrotrophic stages. In all, 4936 genes coding for putative transcription factors (TF) were identified in our library. The most abundant TF family was the NAC group (527), followed by G2-like (440), MYB (372), BHLH (331), bZIP (271) ERF, C3H, and WRKY. We also analyzed the expression of genes involved in pathogen-associated molecular pattern (PAMP) recognition, the activation of effector-triggered immunity, TFs, and hormone biosynthesis, as well as genes that are pathogenesis-related, or have roles in signaling/regulatory functions and cell wall modification. Their differential expression patterns were compared among mock-/inoculated- and resistant/susceptible cotton. Our results suggest that the cotton defense response has significant transcriptional complexity and that large accumulations of defense-related transcripts may contribute to V. dahliae resistance in cotton. Therefore, these data provide a resource for cotton improvement through molecular breeding approaches. Conclusions: This study generated a substantial amount of cotton transcript sequences that are related to defense responses against V. dahliae. These genomics resources and knowledge of important related genes contribute to our understanding of host--pathogen interactions and the defense mechanisms utilized by G. barbadense, a non-model plant system. These tools can be applied in establishing a modern breeding program that uses marker-assisted selections and oligonucleotide arrays to identify candidate genes that can be linked to valuable agronomic traits in cotton, including disease resistance.  


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Rescooped by Rebecca McDougal from of Plants & Bacteria (and sometimes other fellows too)
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First Report of Neofusicoccum australe and N. luteum Associated with Canker and Dieback of Quercus robur in Portugal

First Report of Neofusicoccum australe and N. luteum Associated with Canker and Dieback of Quercus robur in Portugal | plant pathology | Scoop.it

by: C.Barradas, A.Correia and A.Alves

 

Quercus robur L., commonly known as “pedunculate oak,” is a long-lived deciduous tree native to most of Europe. It is of great ecological and forestry importance. It is also commonly cultivated as an ornamental tree in parks and gardens. Since 2009 and most likely related to increased drought periods, diseased ornamental trees have been observed in the campus of the University of Aveiro, Portugal. More than 50% of the trees are already damaged by the disease. The symptoms included twig and branch dieback and sunken necrotic bark lesions that could progress to the trunk, resulting in the death of large sections of the tree. Ascomata and conidiomata typical of Botryosphaeriaceae were observed on branches of symptomatic trees. Ascospores were hyaline, aseptate, ovoid to fusoid, and conidia were hyaline, aseptate, smooth, thin-walled, and fusiform with base truncate. Single spore isolates were obtained from samples. In culture, single ascospore isolates produced conidia similar to the ones found on the host. Diseased branch tissues were surface sterilized with 5% NaOCl, plated on potato dextrose agar (PDA), and incubated at 25°C. Fungal isolates recovered produced white aerial mycelium that darkened with age becoming grey to dark grey and conidia that were similar in all aspects to the ones produced by single spore isolates. All isolates produced on PDA a yellow pigment that diffused into the agar and disappeared after 6 to 7 days. Morphological and cultural aspects of the isolates were similar to the species Neofusicoccum luteum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips and N. australe (Slippers, Crous & M.J. Wingf.) Crous, Slippers & A.J.L. Phillips (2). Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR fingerprinting divided the isolates into two groups (1). Two isolates (CAA352 and CAA392), one from each group, were selected for further identification by sequencing of the internal transcribed spacer (ITS) region of the rDNA and part of the elongation factor 1-alpha gene (EF1-α) (Accession No. ITS: JX975212 JX975213; EF1-α: JX975210 JX975211). BLAST analysis showed that ITS and EF1-α sequences from group 1 and 2 had 99 to 100% similarity to reference cultures (including ex-type) of N. luteum and N. australe, respectively. To confirm pathogenicity and fulfill Koch's postulates, six 2-year-old seedlings of Q. robur were artificially infected with isolates CAA352 and CAA392 and kept at approximately 20 to 25°C. A shallow wound was done with a scalpel on the basal part of the stem of each seedling, a bark portion was removed aseptically and a PDA disc (0.5 cm) of an actively growing culture was placed on the wound. Control seedlings received sterile PDA discs. The inoculation site was wrapped in Parafilm to prevent desiccation. Within 8 weeks, infected seedlings developed canker lesions associated with vascular necrosis around the inoculation point. A third of the seedlings died and developed abundant pycnidia on the stem. Control seedlings remained symptomless. Both pathogens were successfully reisolated from the infected tissue. N. luteum and N. australe are increasingly reported as causing diseases to a wide range of woody hosts of economic and forestry importance (3). To our knowledge, this is the first report of both species causing dieback and canker disease on Q. robur.


Via Freddy Monteiro
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Freddy Monteiro's curator insight, March 10, 2013 7:23 AM

Aveiro is my home-town in Portugal and I am so glad to see this disease report from a local research group. I'm looking forward getting in contact with them and get to know more about what they do.

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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild | plant pathology | Scoop.it
Fungi typically live in highly diverse communities composed of multiple ecological guilds. Although high-throughput sequencing has greatly increased the ability to quantify the diversity of fungi in environmental samples, researchers currently lack a simple and consistent way to sort large sequence pools into ecologically meaningful categories. We address this issue by introducing FUNGuild, a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline. Using a database and an accompanying bioinformatics script, we demonstrate the application of FUNGuild to three high-throughput sequencing datasets from different habitats: forest soils, grassland soils, and decomposing wood. We found that guilds characteristic of each habitat (i.e., saprotrophic and ectomycorrhizal fungi in forest soils, saprotrophic and arbuscular mycorrhizal fungi in grassland soils, saprotrophic, wood decomposer, and plant pathogenic fungi in decomposing wood) were each well represented. The example datasets demonstrate that while we could quickly and efficiently assign a large portion of the data to guilds, another large portion could not be assigned, reflecting the need to expand and improve the database as well as to gain a better understanding of natural history for many described and undescribed fungal species. As a community resource, FUNGuild is dependent on third-party annotation, so we invite researchers to populate it with new categories and records as well as refine those already in existence.

Via Alejandro Rojas, Niklaus Grunwald
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The invisible dimension of fungal diversity

The invisible dimension of fungal diversity | plant pathology | Scoop.it
Taxonomy plays a central role in understanding the diversity of life, translating the products of biological exploration and discovery—specimens and observations—into systems of names that capture the relationships between species. Taxonomic names facilitate communication among scientists and the public and provide conceptual handles for complex phylogenetic hypotheses. However, taxonomy can be challenging, particularly for fungi and other microorganisms, which are morphologically simple and extremely diverse (1). Molecular environmental surveys have revealed previously unknown branches of the fungal tree of life (2–5) and illuminated biogeographic patterns across all groups of fungi (6, 7). Yet the products of this research are not being translated into formal species names, in part because of the very rules designed to facilitate taxonomy.

Via Steve Marek, Niklaus Grunwald
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bioRxiv: A bacterial parasite effector mediates insect vector attraction in host plants independently of developmental changes (2016)

bioRxiv: A bacterial parasite effector mediates insect vector attraction in host plants independently of developmental changes (2016) | plant pathology | Scoop.it

Parasites can take over their hosts and trigger dramatic changes in host appearance and behaviour that are typically interpreted as extended phenotypes to promote parasite survival and fitness. For example, Toxoplasma gondii manipulates the behaviour of infected rodents to aid transmission to cats and parasitic trematodes of the genus Ribeiroia alter limb development in their amphibian hosts to facilitate predation by birds. Plant parasites and pathogens also reprogram host development and morphology. Phytoplasma parasites of plants induce extensive leaf-like flower phenotype (phyllody) in their host plants, presumably to attract insect vectors on which these bacteria depend for transmission. However, it remains debatable whether morphological phenotypes, such as phyllody, are directly beneficial to the parasites or are side-products of parasite infection. Previously, we found that phytoplasma virulence protein (effector) SAP54 binds and mediates degradation of host MADS-box transcription factors (MTFs), regulatory hubs of plant development and hormone physiology, to induce phyllody and promote insect vector colonisation. Here we show that plants heterologously expressing SAP54 are strongly attractive to insects, but surprisingly, insect attraction was independent of the presence of leaf-like flowers. Moreover, plants that produce leaf-like flowers in the absence of SAP54 did not attract insects. We conclude that the SAP54 effector mediates insect vector attraction in host plants by exploiting the role of its MTF targets in insect defence and that perturbation of floral development may be a secondary effect of the effector activity.


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A new species of rust fungus on the New Zealand endemic plant, Myosotidium, from the isolated Chatham Islands

Pucciniastrum myosotidii sp. nov. is described from plants of the Chatham Island forget-me-not (Myosotidium hortensium), a host plant that has a conservation status of “nationally endangered”. The rust has been found only on cultivated plants and not on wild plants. Although no teliospores were found, LSU and SSU sequence analysis showed that the new rust is closely related to some species of Pucciniastrum and Thekopsora forming a weakly supported clade together with P. boehmeriae, P. epilobii, P. ircaeae, P. goeppertianum, P. guttatum, P. pustulatum, T. minima and Melampsorella symphyti. If this rust is endemic to Chatham Islands, then it must be accepted as a species of conservation value since the host plant is under threat from grazing animals and habitat loss.


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Microbiomes: Curating communities from plants : Nature : Nature Publishing Group

Microbiomes: Curating communities from plants : Nature : Nature Publishing Group | plant pathology | Scoop.it

Large-scale cultivation and genome sequencing of the bacteria that inhabit the leaves and roots of Arabidopsis plants have paved the way for probing how microbial communities assemble and function.


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New naming rules for fungi? Genetic advances spur mycologists to put their kingdom in order

New naming rules for fungi? Genetic advances spur mycologists to put their kingdom in order | plant pathology | Scoop.it
A rebellion has broken out against the traditional way of naming species in the peculiar, shape-shifting world of fungi.

 

Many fungi are shape-shifters seemingly designed to defy human efforts at categorization. The same species, sometimes the same individual, can reproduce two ways: sexually, by mixing genes with a partner of the same species, or asexually, by cloning to produce genetically identical offspring.

 

The problem is that reproductive modes can take entirely different anatomical forms. A species that looks like a miniature corn dog when it is reproducing sexually might look like fuzzy white twigs when it is in cloning mode. A gray smudge on a sunflower seed head might just be the asexually reproducing counterpart of a tiny satellite dish–shaped thing. Just by looking at them, you’d never know.

 

When many of these pairs were discovered, sometimes decades apart, sometimes growing right next to each other, it was difficult or impossible to demonstrate that they were the same thing. So one species would get two names. Careful observation later suggested that officially different species are actually one, but the pairs of names remained. In fact, it soon became standard mycological practice to name many species twice — once for the sexual form, once for the asexual one.

 

Now, mycologists have a chance to set the record straight. A group of upstart scientists has rebelled against the dual-naming system, arguing that DNA analysis can endow fungi with a one-species, one-name system. Having won a major victory at a recent international scientific congress, they are poised to bring their field into a new era of genetic nomenclature. But however justified genetically, their project is not without perils.


Via Dr. Stefan Gruenwald
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Pathogenicity of Phytophthora pluvialis to Pinus radiata and its relation with red needle cast disease in New Zealand - Springer

Pathogenicity of Phytophthora pluvialis to Pinus radiata and its relation with red needle cast disease in New Zealand - Springer | plant pathology | Scoop.it

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Nari Williams's curator insight, July 8, 2014 9:01 PM

Link to paper: http://link.springer.com/article/10.1186/s40490-014-0006-7

 

Check out our other RNC publications:

Decline in vitality of propagules of Phytophthora pluvialis and Phytophthora kernoviae and their inability to contaminate or colonise bark and sapwood in Pinus radiata export log simulation studies. http://link.springer.com/article/10.1186/s40490-014-0007-6

 

The use of adjuvants to improve uptake of phosphorous acid applied to Pinus radiata needles for control of foliar Phytophthora diseases. http://link.springer.com/article/10.1186/s40490-014-0008-5/fulltext.html

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Strategies of attack and defence in woody plant–Phytophthora interactions

Strategies of attack and defence in woody plant–Phytophthora interactions | plant pathology | Scoop.it

This review comprises both well-known and recently described Phytophthora species and concentrates on Phytophthora–woody plant interactions. First, comprehensive data on infection strategies are presented which were the basis for three models that explain invasion and spread of Phytophthora pathogens in different woody host plants. The first model describes infection of roots, the second concentrates on invasion of the trunk, and the last one summarizes infection and invasion of host plants via leaves. On the basis of morphological, physiological, biochemical and molecular data, scenarios are suggested which explain the sequences of reactions that occur in susceptible and tolerant plants following infections of roots or of stem bark. Particular emphasis is paid to the significance ofPhytophthora elicitins for such host–pathogen interactions. The overall goal is to shed light on the sequences of pathogenesis to better understand how Phytophthora pathogens harm their host plants.


Via Alejandro Rojas, David Studholme, Richard Hamelin
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Nari Williams's curator insight, July 8, 2014 5:39 PM

Great paper and a must read for all of us working in Phytophthora-tree interactions.

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Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao

Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease.


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Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction | plant pathology | Scoop.it

“ Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.”;


Via Niklaus Grunwald, Francis Martin, Richard Hamelin
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Trends in Plant Science: Susceptibility to plant disease: more than a failure of host immunity (2013)

Trends in Plant Science: Susceptibility to plant disease: more than a failure of host immunity (2013) | plant pathology | Scoop.it

Susceptibility to infectious diseases caused by pathogens affects most plants in their natural habitat and leads to yield losses in agriculture. However, plants are not helpless because their immune system can deal with the vast majority of attackers. Nevertheless, adapted pathogens are able to circumvent or avert host immunity making plants susceptible to these uninvited guests. In addition to the failure of the plant immune system, there are other host processes that contribute to plant disease susceptibility. In this review, we discuss recent studies that show the active role played by the host in supporting disease, focusing mainly on biotrophic stages of infection. Plants attract pathogens, enable their entry and accommodation, and facilitate nutrient provision.


Via Kamoun Lab @ TSL
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