Plant pathogenic fungi
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pH Signaling in Human Fungal Pathogens: a New Target for Antifungal Strategies

pH Signaling in Human Fungal Pathogens: a New Target for Antifungal Strategies | Plant pathogenic fungi | Scoop.it

Fungi are exposed to broadly fluctuating environmental conditions, to which adaptation is crucial for their survival. An ability to respond to a wide pH range, in particular, allows them to cope with rapid changes in their extracellular settings. PacC/Rim signaling elicits the primary pH response in both model and pathogenic fungi and has been studied in multiple fungal species. In the predominant human pathogenic fungi, namely, Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans, this pathway is required for many functions associated with pathogenesis and virulence. Aspects of this pathway are fungus specific and do not exist in mammalian cells. In this review, we highlight recent advances in our understanding of PacC/Rim-mediated functions and discuss the growing interest in this cascade and its factors as potential drug targets for antifungal strategies. We focus on both conserved and distinctive features in model and pathogenic fungi, highlighting the specificities of PacC/Rim signaling in C. albicans, A. fumigatus, and C. neoformans. We consider the role of this pathway in fungal virulence, including modulation of the host immune response. Finally, as now recognized for other signaling cascades, we highlight the role of pH in adaptation to antifungal drug pressure. By acting on the PacC/Rim pathway, it may therefore be possible (i) to ensure fungal specificity and to limit the side effects of drugs, (ii) to ensure broad-spectrum efficacy, (iii) to attenuate fungal virulence, (iv) to obtain additive or synergistic effects with existing antifungal drugs through tolerance inhibition, and (v) to slow the emergence of resistant mutants.

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Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection

Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection | Plant pathogenic fungi | Scoop.it
Aggressive fungal pathogens such as Botrytis and Verticillium spp. cause severe crop losses worldwide. We recently discovered that Botrytis cinerea delivers small RNAs (Bc–sRNAs) into plant cells to silence host immunity genes. Such sRNA effectors are mostly produced by Botrytis cinerea Dicer-like protein 1 (Bc-DCL1) and Bc-DCL2. Here we show that expressing sRNAs that target Bc-DCL1 and Bc-DCL2 in Arabidopsis and tomato silences Bc-DCL genes and attenuates fungal pathogenicity and growth, exemplifying bidirectional cross-kingdom RNAi and sRNA trafficking between plants and fungi. This strategy can be adapted to simultaneously control multiple fungal diseases. We also show that Botrytis can take up external sRNAs and double-stranded RNAs (dsRNAs). Applying sRNAs or dsRNAs that target Botrytis DCL1 and DCL2 genes on the surface of fruits, vegetables and flowers significantly inhibits grey mould disease. Such pathogen gene-targeting RNAs represent a new generation of environmentally friendly fungicides.

Via Pierre-Marc Delaux
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A Novel Population of Fusarium fujikuroi Isolated from Southeastern U.S. Winegrapes Reveals the Need to Re-Evaluate the Species’ Fumonisin Production

A Novel Population of Fusarium fujikuroi Isolated from Southeastern U.S. Winegrapes Reveals the Need to Re-Evaluate the Species’ Fumonisin Production | Plant pathogenic fungi | Scoop.it
Mycotoxins pose a challenge to a safe food supply worldwide, and their threat is expected to worsen with our changing climate. The need for diligence is exemplified by the discovery of fumonisin B2 in wine, which joins ochratoxin A as a mycotoxin of concern in the grape-wine chain. To elucidate the mycotoxin risk in southeastern American wine, grape samples were collected from vineyards during harvest in 2013 and potentially mycotoxigenic fungi (Fusarium and Aspergillus) were isolated from the samples. Numerous Fusarium isolates were recovered and identified to the species level by comparison of translation elongation factor 1-α gene sequences to verified strains. Fusarium fujikuroi was the most abundant species recovered (239 isolates), followed by F. proliferatum (52), F. incarnatum-equiseti (14), F. oxysporum (7), F. concentricum (1), and F. solani (1). In vitro assays quantified fumonisin production for representative isolates via liquid chromatography-tandem mass spectrometry. Surprisingly, nearly all F. fujikuroi isolates produced fumonisins B1, B2, and B3 at levels comparable to both the F. proliferatum isolates and the positive control, Fusarium verticillioides. Such capacity for fumonisin production refutes the generally accepted notion that F. fujikuroi produces undetectable or low levels of fumonisins and provides evidence to reconsider this species as a mycotoxigenic threat to economically significant crops.
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Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease

Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease | Plant pathogenic fungi | Scoop.it

Here, we characterized the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in multiplex families with CD and healthy relatives and defined the microbial interactions leading to dysbiosis in CD. We identified fungal (Candida tropicalis) and bacterial (Serratia marcescens and Escherichia coli) species that are associated with CD dysbiosis. Additionally, we found that the level of anti-Saccharomyces cerevisiae antibodies (ASCA; a known CD biomarker) was associated with the abundance of C. tropicalis. We also identified positive interkingdom correlations between C. tropicalis, E. coli, and S. marcescens in CD patients and validated these correlations using in vitro biofilms. These results provide insight into the roles of bacteria and fungi in CD and may lead to the development of novel treatment approaches and diagnostic assays.

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Down-regulation of the glucan synthase-like 6 gene (HvGsl6) in barley leads to decreased callose accumulation and increased cell wall penetration by Blumeria graminis f. sp. hordei - Chowdhury - 20...

Down-regulation of the glucan synthase-like 6 gene (HvGsl6) in barley leads to decreased callose accumulation and increased cell wall penetration by Blumeria graminis f. sp. hordei - Chowdhury - 20... | Plant pathogenic fungi | Scoop.it

The recent characterization of the polysaccharide composition of papillae deposited at the barley cell wall during infection by the powdery mildew pathogen, Blumeria graminis f. sp. hordei (Bgh), has provided new targets for the generation of enhanced disease resistance. The role of callose in papilla-based penetration resistance of crop species is largely unknown because the genes involved in the observed callose accumulation have not been identified unequivocally.
We have employed both comparative and functional genomics approaches to identify the functional orthologue of AtGsl5 in the barley genome. HvGsl6 (the barley glucan synthase-like 6 gene), which has the highest sequence identity to AtGsl5, is the only Bgh-induced gene among the HvGsls examined in this study.
Through double-stranded RNA interference (dsRNAi)-mediated silencing of HvGsl6, we have shown that the down-regulation of HvGsl6 is associated with a lower accumulation of papillary and wound callose and a higher susceptibility to penetration of the papillae by Bgh, compared with control lines.
The results indicate that the HvGsl6 gene is a functional orthologue of AtGsl5 and is involved in papillary callose accumulation in barley. The increased susceptibility of HvGsl6 dsRNAi transgenic lines to infection indicates that callose positively contributes to the barley fungal penetration resistance mechanism.

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The elusive predisposition to mycoheterotrophy in Ericaceae - Lallemand - 2016 - New Phytologist - Wiley Online Library

The elusive predisposition to mycoheterotrophy in Ericaceae - Lallemand - 2016 - New Phytologist - Wiley Online Library | Plant pathogenic fungi | Scoop.it
The rise and diversification of land plants was accompanied by mycorrhizal symbiosis, from their emergence to their adaptation to various biomes and ecological situations (Selosse et al., 2015). In most mycorrhizal associations, fungi provide soil minerals to the plant, in exchange for sugars derived from photosynthesis (Smith & Read, 2008; van der Heijden et al., 2015). However, several plant species adapted to shaded forest conditions by secondarily reversing this exchange of carbohydrates: they became achlorophyllous thanks to carbon provided by the fungus. This so-called mycoheterotrophic nutrition is described in over 400 species and evolved at least 40 times independently (Merckx, 2013), raising the question of what predispositions underlie these convergences.
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Frontiers | Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis | Evolutionary and Genomic Micr...

Frontiers | Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis | Evolutionary and Genomic Micr... | Plant pathogenic fungi | Scoop.it
Amphibian populations are experiencing catastrophic declines driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Although horizontal gene transfer (HGT) facilitates the evolution and adaptation in many fungi by conferring novel function genes to the recipient fungi, inter-kingdom HGT in Bd remains largely unexplored. In this study, our investigation detects 19 bacterial genes transferred to Bd, including metallo-beta-lactamase and arsenate reductase that play important roles in the resistance to antibiotics and arsenates. Moreover, three probable HGT gene families in Bd are from plants and one gene family coding the ankyrin repeat-containing protein appears to come from oomycetes. The observed multi-copy gene families associated with HGT are probably due to the independent transfer events or gene duplications. Five HGT genes with extracellular locations may relate to infection, and some other genes may participate in a variety of metabolic pathways, and in doing so add important metabolic traits to the recipient. The evolutionary analysis indicates that all the transferred genes evolved under purifying selection, suggesting that their functions in Bd are similar to those of the donors. Collectively, our results indicate that HGT from diverse donors may be an important evolutionary driver of Bd, and improve its adaptations for infecting and colonizing host amphibians.

Via IPM Lab
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Fungal identification biases in microbiome projects - Tedersoo - 2016 - Environmental Microbiology Reports - Wiley Online Library

Fungal identification biases in microbiome projects - Tedersoo - 2016 - Environmental Microbiology Reports - Wiley Online Library | Plant pathogenic fungi | Scoop.it

Asterisks indicate significant differences between ITS1 and ITS2 region, accounting for false discovery rate using Benjamini–Hochberg correction (*P < 0.05; **P < 0.01; ***P < 0.001)


Fungi are the key players in ecosystems as well as in plant and human health. High-throughput molecular identification of fungi has greatly progressed our understanding about the diversity of mutualists, saprotrophs, and pathogens. We argue that the methods promoted by the microbiome consortia are suboptimal for detection of the most important fungal pathogens and ecologically important degraders. We recommend several sets of optimized primers for analysis of fungi or all eukaryote groups based on either short or long amplicons that cover the ITS region as well as part of 18S and 28S rDNA.

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Fusarium praegraminearum sp. nov., a novel nivalenol mycotoxin-producing pathogen from New Zealand can induce head blight on wheat

Fusarium praegraminearum sp. nov., a novel nivalenol mycotoxin-producing pathogen from New Zealand can induce head blight on wheat | Plant pathogenic fungi | Scoop.it
We report on the molecular and morphological characterization of a novel type B trichothecene toxin-producing species (i.e. B clade) recovered from litter in a maize field near Wellington, New Zealand, which is described as Fusarium praegraminearum sp. nov. This species was initially identified as F. acuminatum based on morphological characters. However, it differs from this species by producing longer, slightly asymmetrically curved macroconidia in which the apical cell is not as pointed and by its much faster colony growth rate on agar. Molecular phylogenetic analyses of portions of 13 genes resolved F. praegraminearum as the most basal species within the B clade. Mycotoxin analyses demonstrated that it was able to produce 4-acetylnivalenol and 4,15-diacetylnivalenol trichothecenes, the nontrichothecene sesquiterpenes culmorin and hydroxy-culmorins, and the estrogen zearalenone in vitro. Results of a pathogenicity experiment revealed that F. praegraminearum induced moderate head blight on wheat.

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Editorial special issue: soil, plants and endophytes - Plant and Soil, Volume 405, Issue 1 - Springer

Editorial special issue: soil, plants and endophytes - Plant and Soil, Volume 405, Issue 1 - Springer | Plant pathogenic fungi | Scoop.it
In this Special Issue, contributors from around the world improve our understanding of the mechanisms of endophytic colonization, soil-plant-endophyte interactions, how endophytes exploit niches inside the plant, how plants respond to endophyte establishment, and how we can decipher mechanisms of plant-endophyte interactions, both for bacteria and fungi. Additional studies were also done on plant-associated endophytic communities when subjected to various stresses.
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bZIP transcription factor CgAP1 is essential for oxidative stress tolerance and full virulence of the poplar anthracnose fungus Colletotrichum gloeosporioides

bZIP transcription factor CgAP1 is essential for oxidative stress tolerance and full virulence of the poplar anthracnose fungus Colletotrichum gloeosporioides | Plant pathogenic fungi | Scoop.it

Highlights
• The expression and nuclear localization of CgAP1 is induced by ROS.
• CgAP1 deletion mutants are hypersensitive to oxidative stress and attenuated in virulence.
• CgAP1 acts as a positive regulator of ROS detoxification in Colletotrichum gloeosporioides.

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The geographic distribution and complex evolutionary history of the NX-2 trichothecene chemotype from Fusarium graminearum

The geographic distribution and complex evolutionary history of the NX-2 trichothecene chemotype from Fusarium graminearum | Plant pathogenic fungi | Scoop.it

Highlights
• NX-2 F. graminearum may be endemic to southern Canada and the northern U.S.
• TRI1 variation within FSAMSC-1 was shaped by trans-species evolution.
• The NX-2 chemotype evolved relatively recently from a type B ancestor.
• NX-2 evolved in association with a significant change in selection pressure on Tri1.
• NX-2 strains may occupy an evolutionary niche distinct from type B F. graminearum.

Abstract
Fusarium graminearum and 21 related species comprising the F. sambucinum species complex lineage 1 (FSAMSC-1) are the most important Fusarium Head Blight pathogens of cereal crops world-wide. FSAMSC-1 species typically produce type B trichothecenes. However, some F. graminearum strains were recently found to produce a novel type A trichothecene (NX-2) resulting from functional variation in the trichothecene biosynthetic enzyme Tri1. We used a PCR-RFLP assay targeting the TRI1 gene to identify the NX-2 allele among a global collection of 2515 F. graminearum. NX-2 isolates were only found in southern Canada and the northern U.S., where they were observed at low frequency (1.8%), but over a broader geographic range and set of cereal hosts than previously recognized. Phylogenetic analyses of TRI1 and adjacent genes produced gene trees that were incongruent with the history of species divergence within FSAMSC-1, indicating trans-species evolution of ancestral polymorphism. In addition, placement of NX-2 strains in the TRI1 gene tree was influenced by the accumulation of nonsynonymous substitutions associated with the evolution of the NX-2 chemotype, and a significant (P < 0.001) change in selection pressure was observed along the NX-2 branch (ω = 1.16) in comparison to other branches (ω = 0.17) in the TRI1 phylogeny. Parameter estimates were consistent with positive selection for specific amino-acid changes during the evolution of NX-2, but direct tests of positive selection were not significant. Phylogenetic analyses of fourfold degenerate sites and intron sequences in TRI1 indicated the NX-2 chemotype had a single evolutionary origin and evolved recently from a type B ancestor. Our results indicate the NX-2 chemotype may be indigenous, and possibly endemic, to southern Canada and the northern U.S. In addition, we demonstrate that the evolution of TRI1 within FSAMSC-1 has been complex, with evidence of trans-species evolution and chemotype-specific shifts in selective constraint.

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Effectors from wheat rust fungi suppress multiple plant defense responses — Phytopathology

Effectors from wheat rust fungi suppress multiple plant defense responses — Phytopathology | Plant pathogenic fungi | Scoop.it
Fungi that cause cereal rust diseases (genus Puccinia) are important pathogens of wheat globally. Upon infection the fungus secretes a number of effector proteins. Although a large repository of putative effectors have been predicted using bioinformatic pipelines, the lack of available high-throughput effector screening systems has limited functional studies on these proteins. In this study we mined the available transcriptomes of Puccinia graminis and Puccinia striiformis to look for potential effectors that suppress host hypersensitive response (HR). Twenty small (<300 amino acids), secreted proteins, with no predicted functions were selected for the HR suppression assay using Nicotiana benthamiana, in which each of the proteins were transiently expressed and evaluated for their ability to suppress HR caused by four cytotoxic effector‐R gene combinations (Cp/Rx, ATR13/RPP13, Rpt2/RPS‐2 and GPA/RBP‐1) and one mutated R gene - Pto (Y207D). Nine out of twenty proteins, designated Shr1- Shr9 (Suppressors of Hypersensitive Response), were found to suppress HR in Nicotiana benthamiana. These effectors varied in the effector-R gene defenses they suppressed, indicating these pathogens can interfere with a variety of host defense pathways. In addition to HR suppression, effector Shr7 also suppressed PAMP-triggered immune response triggered by flg22. Finally, delivery of Shr7 through Pseudomonas fluorescens EtHAn suppressed non-specific hypersensitive response induced by P. syringae DC3000 in wheat, confirming its activity in a homologous system. Overall, this study provides the first evidence for the presence of effectors in Puccinia species suppressing multiple plant defense responses.

Via Yogesh Gupta
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Nuclear Pore Permeabilization Is a Convergent Signaling Event in Effector-Triggered Immunity

Nuclear Pore Permeabilization Is a Convergent Signaling Event in Effector-Triggered Immunity | Plant pathogenic fungi | Scoop.it

Highlights
•CPR5 is a component of the nuclear pore complex (NPC)
•CPR5 regulates nuclear transport through the selective barrier of the NPC
•The CPR5 homomer is disrupted upon induction of effector-triggered immunity (ETI)
•Conformational change in CPR5 leads to CKI release and NPC permeabilization for ETI

Summary
Nuclear transport of immune receptors, signal transducers, and transcription factors is an essential regulatory mechanism for immune activation. Whether and how this process is regulated at the level of the nuclear pore complex (NPC) remains unclear. Here, we report that CPR5, which plays a key inhibitory role in effector-triggered immunity (ETI) and programmed cell death (PCD) in plants, is a novel transmembrane nucleoporin. CPR5 associates with anchors of the NPC selective barrier to constrain nuclear access of signaling cargos and sequesters cyclin-dependent kinase inhibitors (CKIs) involved in ETI signal transduction. Upon activation by immunoreceptors, CPR5 undergoes an oligomer to monomer conformational switch, which coordinates CKI release for ETI signaling and reconfigures the selective barrier to allow significant influx of nuclear signaling cargos through the NPC. Consequently, these coordinated NPC actions result in simultaneous activation of diverse stress-related signaling pathways and constitute an essential regulatory mechanism specific for ETI/PCD induction.

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Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus

Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus | Plant pathogenic fungi | Scoop.it

Background
Aspergillus cristatus is the dominant fungus involved in the fermentation of Chinese Fuzhuan brick tea. Aspergillus cristatus is a homothallic fungus that undergoes a sexual stage without asexual conidiation when cultured in hypotonic medium. The asexual stage is induced by a high salt concentration, which completely inhibits sexual development. The taxon is therefore appropriate for investigating the mechanisms of asexual and sexual reproduction in fungi. In this study, de novo genome sequencing and analysis of transcriptomes during culture under high- and low-osmolarity conditions were performed. These analyses facilitated investigation of the evolution of mating-type genes, which determine the mode of sexual reproduction, in A. cristatus, the response of the high-osmolarity glycerol (HOG) pathway to osmotic stimulation, and the detection of mycotoxins and evaluation of the relationship with the location of the encoding genes.

Results
The A. cristatus genome comprised 27.9 Mb and included 68 scaffolds, from which 10,136 protein-coding gene models were predicted. A phylogenetic analysis suggested a considerable phylogenetic distance between A. cristatus and A. nidulans. Comparison of the mating-type gene loci among Aspergillus species indicated that the mode in A. cristatus differs from those in other Aspergillus species. The components of the HOG pathway were conserved in the genome of A. cristatus. Differential gene expression analysis in A. cristatus using RNA-Seq demonstrated that the expression of most genes in the HOG pathway was unaffected by osmotic pressure. No gene clusters associated with the production of carcinogens were detected.

Conclusions
A model of the mating-type locus in A. cristatus is reported for the first time. Aspergillus cristatus has evolved various mechanisms to cope with high osmotic stress. As a fungus associated with Fuzhuan tea, it is considered to be safe under low- and high-osmolarity conditions.

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Immunity to Rice Blast Disease by Suppression of Effector-Triggered Necrosis

Immunity to Rice Blast Disease by Suppression of Effector-Triggered Necrosis | Plant pathogenic fungi | Scoop.it

Highlights

•AvrPiz-t interacts and co-localizes with APIP5 in the cytoplasm
•AvrPiz-t suppresses APIP5 transcriptional activity and protein accumulation
•APIP5, a negative regulator of cell death, interacts with the NLR receptor Piz-t
•Piz-t suppresses the AvrPiz-t-mediated APIP5 turnover

Summary
Hemibiotrophic pathogens are some of the most destructive plant pathogens, causing huge economic losses and threatening global food security. Infection with these organisms often involves an initial biotrophic infection phase, during which the pathogen spreads in host tissue asymptomatically, followed by a necrotrophic phase, during which host-cell death is induced. How hemibiotrophic pathogens trigger host necrosis and how plants inhibit the transition from the biotrophic stage to the necrotrophic stage in disease symptom expression are mainly unknown. The rice blast fungus Magnaporthe oryzae spreads in rice biotrophically early during infection, but this biotrophic stage is followed by a pronounced switch to cell death and lesion formation. Here, we show that the M. oryzae effector AvrPiz-t interacts with the bZIP-type transcription factor APIP5 in the cytoplasm and suppresses its transcriptional activity and protein accumulation at the necrotrophic stage. Silencing of APIP5 in transgenic rice leads to cell death, and the phenotype is enhanced by the expression of AvrPiz-t. Conversely, Piz-t interacts with and stabilizes APIP5 to prevent necrosis at the necrotrophic stage. At the same time, APIP5 is essential for Piz-t stability. These results demonstrate a novel mechanism for the suppression of effector-triggered necrosis at the necrotrophic stage by an NLR receptor in plants.


Via Christophe Jacquet
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The barley (Hordeum vulgare) cellulose synthase-like D2 gene (HvCslD2) mediates penetration resistance to host-adapted and nonhost isolates of the powdery mildew fungus - Douchkov - 2016 - New Phyt...

The barley (Hordeum vulgare) cellulose synthase-like D2 gene (HvCslD2) mediates penetration resistance to host-adapted and nonhost isolates of the powdery mildew fungus - Douchkov - 2016 - New Phyt... | Plant pathogenic fungi | Scoop.it
Cell walls and cellular turgor pressure shape and suspend the bodies of all vascular plants. In response to attack by fungal and oomycete pathogens, which usually breach their host's cell walls by mechanical force or by secreting lytic enzymes, plants often form local cell wall appositions (papillae) as an important first line of defence. The involvement of cell wall biosynthetic enzymes in the formation of these papillae is still poorly understood, especially in cereal crops.
To investigate the role in plant defence of a candidate gene from barley (Hordeum vulgare) encoding cellulose synthase-like D2 (HvCslD2), we generated transgenic barley plants in which HvCslD2 was silenced through RNA interference (RNAi).
The transgenic plants showed no growth defects but their papillae were more successfully penetrated by host-adapted, virulent as well as avirulent nonhost isolates of the powdery mildew fungus Blumeria graminis. Papilla penetration was associated with lower contents of cellulose in epidermal cell walls and increased digestion by fungal cell wall degrading enzymes.
The results suggest that HvCslD2-mediated cell wall changes in the epidermal layer represent an important defence reaction both for nonhost and for quantitative host resistance against nonadapted wheat and host-adapted barley powdery mildew pathogens, respectively.
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Alternative splicing – an elegant way to diversify the function of repeat-containing effector proteins? - Betz - 2016 - New Phytologist - Wiley Online Library

Alternative splicing – an elegant way to diversify the function of repeat-containing effector proteins? - Betz - 2016 - New Phytologist - Wiley Online Library | Plant pathogenic fungi | Scoop.it

Plants are subjected to associations with organisms throughout all kingdoms, and colonization is often accompanied by the secretion of effector proteins which results in alterations to plant physiology and immune responses to facilitate colonization. In recent years evidence has arisen that many plant-associated organisms make use of repeat-containing effectors, which often seem to be organized in larger protein families with characteristic distribution of repeat elements (Mesarich et al., 2015). RXLR effectors from plant pathogenic oomycetes, for instance, comprise a conserved but highly degenerate C-terminal WYL domain that is often organized in tandem repeats (Jiang et al., 2008). Conversely, there are effectors harbouring perfect, or almost perfect, repeats; for example MpC002, which is an effector from the peach-potato aphid Myzus persicae that contains five hydrophilic perfect tandem repeats, consisting of seven amino acids (Bos et al., 2010). Certainly the most common repeat-containing effectors are the so-called TAL effectors derived from plant-pathogenic Xanthomonas species, whose characteristic feature is a central domain of nearly identical tandem repeats (Boch et al., 2009). Each repeat harbours a variable amino acid pair, termed repeat-variable di-residues (RVDs), which determines nucleotide binding specificity of the effector. In this issue of New Phytologist, Noon et al. (pp. 444–460) identify HgGLAND18 as a novel tandem repeat-containing effector from the soybean cyst nematode Heterodera glycines. Interestingly, HgGLAND18 exists in different isoforms and transcript variants. The isoforms contain different polymorphisms and the variants show irregular numbers of repeats. As a basic structure, HgGLAND18 isoforms are composed of a signal peptide, followed by a series of zero to five tandem repeats, a supercharged stretch of 43 amino acids (aa) terminating the N-terminal region, and a C-terminus of 49 aa. The different transcript versions of HgGLAND18 are herein proposed to be generated either by allelic variations and/or by alternative splicing (AS). This raises the question whether, and to what extent, AS might participate in the synthesis of multiple effector proteins with possible different biological functions.

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Frontiers | Comparative genomic analysis among four representative isolates of Phytophthora sojae reveals genes under evolutionary selection | Plant Biotic Interactions

Frontiers | Comparative genomic analysis among four representative isolates of Phytophthora sojae reveals genes under evolutionary selection | Plant Biotic Interactions | Plant pathogenic fungi | Scoop.it
Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related studies is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. 153 positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative P. sojae isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in P. sojae and will provide clues for identification of new virulence factors in the oomycete plant pathogens.
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The frequency of sex in fungi

The frequency of sex in fungi | Plant pathogenic fungi | Scoop.it

Fungi are a diverse group of organisms with a huge variation in reproductive strategy. While almost all species can reproduce sexually, many reproduce asexually most of the time. When sexual reproduction does occur, large variation exists in the amount of in- and out-breeding. While budding yeast is expected to outcross only once every 10 000 generations, other fungi are obligate outcrossers with well-mixed panmictic populations. In this review, we give an overview of the costs and benefits of sexual and asexual reproduction in fungi, and the mechanisms that evolved in fungi to reduce the costs of either mode. The proximate molecular mechanisms potentiating outcrossing and meiosis appear to be present in nearly all fungi, making them of little use for predicting outcrossing rates, but also suggesting the absence of true ancient asexual lineages. We review how population genetic methods can be used to estimate the frequency of sex in fungi and provide empirical data that support a mixed mode of reproduction in many species with rare to frequent sex in between rounds of mitotic reproduction. Finally, we highlight how these estimates might be affected by the fungus-specific mechanisms that evolved to reduce the costs of sexual and asexual reproduction.


Via Pierre Gladieux
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New luminescent mycenoid fungi (Basidiomycota, Agaricales) from São Paulo State, Brazil

New luminescent mycenoid fungi (Basidiomycota, Agaricales) from São Paulo State, Brazil | Plant pathogenic fungi | Scoop.it

Four species of mycenoid fungi are reported as luminescent (or putatively luminescent) on the basis of specimens collected from São Paulo State, Brazil. Two of them represent new species (Mycena oculisnymphae, Resinomycena petarensis), and two represent new reports of luminescence in previously described species (M. deformis, M. globulispora). Comprehensive descriptions, illustrations, photographs, and comparisons with phenetically similar species are provided. Sequences of nuc rDNA internal transcribed spacer regions were generated for barcoding purposes and for comparisons with similar species.

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Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae

Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae | Plant pathogenic fungi | Scoop.it
In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,741 hectares, about 16% of cultivated wheat area in Bangladesh, with yield losses reaching up to 100%. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. Population genomics analyses revealed that the outbreak was caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. We show that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.

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Rescooped by Steve Marek from Plants and Microbes
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New Phytologist: Fundamental wheat stripe rust research in the 21st century (2016)

New Phytologist: Fundamental wheat stripe rust research in the 21st century (2016) | Plant pathogenic fungi | Scoop.it

In the 21st century, the wheat stripe rust fungus has evolved to be the largest biotic limitation to global wheat production. New pathogen genotypes are more aggressive and able to infect previously resistant wheat varieties, leading to rapid pathogen migration across and between continents. We now know the full life cycle, microevolutionary relationships and past migration routes on a global scale. Current sequencing technologies have provided the first fungal draft genomes and simplified plant resistance gene cloning. Yet, we know nothing about the molecular and microevolutionary mechanisms that facilitate the infection process and cause new devastating pathogen races. These are the questions that need to be addressed by exploiting the synergies between novel 21st century biology tools and decades of dedicated pathology work.


Via Kamoun Lab @ TSL
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Suppressor of fusion, a Fusarium oxysporum homolog of Ndt80, is required for nutrient-dependent regulation of anastomosis

Suppressor of fusion, a Fusarium oxysporum homolog of Ndt80, is required for nutrient-dependent regulation of anastomosis | Plant pathogenic fungi | Scoop.it

Highlights
• Fusarium oxysporum contains an ortholog of Vegetative Incompatibility Blocked VIB-1.
• Deletion of this ortholog, called SUF, leads to enhanced hyphal fusion.
• In one strain, deletion of SUF also leads to more conidial anastomosis tube-fusion.
• SUF is not required for vegetative incompatibility nor for secretion of proteases.

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Rescooped by Steve Marek from Ecology, evolution, pathogens, genomics, fungi, biotic interactions, human history ...
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pong: fast analysis and visualization of latent clusters in population genetic data

pong: fast analysis and visualization of latent clusters in population genetic data | Plant pathogenic fungi | Scoop.it
Motivation: A series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining. Results: We introduce pong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native interactive D3.js visualization. pong leverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared with other methods that process output from mixed-membership models. We apply pong to 225 705 unlinked genome-wide single-nucleotide variants from 2426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show that pong outpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools. Availability and Implementation: pong is freely available and can be installed using the Python package management system pip. pong’s source code is available at https://github.com/abehr/pong.

Via Pierre Gladieux
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Rescooped by Steve Marek from Plant Pathogens
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Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates  - New Phytologist - Wiley Online Library

Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates  - New Phytologist - Wiley Online Library | Plant pathogenic fungi | Scoop.it
Summary 

• Blast disease (causal agent Magnaporthe oryzae) has presented as a new and serious field disease of wheat in South America. Here, we investigated the responses of wheat to both adapted and nonadapted isolates of the blast fungus Magnaporthe, examining cellular defence and transcriptional changes. 
• Resistance towards the nonadapted isolate was associated with the formation of appositions, here termed halos, beneath attempted Magnaporthe grisea penetration sites that wheat-adapted, M. oryzae isolates were able to breach. 
• Transcriptome analysis indicated extensive transcriptional reprogramming following inoculation with both wheat-adapted and nonadapted isolates of Magnaporthe. Functional annotation of many of the differentially expressed transcripts classified into the categories: cell rescue and defence, plant metabolism, cellular transport and regulation of transcription (although a significant number of transcripts remain unclassified). 
• Defence-related transcripts induced in common by adapted and nonadapted isolates were differentially regulated in response to M. oryzae and M. grisea isolates over time. Differential expression of genes involved in cellular transport indicated the importance of this process in plant defence. Functional characterisation of these transcripts and their role in defence may eventually lead to the identification of broad-spectrum resistance mechanisms in wheat towards Magnaporthe.

Via Yogesh Gupta
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