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BioEssays: Sex or no sex: Evolutionary adaptation occurs regardless (2014)

BioEssays: Sex or no sex: Evolutionary adaptation occurs regardless (2014) | Plant pathogenic fungi | Scoop.it

All species continuously evolve to adapt to changing environments. The genetic variation that fosters such adaptation is caused by a plethora of mechanisms, including meiotic recombination that generates novel allelic combinations in the progeny of two parental lineages. However, a considerable number of eukaryotic species, including many fungi, do not have an apparent sexual cycle and are consequently thought to be limited in their evolutionary potential. As such organisms are expected to have reduced capability to eliminate deleterious mutations, they are often considered as evolutionary dead ends. However, inspired by recent reports we argue that such organisms can be as persistent as organisms with conventional sexual cycles through the use of other mechanisms, such as genomic rearrangements, to foster adaptation.


Via Kamoun Lab @ TSL
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Knapco's curator insight, February 19, 2:08 AM

Verticillium dahliae is among 20% of fungal species lacking sexual cycle of reproduction. However, the authors suggest that its genome contains a high amount of transposable elements (TE) which may drive genome evolution in this pathogen. TEs are DNA sequences that can change their position within genome and can impact the genome by inducing gene knockouts, modulating gene regulation or causing double-stranded DNA breaks. These sources of variability enable evolution: selection and adaptaion to plant hosts and evolution of fungal aggressiveness.

Similar asexual mechanisms facilitate genome evolution in other eukaryotes, known to be plant pathogens: Phytophthora infestans causing potato blight, Leptosphaeria maculans causing stem canker on Brassica, Blumeria graminis causing powdery mildew, Alternaria spp., Fusarium spp., Mycosphaerella graminicola...

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Genome Editing Cuts Out HIV | The Scientist Magazine®

Genome Editing Cuts Out HIV | The Scientist Magazine® | Plant pathogenic fungi | Scoop.it
Researchers use the CRISPR/Cas9 method to remove the virus from the host genome in human cell lines.
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Off topic, but great research!

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Characterization of the Largest Effector Gene Cluster of Ustilago maydis

Characterization of the Largest Effector Gene Cluster of Ustilago maydis | Plant pathogenic fungi | Scoop.it

In this study, we provide the first step to the functional analysis of the largest gene cluster in the Ustilago maydis genome encoding 24 secreted effectors. While the deletion of the entire cluster dramatically affected tumor formation and abolished anthocyanin induction, only one of the genes had a large contribution to tumor formation, while another effector gene was primarily responsible for the anthocyanin induction. Unexpectedly, the cluster mutant could still colonize plants and complete the life cycle, i.e. behaves like an endophyte. Despite only small contributions to tumor formation, individual effector mutants caused distinct plant responses, suggesting that they affect discrete plant processes. On these grounds we are proposing to use plant responses as a general readout to assess and compare effector gene function.

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Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans

Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans | Plant pathogenic fungi | Scoop.it

Effectors are key players in pathogenicity of microbes toward plants. Effector genes usually show concerted expression during plant infection but how this concerted expression is generated remains a largely unexplored research topic. Epigenetic mechanisms are involved in genome maintenance and integrity but are increasingly considered as important for regulation of gene expression in numerous and diverse organisms. Here we show that the genomic environment has impact on expression of Leptosphaeria maculans effector genes, and that an epigenetic mechanism that relies on two proteins involved in heterochromatin formation and maintenance, HP1 and DIM-5, modulates this expression, leading to repression during growth in axenic culture. Chromatin decondensation by removal of histone H3 lysine 9 methylation and/or HP1 is presumably a prerequisite for effector gene expression during primary infection of oilseed rape. Thus we show chromatin-based transcriptional regulation that can act on effector gene expression in fungi. Our study highlights the importance of heterochromatic landscapes, not only for genome maintenance but also in rapid and efficient adaptation of organisms to changing environmental situations.

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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 pathogenic fungi | 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.

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The Triphenylethylenes, a Novel Class of Antifungals

The Triphenylethylenes, a Novel Class of Antifungals | Plant pathogenic fungi | Scoop.it

New antifungals are needed, particularly in the developing world, to treat life-threatening fungal infections, such as cryptococcosis. Drug repurposing is one strategy to identify new drug-like compounds, but it is often difficult to identify a mechanism of action. Here we discuss the outstanding effort by Butts et al. to identify calmodulin as an antifungal target of repurposed estrogen receptor antagonists [A. Butts, K. Koselny, Y. Chabrier-Roselló, C. P. Semighini, Y. C. S. Brown, et al., mBio 5(1):e00765-13, 2014, doi:10.1128/mBio.00765-13]. The authors show that these compounds bind to and directly inhibit fungal calmodulin and also reduce fungal burden in an animal disease model. These studies thus establish both the key preclinical efficacy and the antifungal mechanism of action, which will allow these compounds to progress toward development of novel antifungal therapies.

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Fungi borrowed bacterial gene again and again

Fungi borrowed bacterial gene again and again | Plant pathogenic fungi | Scoop.it
Multiple independent gene transfers gave fungi ability to colonize plant roots.

Muller and his colleagues scanned the genomes of 149 eukaryotes, and found acdS-like genes in 65 of them — 61 in fungi and 4 in parasitic microorganisms called oomycetes, including Phytophthora infestans, the microbe responsible for the Irish potato famine. After analysing the organisms' genetic family trees, the researchers determined that the most likely explanation was that three different kinds of bacterium had donated the gene to the fungi and oomycetes in a total of 15 different horizontal-gene-transfer events.


Via Francis Martin
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Colletotrichum orbiculare Secretes Virulence Effectors to a Biotrophic Interface at the Primary Hyphal Neck via Exocytosis Coupled with SEC22-Mediated Traffic

Colletotrichum orbiculare Secretes Virulence Effectors to a Biotrophic Interface at the Primary Hyphal Neck via Exocytosis Coupled with SEC22-Mediated Traffic | Plant pathogenic fungi | Scoop.it

The hemibiotrophic pathogen Colletotrichum orbiculare develops biotrophic hyphae inside cucumber (Cucumis sativus) cells via appressorial penetration; later, the pathogen switches to necrotrophy. C. orbiculare also expresses specific effectors at different stages. Here, we found that virulence-related effectors of C. orbiculare accumulate in a pathogen–host biotrophic interface. Fluorescence-tagged effectors accumulated in a ring-like region around the neck of the biotrophic primary hyphae. Fluorescence imaging of cellular components and transmission electron microscopy showed that the ring-like signals of the effectors localized at the pathogen–plant interface. Effector accumulation at the interface required induction of its expression during the early biotrophic phase, suggesting that transcriptional regulation may link to effector localization. We also investigated the route of effector secretion to the interface. An exocytosis-related component, the Rab GTPase SEC4, localized to the necks of biotrophic primary hyphae adjacent to the interface, thereby suggesting focal effector secretion. Disruption of SEC4 in C. orbiculare reduced virulence and impaired effector delivery to the ring signal interface. Disruption of the v-SNARE SEC22also reduced effector delivery. These findings suggest that biotrophy-expressed effectors are secreted, via the endoplasmic reticulum-to-Golgi route and subsequent exocytosis, toward the interface generated between C. orbiculare and the host cell.


Via Francis Martin
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Yeast metacaspase: Grim Reaper or savior?

Yeast metacaspase: Grim Reaper or savior? | Plant pathogenic fungi | Scoop.it

Yeast metacaspases are structural and possibly functional homologs of caspases that execute apoptosis—programmed cell death—in higher organisms. Malmgren Hill et al. tested whether yeast metacaspase Mca1 acts as an executioner or beneficial protein during replicative aging of yeast (see the Perspective by Kampinga). Boosting metacaspase levels caused a substantial and robust extension of life span. This lifespan extension was only partly dependent on the caspase activity of Mca1 but required the presence of the protein disaggregase Hsp104. Consistent with a role in proteostasis, Mca1 was recruited to chaperone-enriched aggregates during aging. Mca1 increased aggregate asymmetry during yeast cytokinesis and counteracted the age-associated accumulation of inclusions.

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Australia: New leaf rust threat to popular wheat varieties (2014)

Australia: New leaf rust threat to popular wheat varieties (2014) | Plant pathogenic fungi | Scoop.it

WA wheatgrowers have been advised to monitor crops throughout the season for signs of leaf rust following testing which confirmed an increased risk of rust in popular wheat varieties. Department of Agriculture and Food plant pathologist Geoff Thomas said that in 2013, wheat leaf rust with increased virulence for several popular varieties was discovered in WA. Testing through the Australian Cereal Rust Control Program at Sydney University confirmed the presence of the leaf rust pathotype named 76-1, 3, 5, 7, 9, 10, 12 +Lr 37. "This represents the first occurrence in WA of virulence for varieties which contain Lr13 resistance," Mr Thomas said. "As a result, several varieties, including Mace, are expected to have an altered response in the presence of this pathotype. "In order to gauge the rust response of wheat varieties popular in WA, the Department recently completed glasshouse trials to test the seedling and adult reactions of varieties to this new pathotype. "Our pathology tests confirmed that varieties Mace, Wyalkatchem and Corack, which all carry Lr13, are susceptible (S) as seedlings and moderately susceptible to susceptible (MS-S) as adult plants. "This result signifies a significant reduction in resistance from the moderately-resistant (MR) response of these varieties to the former dominant rust pathotype in WA.


Via CIMMYT, Int., Kamoun Lab @ TSL
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South American science: Big players

South American science: Big players | Plant pathogenic fungi | Scoop.it
Despite myriad problems in many countries, pockets of excellence thrive in South American science.
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Buzzfeed: 11 Plant Diseases That Could Make Your Favorite Foods Disappear (2014)

Buzzfeed: 11 Plant Diseases That Could Make Your Favorite Foods Disappear (2014) | Plant pathogenic fungi | Scoop.it

You know people and animals get sick, but plants also get sick. Plant diseases threaten some of the world’s favorite food sources. Luckily, plant pathologists (plant doctors) stand between plant diseases and the world’s food supply.


Via Kamoun Lab @ TSL
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Rusty Waves of Grain | The Scientist Magazine®

Rusty Waves of Grain | The Scientist Magazine® | Plant pathogenic fungi | Scoop.it
See how a ruinous fungus that attacks wheat wreaks its damage.
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more from the Scientist

Includes a great video about wheat stem rust.

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Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii

Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii | Plant pathogenic fungi | Scoop.it

The ever-increasing demand for transportation fuels, the decrease in global petroleum reserves, and the negative impact of greenhouse gases resulting from burning petroleum make renewable and sustainable biofuels an imperative for the future. First-generation biofuels produced from food crops are limited by cost and competition with food supply. Considerable effort has been made to produce fuels from lignocellulosic biomass, but the need for chemical and enzymatic pretreatment to solubilize the biomass prior to microbial bioconversion is a major economic barrier to the development of an industrial process. Here we report the metabolic engineering of a bacterium, Caldicellulosiruptor bescii, that is capable of using unprocessed switchgrass, an abundant, environmentally desirable, and economically sustainable lignocellulosic plant biomass, as feedstock to produce ethanol.

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Illuminating Fungal Infections with Bioluminescence

Illuminating Fungal Infections with Bioluminescence | Plant pathogenic fungi | Scoop.it
From molecules to physiology
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Frontiers | The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration | Plant-Microbe Interaction

Frontiers | The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration | Plant-Microbe Interaction | Plant pathogenic fungi | Scoop.it
Plant diseases are one of the most studied subjects in the field of plant science due to their impact on crop yield and food security. Our increased understanding of plant–pathogen interactions was mainly driven by the development of new techniques that facilitated analyses on a subcellular and molecular level. The development of labeling technologies, which allowed the visualization and localization of cellular structures and proteins in live cell imaging, promoted the use of fluorescence and laser-scanning microscopy in the field of plant–pathogen interactions. Recent advances in new microscopic technologies opened their application in plant science and in the investigation of plant diseases. In this regard, in planta Förster/Fluorescence resonance energy transfer has demonstrated to facilitate the measurement of protein-protein interactions within the living tissue, supporting the analysis of regulatory pathways involved in plant immunity and putative host-pathogen interactions on a nanoscale level. Localization microscopy, an emerging, non-invasive microscopic technology, will allow investigations with a nanoscale resolution leading to new possibilities in the understanding of molecular processes.
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New mushrooms found in porcini packet | Kew News

New mushrooms found in porcini packet | Kew News | Plant pathogenic fungi | Scoop.it
Kew mycologists Bryn Dentinger and Laura Martinez-Suz have discovered three species of mushrooms that are new to science in a commercial packet of dried Chinese porcini purchased from a shop in London.
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Noisy Predators Put Plants on Alert, Study Finds

Noisy Predators Put Plants on Alert, Study Finds | Plant pathogenic fungi | Scoop.it
Plants respond to sound, but why? Researchers who exposed plants to the vibrations of chomping caterpillars say the reason is self-defense.
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?!

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One lichen is actually 126 species and counting | Science News

One lichen is actually 126 species and counting | Science News | Plant pathogenic fungi | Scoop.it
One supposedly well-known tropical lichen could really be several hundred kinds.
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Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data

Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data | Plant pathogenic fungi | Scoop.it

•We evaluated the oldest available fossil ascomycetes from amber and chert.

•We solely used fossil ascomycetes to model a molecular clock with BEAST.

•Our results suggest an initial diversification of ascomycetes in the Ordovician.

•Continuous diversification within ascomycete classes occurred during the Phanerozoic.

•Taxa of each lineage probably survived crises due to their ecological diversity.

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Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic

Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic | Plant pathogenic fungi | Scoop.it

Fungi are abundant and functionally important in the Arctic, yet comprehensive studies of their diversity in relation to geography and environment are not available. We sampled soils in paired plots along the North American Arctic Transect (NAAT), which spans all five bioclimatic subzones of the Arctic. Each pair of plots contrasted relatively bare, cryoturbated patterned-ground features (PGFs) and adjacent vegetated between patterned-ground features (bPGFs). Fungal communities were analysed via sequencing of 7834 ITS-LSU clones. We recorded 1834 OTUs – nearly half the fungal richness previously reported for the entire Arctic. These OTUs spanned eight phyla, 24 classes, 75 orders and 120 families, but were dominated by Ascomycota, with one-fifth belonging to lichens. Species richness did not decline with increasing latitude, although there was a decline in mycorrhizal taxa that was offset by an increase in lichen taxa. The dominant OTUs were widespread even beyond the Arctic, demonstrating no dispersal limitation. Yet fungal communities were distinct in each subzone and were correlated with soil pH, climate and vegetation. Communities in subzone E were distinct from the other subzones, but similar to those of the boreal forest. Fungal communities on disturbed PGFs differed significantly from those of paired stable areas in bPGFs. Indicator species for PGFs included lichens and saprotrophic fungi, while bPGFs were characterized by ectomycorrhizal and pathogenic fungi. Our results suggest that the Arctic does not host a unique mycoflora, while Arctic fungi are highly sensitive to climate and vegetation, with potential to migrate rapidly as global change unfolds.


Via Francis Martin
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World Food Prize organizations announces Sanjaya Rajaram will be 2014 World Food Prize laureate | Delta Farm Press

World Food Prize organizations announces Sanjaya Rajaram will be 2014 World Food Prize laureate | Delta Farm Press | Plant pathogenic fungi | Scoop.it
“I felt highly honored to receive the news that the 2014 World Food Prize would be awarded to me, and through me, to hundreds and thousands of wheat researchers and farmers around the world. I believe that the challenges of 21st-century agriculture and food production are surmountable compared to the past and can be overcome provided we can bring together new knowledge and delivery systems to farmers in a very sustainable manner. Future crop production is bound to decline unless we fully factor in the issues related to climate change, soil fertility and water deficits, and utilize advanced genetics in the next 20 to 30 years. It will require all the resources from international research centers, national governments, foundations, NGOs and farmer groups together to synergize future agricultural technologies and food production.” – Dr. Sanjaya Rajaram
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Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing

Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing | Plant pathogenic fungi | Scoop.it

Although the number of studies investigating mycorrhizal associations in orchids has increased in recent years, the fungal communities associating with orchids and how they differ between species and sites remain unclear. Recent research has indicated that individual orchid plants may associate with several fungi concurrently, implying that to study mycorrhizal associations in orchids the fungal community should be assessed, rather than the presence of individual dominant fungal species or strains. High-throughput sequencing methods, such as 454 pyrosequencing, are increasingly used as the primary tool for such analyses. However, many studies combine universal primers from previous phylogenetic or ecological studies to generate amplicons suitable for 454 pyrosequencing without first critically evaluating their performance, potentially resulting in biased fungal community descriptions. Here, following in silico primer analysis we evaluated the performance of different combinations of existing PCR primers to characterize orchid mycorrhizal communities using 454 pyrosequencing by analysis of both an artificially assembled community of mycorrhizal fungi isolated from diverse orchid species and root samples from three different orchid species (Anacamptis morio, Ophrys tenthredinifera and Serapias lingua). Our results indicate that primer pairs ITS3/ITS4OF and ITS86F/ITS4, targeting the internal transcribed spacer-2 (ITS-2) region, outperformed other tested primer pairs in terms of number of reads, number of operational taxonomic units recovered from the artificial community and number of different orchid mycorrhizal associating families detected in the orchid samples. Additionally, we show the complementary specificity of both primer pairs, making them highly suitable for tandem use when studying the diversity of orchid mycorrhizal communities.


Via Francis Martin, Niklaus Grunwald
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A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding | Plant pathogenic fungi | Scoop.it

Gumei 4/R608 BC4F1 plants. Black arrow above Gumei 4 indicates the locus of Pigm(t)

 

 

Here we report the development of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.


Via Christophe Jacquet, Elsa Ballini
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Curr Opin Plant Biol: Cross-interference of plant development and plant–microbe interactions (2014)

Curr Opin Plant Biol: Cross-interference of plant development and plant–microbe interactions (2014) | Plant pathogenic fungi | Scoop.it

Plant roots are host to a multitude of filamentous microorganisms. Among these, arbuscular mycorrhizal fungi provide benefits to plants, while pathogens trigger diseases resulting in significant crop yield losses. It is therefore imperative to study processes which allow plants to discriminate detrimental and beneficial interactions in order to protect crops from diseases while retaining the ability for sustainable bio-fertilisation strategies. Accumulating evidence suggests that some symbiosis processes also affect plant–pathogen interactions. A large part of this overlap likely constitutes plant developmental processes. Moreover, microbes utilise effector proteins to interfere with plant development. Here we list relevant recent findings on how plant–microbe interactions intersect with plant development and highlight future research leads.


Via Kamoun Lab @ TSL, IvanOresnik
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Rakesh Yashroy's curator insight, July 2, 7:54 AM

Microbe-macrobe or host-pathogen interface determines the cell-cell interactions largely @ http://en.wikipedia.org/wiki/Host-pathogen_interface

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Plant Scourges | The Scientist Magazine®

Plant Scourges | The Scientist Magazine® | Plant pathogenic fungi | Scoop.it
A sampling of some of the most devastating crop pathogens
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a rogues' gallery

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