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DOE Joint Genome Institute - My submission for the DOE Joint Genome Institute Poetry…

DOE Joint Genome Institute - My submission for the DOE Joint Genome Institute Poetry… | MycorWeb Plant-Microbe Interactions | Scoop.it
ENERGY IN THE TREES

Poplar tree growing fast and tall:
how do your genes make your cell walls?

Enzymes string together sugars into rows,
to make straight fibers you know as cellulose;

Reverse this process during cell wall degradation,
and you get sugars for biofuel creation!

Alas there’s also lignin, an amorphous beast;
lignin linked to cellulose blocks sugar release.

To solve this recalcitrance, the genome holds the key,
let’s make better poplar — for sustainable energy!
Francis Martin's insight:

Poem by Kelsey Wood was inspired in part by a talk by Gerald Tuskan (Oak Rigde) at JGI 2014 User's Meeting and is 10 lines long to mark a decade of the Community Science Program.

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Rescooped by Francis Martin from Plant-Microbe Symbioses
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The Potential of Dark Septate Endophytes to Form Root Symbioses with Ectomycorrhizal and Ericoid Mycorrhizal Middle European Forest Plants

The Potential of Dark Septate Endophytes to Form Root Symbioses with Ectomycorrhizal and Ericoid Mycorrhizal Middle European Forest Plants | MycorWeb Plant-Microbe Interactions | Scoop.it
The unresolved ecophysiological significance of Dark Septate Endophytes (DSE) may be in part due to existence of morphologically indistinguishable cryptic species in the most common Phialocephala fortinii s. l.—Acephala applanata species complex (PAC). We inoculated three middle European forest plants (European blueberry, Norway spruce and silver birch) with 16 strains of eight PAC cryptic species and other DSE and ectomycorrhizal/ericoid mycorrhizal fungi and focused on intraradical structures possibly representing interfaces for plant-fungus nutrient transfer and on host growth response. The PAC species Acephala applanata simultaneously formed structures resembling ericoid mycorrhiza (ErM) and DSE microsclerotia in blueberry. A. macrosclerotiorum, a close relative to PAC, formed ectomycorrhizae with spruce but not with birch, and structures resembling ErM in blueberry. Phialocephala glacialis, another close relative to PAC, formed structures resembling ErM in blueberry. In blueberry, six PAC strains significantly decreased dry shoot biomass compared to ErM control. In birch, one A. macrosclerotiorum strain increased root biomass and the other shoot biomass in comparison with non-inoculated control. The dual mycorrhizal ability of A. macrosclerotiorum suggested that it may form mycorrhizal links between Ericaceae and Pinaceae. However, we were unable to detect this species in Ericaceae roots growing in a forest with presence of A. macrosclerotiorum ectomycorrhizae. Nevertheless, the diversity of Ericaceae mycobionts was high (380 OTUs) with individual sites often dominated by hitherto unreported helotialean and chaetothyrialean/verrucarialean species; in contrast, typical ErM fungi were either absent or low in abundance. Some DSE apparently have a potential to form mycorrhizae with typical middle European forest plants. However, except A. applanata, the tested representatives of all hitherto described PAC cryptic species formed typical DSE colonization without specific structures necessary for mycorrhizal nutrient transport. A. macrosclerotiorum forms ectomycorrhiza with conifers but not with broadleaves and probably does not form common mycorrhizal networks between conifers with Ericaceae.

Via Jean-Michel Ané
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Genomics in a changing arctic: critical questions await the molecular ecologist

Genomics in a changing arctic: critical questions await the molecular ecologist | MycorWeb Plant-Microbe Interactions | Scoop.it

Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high-latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate.

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YouTube: Sophien Kamoun at the 2015 DOE JGI Genomics of Energy & Environment Meeting

Sophien Kamoun, The Sainsbury Laboratory, at the 10th Annual Genomics of Energy & Environment Meeting held March 24-26, 2015 in Walnut Creek, Calif.


Via Kamoun Lab @ TSL
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Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches

Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches | MycorWeb Plant-Microbe Interactions | Scoop.it
Most fungi from the Mucoromycotina lineage occur in ecosystems as saprobes, although some species are phytopathogens or may induce human mycosis. Mucoromycotina represent early diverging models that are most valuable for understanding fungal evolution. Here we reveal the uniqueness of the cell wall structure of the Mucoromycotina Rhizopus oryzae and Phycomyces blakesleeanus compared with the better characterized cell wall of the ascomycete Neurospora crassa. We have analysed the corresponding polysaccharide biosynthetic and modifying pathways, and highlight their evolutionary features and higher complexity in terms of gene copy numbers compared with species from other lineages. This work uncovers the presence in Mucoromycotina of abundant fucose-based polysaccharides similar to algal fucoidans. These unexpected polymers are associated with unusually low amounts of glucans and a higher proportion of chitin compared with N. crassa. The specific structural features are supported by the identification of genes potentially involved in the corresponding metabolic pathways. Phylogenomic analyses of genes encoding carbohydrate synthases, polysaccharide modifying enzymes and enzymes involved in nucleotide-sugar formation provide evidence for duplication events during evolution of cell wall metabolism in fungi. Altogether, the data highlight the specificity of Mucoromycotina cell walls and pave the way for a finer understanding of their metabolism.
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Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species

Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species | MycorWeb Plant-Microbe Interactions | Scoop.it

Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies.

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Evolving new organisms via symbiosis

Evolving new organisms via symbiosis | MycorWeb Plant-Microbe Interactions | Scoop.it
Symbiotic partnerships are a major source of evolutionary innovation. They have driven rapid diversification of organisms, allowed hosts to harness new forms of energy, and radically modified Earth's nutrient cycles. The application of next-generation sequencing and advanced microscopic techniques has revealed not only the ubiquity of symbiotic partnerships, but the extent to which partnerships can become physically, genomically, and metabolically integrated (1). When and why does this integration of once free-living organisms happen?
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Rescooped by Francis Martin from Plants and Microbes
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Plant Cell: A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors (2015)

Plant Cell: A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors (2015) | MycorWeb Plant-Microbe Interactions | Scoop.it

The biotrophic smut fungus Ustilago maydis infects all aerial organs of maize (Zea mays) and induces tumors in the plant tissues. U. maydis deploys many effector proteins to manipulate its host. Previously, deletion analysis demonstrated that several effectors have important functions in inducing tumor expansion specifically in maize leaves. Here, we present the functional characterization of the effector See1 (Seedling efficient effector1). See1 is required for the reactivation of plant DNA synthesis, which is crucial for tumor progression in leaf cells. By contrast, See1 does not affect tumor formation in immature tassel floral tissues, where maize cell proliferation occurs independent of fungal infection. See1 interacts with a maize homolog of SGT1 (Suppressor of G2 allele of skp1), a factor acting in cell cycle progression in yeast (Saccharomyces cerevisiae) and an important component of plant and human innate immunity. See1 interferes with the MAPK-triggered phosphorylation of maize SGT1 at a monocot-specific phosphorylation site. We propose that See1 interferes with SGT1 activity, resulting in both modulation of immune responses and reactivation of DNA synthesis in leaf cells. This identifies See1 as a fungal effector that directly and specifically contributes to the formation of leaf tumors in maize.


Via Kamoun Lab @ TSL
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Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis

Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis | MycorWeb Plant-Microbe Interactions | Scoop.it
Batrachochytrium dendrobatidis (Bd) is the causative agent of chytridiomycosis responsible for worldwide decline in amphibian populations. Previous analysis of the Bd genome revealed a unique expansion of the carbohydrate-binding module family 18 (CBM18) predicted to be a sub-class of chitin recognition domains. CBM expansions have been linked to the evolution of pathogenicity in a variety of fungal species by protecting the fungus from the host. Based on phylogenetic analysis and presence of additional protein domains, the gene family can be classified into 3 classes: Tyrosinase-, Deacetylase-, and Lectin-like. Examination of the mRNA expression levels from sporangia and zoospores of nine of the cbm18 genes found that the Lectin-like genes had the highest expression while the Tyrosinase-like genes showed little expression, especially in zoospores. Heterologous expression of GFP-tagged copies of four CBM18 genes in Saccharomyces cerevisiae demonstrated that two copies containing secretion signal peptides are trafficked to the cell boundary. The Lectin-like genes cbm18-ll1 and cbm18-ll2 co-localized with the chitinous cell boundaries visualized by staining with calcofluor white. In vitro assays of the full length and single domain copies from CBM18-LL1 demonstrated chitin binding and no binding to cellulose or xylan. Expressed CBM18 domain proteins were demonstrated to protect the fungus, Trichoderma reeseii, in vitro against hydrolysis from exogenously added chitinase, likely by binding and limiting exposure of fungal chitin. These results demonstrate that cbm18 genes can play a role in fungal defense and expansion of their copy number may be an important pathogenicity factor of this emerging infectious disease of amphibians.
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The Top 10 oomycete pathogens in molecular plant pathology

The Top 10 oomycete pathogens in molecular plant pathology | MycorWeb Plant-Microbe Interactions | Scoop.it
Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
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Rescooped by Francis Martin from Insights into Soil Ecology
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The role of symbiosis in the transition of some eukaryotes from aquatic to terrestrial environments

The role of symbiosis in the transition of some eukaryotes from aquatic to terrestrial environments | MycorWeb Plant-Microbe Interactions | Scoop.it
Symbiosis may have played a far greater role in biological evolution than was previously thought. The symbiosis that made the colonization of land by plants possible was as a consequence of the development of arbuscular mycorrhizae. However, the present review draws attention to the role of lichens in assisting in this transition and to the phenomenon of lichenization. The recent discovery of lichen fossils in marine phosphorites in China and molecular clock estimates indicate that lichenized fungi were already present in Precambrian seas and, like contemporary species, played a role as pioneers in occupying new habitats. There is evidence that the holistic properties of associations between fungi and cyanobacteria and/or green algae facilitated the transition onto land and the subsequent colonization of terrestrial habitats. A key role in this process was played by poikilohydry. The algal components of delichenized fungi, along with lichens and photosynthetic aquatic organisms all contributed to the increase in atmospheric oxygen. Lichens, fungi and cyanobacteria settling on land were undoubtedly important in the formation of soils and thereafter enhancing their fertility. It is suggested that vascular and other green plants were able grow on these primitive soils that were stabilized by the growth of lichens, algae and cyanobacteria in a similar way to those which play a role in desert crusts at the present time.

Via Jean-Michel Ané, Pedobiologia: Journal of Soil Ecology
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Self-DNA: a blessing in disguise?

Self-DNA: a blessing in disguise? | MycorWeb Plant-Microbe Interactions | Scoop.it
Mazzoleni et al. (2015a,b) in two recent papers provided novel and rigorous evidence for a unique detrimental effect of self-DNA (i.e. DNA originating from conspecifics) on organismal growth. The authors investigated the effect as a means of explaining plant–soil feedbacks via plant litter (Mazzoleni et al., 2015a) and subsequently convincingly generalized their observations to a range of additional organisms including protozoa, algae, fungi and animals. The authors explain the growth suppression on the basis of inhibitory effects of self-DNA. They argue that this inhibition mechanism, through facilitating coexistence, represents a mechanism of maintaining diversity. The ecological, physiological and molecular significance of the observations of Mazzoleni et al. (2015a,b) is thought-provoking. A priority now is to start a discourse on the interpretation of the results of these studies, because this will help design focused experiments to further investigate the role of self-DNA on growth.
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Jean-Michel Ané's curator insight, April 21, 9:45 AM
That's really a provoking idea indeed...
Pedobiologia: Journal of Soil Ecology's curator insight, April 21, 6:15 PM

Can self-DNA act as a signal of conspecific density? An excellent and contextual mechanistic proposal.

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Global Genome and Transcriptome Analyses of Magnaporthe oryzae Epidemic Isolate 98-06 Uncover Novel Effectors and Pathogenicity-Related Genes, Revealing Gene Gain and Lose Dynamics in Genome Evol...

Global Genome and Transcriptome Analyses of  Magnaporthe oryzae  Epidemic Isolate 98-06 Uncover Novel Effectors and Pathogenicity-Related Genes, Revealing Gene Gain and Lose Dynamics in Genome Evol... | MycorWeb Plant-Microbe Interactions | Scoop.it
Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution, in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates. This same principle applies to the rice blast pathogen Magnaporthe oryzae and the rice host; however, genetic variations among different isolates of M. oryzae remain largely unknown, particularly at genome and transcriptome levels. Here, we applied genomic and transcriptomic analytical tools to investigate M. oryzae isolate 98-06 that is the most aggressive in infection of susceptible rice cultivars. A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15. Genome-wide expression profiling revealed the presence of two critical expression patterns of M. oryzae based on 64 known pathogenicity-related (PaR) genes. In addition, 134 candidate effectors with various segregation patterns were identified. Five tested proteins could suppress BAX-mediated programmed cell death in Nicotiana benthamiana leaves. Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity. Moreover, Iug6 and Iug9 are located exclusively in the biotrophic interfacial complex (BIC) and their overexpression leads to suppression of defense-related gene expression in rice, suggesting that they might participate in biotrophy by inhibiting the SA and ET pathways within the host. Thus, our studies identify novel effector and PaR proteins involved in pathogenicity of the highly aggressive M. oryzae field isolate 98-06, and reveal molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions.
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Evolutionary innovation and ecology in marine tetrapods from the Triassic to the Anthropocene

Evolutionary innovation and ecology in marine tetrapods from the Triassic to the Anthropocene | MycorWeb Plant-Microbe Interactions | Scoop.it

Many top consumers in today’s oceans are marine tetrapods, a collection of lineages independently derived from terrestrial ancestors. The fossil record illuminates their transitions from land to sea, yet these initial invasions account for a small proportion of their evolutionary history. We review the history of marine invasions that drove major changes in anatomy, physiology, and ecology over more than 250 million years. Many innovations evolved convergently in multiple clades, whereas others are unique to individual lineages. The evolutionary arcs of these ecologically important clades are framed against the backdrop of mass extinctions and regime shifts in ocean ecosystems. Past and present human disruptions to marine tetrapods, with cascading impacts on marine ecosystems, underscore the need to link macroecology with evolutionary change.

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SNP genotyping and population genomics from expressed sequences – current advances and future possibilities

SNP genotyping and population genomics from expressed sequences – current advances and future possibilities | MycorWeb Plant-Microbe Interactions | Scoop.it

With the rapid increase in production of genetic data from new sequencing technologies, a myriad of new ways to study genomic patterns in nonmodel organisms are currently possible. Because genome assembly still remains a complicated procedure, and because the functional role of much of the genome is unclear, focusing on SNP genotyping from expressed sequences provides a cost-effective way to reduce complexity while still retaining functionally relevant information. This review summarizes current methods, identifies ways that using expressed sequence data benefits population genomic inference and explores how current practitioners evaluate and overcome challenges that are commonly encountered. We focus particularly on the additional power of functional analysis provided by expressed sequence data and how these analyses push beyond allele pattern data available from nonfunction genomic approaches. The massive data sets generated by these approaches create opportunities and problems as well – especially false positives. We discuss methods available to validate results from expressed SNP genotyping assays, new approaches that sidestep use of mRNA and review follow-up experiments that can focus on evolutionary mechanisms acting across the genome.

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PNAS: The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop (2015)

PNAS: The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop (2015) | MycorWeb Plant-Microbe Interactions | Scoop.it

Agrobacterium rhizogenes and Agrobacterium tumefaciens are plant pathogenic bacteria capable of transferring DNA fragments [transfer DNA (T-DNA)] bearing functional genes into the host plant genome. This naturally occurring mechanism has been adapted by plant biotechnologists to develop genetically modified crops that today are grown on more than 10% of the world’s arable land, although their use can result in considerable controversy. While assembling small interfering RNAs, or siRNAs, of sweet potato plants for metagenomic analysis, sequences homologous to T-DNA sequences from Agrobacterium spp. were discovered. Simple and quantitative PCR, Southern blotting, genome walking, and bacterial artificial chromosome library screening and sequencing unambiguously demonstrated that two different T-DNA regions (IbT-DNA1 and IbT-DNA2) are present in the cultivated sweet potato (Ipomoea batatas [L.] Lam.) genome and that these foreign genes are expressed at detectable levels in different tissues of the sweet potato plant. IbT-DNA1 was found to contain four open reading frames (ORFs) homologous to the tryptophan-2-monooxygenase (iaaM), indole-3-acetamide hydrolase (iaaH), C-protein (C-prot), and agrocinopine synthase (Acs) genes of Agrobacterium spp. IbT-DNA1 was detected in all 291 cultigens examined, but not in close wild relatives. IbT-DNA2 contained at least five ORFs with significant homology to the ORF14, ORF17n, rooting locus (Rol)B/RolC, ORF13, and ORF18/ORF17n genes of A. rhizogenes. IbT-DNA2 was detected in 45 of 217 genotypes that included both cultivated and wild species. Our finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops.


Via Kamoun Lab @ TSL
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PLoS ONE: Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi

PLoS ONE: Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi | MycorWeb Plant-Microbe Interactions | Scoop.it

Rust fungi are obligate biotrophic pathogens that cause considerable damage on crop plants. Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, and Melampsora larici-populina, the poplar leaf rust pathogen, have strong deleterious impacts on wheat and poplar wood production, respectively. Filamentous pathogens such as rust fungi secrete molecules called disease effectors that act as modulators of host cell physiology and can suppress or trigger host immunity. Current knowledge on effectors from other filamentous plant pathogens can be exploited for the characterisation of effectors in the genome of recently sequenced rust fungi. We designed a comprehensive in silico analysis pipeline to identify the putative effector repertoire from the genome of two plant pathogenic rust fungi. The pipeline is based on the observation that known effector proteins from filamentous pathogens have at least one of the following properties: (i) contain a secretion signal, (ii) are encoded by in planta induced genes, (iii) have similarity to haustorial proteins, (iv) are small and cysteine rich, (v) contain a known effector motif or a nuclear localization signal, (vi) are encoded by genes with long intergenic regions, (vii) contain internal repeats, and (viii) do not contain PFAM domains, except those associated with pathogenicity. We used Markov clustering and hierarchical clustering to classify protein families of rust pathogens and rank them according to their likelihood of being effectors. Using this approach, we identified eight families of candidate effectors that we consider of high value for functional characterization. This study revealed a diverse set of candidate effectors, including families of haustorial expressed secreted proteins and small cysteine-rich proteins. This comprehensive classification of candidate effectors from these devastating rust pathogens is an initial step towards probing plant germplasm for novel resistance components.


Via Kamoun Lab @ TSL
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The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library

The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungal invasions are increasingly recognized as a significant component of global changes, threatening ecosystem health and damaging food production. Invasive fungi also provide excellent models to evaluate the generality of results based on other eukaryotes. We first consider here the reasons why fungal invasions have long been overlooked: they tend to be inconspicuous, and inappropriate methods have been used for species recognition. We then review the information available on the patterns and mechanisms of fungal invasions. We examine the biological features underlying invasion success of certain fungal species. We review population structure analyses, revealing native source populations and strengths of bottlenecks. We highlight the documented ecological and evolutionary changes in invaded regions, including adaptation to temperature, increased virulence, hybridization, shifts to clonality and association with novel hosts. We discuss how the huge census size of most fungi allows adaptation even in bottlenecked, clonal invaders. We also present new analyses of the invasion of the anther-smut pathogen on white campion in North America, as a case study illustrating how an accurate knowledge of species limits and phylogeography of fungal populations can be used to decipher the origin of invasions. This case study shows that successful invasions can occur even when life history traits are particularly unfavourable to long-distance dispersal and even with a strong bottleneck. We conclude that fungal invasions are valuable models to contribute to our view of biological invasions, in particular by providing insights into the traits as well as ecological and evolutionary processes allowing successful introductions.
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Novel findings on the role of signal exchange in arbuscular and ectomycorrhizal symbioses

Novel findings on the role of signal exchange in arbuscular and ectomycorrhizal symbioses | MycorWeb Plant-Microbe Interactions | Scoop.it

The availability of genome sequences from both arbuscular and ectomycorrhizal fungi and their hosts has, together with elegant biochemical and molecular biological analyses, provided new information on signal exchange between the partners in mycorrhizal associations. The progress in understanding cellular processes has been more rapid in arbuscular than ectomycorrhizal symbiosis due to its similarities of early processes with Rhizobium-legume symbiosis. In ectomycorrhiza, the role of auxin and ethylene produced by both fungus and host plant is becoming understood at the molecular level, although the actual ligands and receptors leading to ectomycorrhizal symbiosis have not yet been discovered. For both systems, the functions of small effector proteins secreted from the respective fungus and taken up into the plant cell may be pivotal in understanding the attenuation of host defense. We review the subject by comparing cross-talk between fungal and plant partners during formation and establishment of arbuscular and ectomycorrhizal symbioses.

Francis Martin's insight:

Amazed by the number of review papers released recently on signals, effectors and signaling pathways in mycorrhiza while the number of research papers remains very scarce.

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Jean-Michel Ané's curator insight, April 25, 5:50 PM

Strikingly similar to our latest review in New Phytologist: http://onlinelibrary.wiley.com/doi/10.1111/nph.13423/abstract

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Molecular cartography of the human skin surface in 3D

Molecular cartography of the human skin surface in 3D | MycorWeb Plant-Microbe Interactions | Scoop.it

The human skin is an organ with a surface area of 1.5–2 m2 that provides our interface with the environment. The molecular composition of this organ is derived from host cells, microbiota, and external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance the technologies needed to explore the topographical distribution of skin molecules, using 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal that the molecular composition of skin has diverse distributions and that the composition is defined not only by skin cells and microbes but also by our daily routines, including the application of hygiene products. The technological development of these maps lays a foundation for studying the spatial relationships of human skin with hygiene, the microbiota, and environment, with potential for developing predictive models of skin phenotypes tailored to individual health

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GATA-Dependent Glutaminolysis Drives Appressorium Formation in Magnaporthe oryzae by Suppressing TOR Inhibition of cAMP/PKA Signaling

GATA-Dependent Glutaminolysis Drives Appressorium Formation in  Magnaporthe oryzae  by Suppressing TOR Inhibition of cAMP/PKA Signaling | MycorWeb Plant-Microbe Interactions | Scoop.it
Author Summary Many fungal pathogens destroy important crops by first gaining entrance to the host using specialized appressorial cells. Understanding the molecular mechanisms that control appressorium formation could provide new routes for managing severe plant diseases. Here, we describe a previously unknown regulatory pathway that suppresses appressorium formation by the rice pathogen Magnaporthe oryzae . We provide evidence that a mutant M . oryzae strain, unable to form appressoria,
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Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection

Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection | MycorWeb Plant-Microbe Interactions | Scoop.it
A broad range of parasites rely on the functions of effector proteins to subvert host immune response and facilitate disease development. The notorious Phytophthora pathogens evolved effectors with RNA silencing suppression activity to promote infection in plant hosts. Here we report that the Phytophthora Suppressor of RNA Silencing 1 (PSR1) can bind to an evolutionarily conserved nuclear protein containing the aspartate–glutamate–alanine–histidine-box RNA helicase domain in plants. This protein, designated PSR1-Interacting Protein 1 (PINP1), regulates the accumulation of both microRNAs and endogenous small interfering RNAs in Arabidopsis. A null mutation of PINP1 causes embryonic lethality, and silencing of PINP1 leads to developmental defects and hypersusceptibility to Phytophthora infection. These phenotypes are reminiscent of transgenic plants expressing PSR1, supporting PINP1 as a direct virulence target of PSR1. We further demonstrate that the localization of the Dicer-like 1 protein complex is impaired in the nucleus of PINP1-silenced or PSR1-expressing cells, indicating that PINP1 may facilitate small RNA processing by affecting the assembly of dicing complexes. A similar function of PINP1 homologous genes in development and immunity was also observed in Nicotiana benthamiana. These findings highlight PINP1 as a previously unidentified component of RNA silencing that regulates distinct classes of small RNAs in plants. Importantly, Phytophthora has evolved effectors to target PINP1 in order to promote infection.
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Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses - Garcia - 2015 - New Phytologist - Wiley Online Library

Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses - Garcia - 2015 - New Phytologist - Wiley Online Library | MycorWeb Plant-Microbe Interactions | Scoop.it

Ectomycorrhizal (ECM) symbioses are among the most widespread associations between roots of woody plants and soil fungi in forest ecosystems. These associations contribute significantly to the sustainability and sustainagility of these ecosystems through nutrient cycling and carbon sequestration. Unfortunately, the molecular mechanisms controlling the mutual recognition between both partners are still poorly understood. Elegant work has demonstrated that effector proteins from ECM and arbuscular mycorrhizal (AM) fungi regulate host defenses by manipulating plant hormonal pathways. In parallel, genetic and evolutionary studies in legumes showed that a ‘common symbiosis pathway’ is required for the establishment of the ancient AM symbiosis and has been recruited for the rhizobia–legume association. Given that genes of this pathway are present in many angiosperm trees that develop ectomycorrhizas, we propose their potential involvement in some but not all ECM associations. The maintenance of a successful long-term relationship seems strongly regulated by resource allocation between symbiotic partners, suggesting that nutrients themselves may serve as signals. This review summarizes our current knowledge on the early and late signal exchanges between woody plants and ECM fungi, and we suggest future directions for decoding the molecular basis of the underground dance between trees and their favorite fungal partners.


Via Kevin Garcia
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Rescooped by Francis Martin from Insights into Soil Ecology
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The role of community and population ecology in applying mycorrhizal fungi for improved food security

The role of community and population ecology in applying mycorrhizal fungi for improved food security | MycorWeb Plant-Microbe Interactions | Scoop.it
The global human population is expected to reach ~9 billion by 2050. Feeding this many people represents a major challenge requiring global crop yield increases of up to 100%. Microbial symbionts of plants such as arbuscular mycorrhizal fungi (AMF) represent a huge, but unrealized resource for improving yields of globally important crops, especially in the tropics. We argue that the application of AMF in agriculture is too simplistic and ignores basic ecological principals. To achieve this challenge, a community and population ecology approach can contribute greatly. First, ecologists could significantly improve our understanding of the determinants of the survival of introduced AMF, the role of adaptability and intraspecific diversity of AMF and whether inoculation has a direct or indirect effect on plant production. Second, we call for extensive metagenomics as well as population genomics studies that are crucial to assess the environmental impact that introduction of non-local AMF may have on native AMF communities and populations. Finally, we plead for an ecologically sound use of AMF in efforts to increase food security at a global scale in a sustainable manner.

Via Jean-Michel Ané, Pedobiologia: Journal of Soil Ecology
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Jean-Michel Ané's curator insight, April 21, 3:38 PM

Excellent review

Pedobiologia: Journal of Soil Ecology's curator insight, April 21, 6:33 PM

All are important questions to answer, but what about the question: what are the characteristics that make an AM fungus beneficial in an agricultural context? A trait-based approach would address this and some of the questions posed in the review.

Scooped by Francis Martin
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Contrasting Diversity and Host Association of Ectomycorrhizal Basidiomycetes versus Root-Associated Ascomycetes in a Dipterocarp Rainforest

Contrasting Diversity and Host Association of Ectomycorrhizal Basidiomycetes versus Root-Associated Ascomycetes in a Dipterocarp Rainforest | MycorWeb Plant-Microbe Interactions | Scoop.it
Root-associated fungi, including ectomycorrhizal and root-endophytic fungi, are among the most diverse and important belowground plant symbionts in dipterocarp rainforests. Our study aimed to reveal the biodiversity, host association, and community structure of ectomycorrhizal Basidiomycota and root-associated Ascomycota (including root-endophytic Ascomycota) in a lowland dipterocarp rainforest in Southeast Asia. The host plant chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) region and fungal internal transcribed spacer 2 (ITS2) region were sequenced using tag-encoded, massively parallel 454 pyrosequencing to identify host plant and root-associated fungal taxa in root samples. In total, 1245 ascomycetous and 127 putative ectomycorrhizal basidiomycetous taxa were detected from 442 root samples. The putative ectomycorrhizal Basidiomycota were likely to be associated with closely related dipterocarp taxa to greater or lesser extents, whereas host association patterns of the root-associated Ascomycota were much less distinct. The community structure of the putative ectomycorrhizal Basidiomycota was possibly more influenced by host genetic distances than was that of the root-associated Ascomycota. This study also indicated that in dipterocarp rainforests, root-associated Ascomycota were characterized by high biodiversity and indistinct host association patterns, whereas ectomycorrhizal Basidiomycota showed less biodiversity and a strong host phylogenetic preference for dipterocarp trees. Our findings lead to the working hypothesis that root-associated Ascomycota, which might be mainly represented by root-endophytic fungi, have biodiversity hotspots in the tropics, whereas biodiversity of ectomycorrhizal Basidiomycota increases with host genetic diversity.
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Rescooped by Francis Martin from Plant & Evolution
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Evolution of mycoheterotrophy in Polygalaceae: The case of Epirixanthes

• Premise of the study: The mycoheterotrophic lifestyle has enabled some plant lineages to obtain carbon from their mycorrhizal symbionts. The mycoheterotrophic genus Epirixanthes (Polygalaceae) consists of six species from tropical Asia. Although it is probably closely related to the chlorophyllous genus Salomonia and linked to arbuscular mycorrhizal fungi, lack of DNA sequence data has thus far prevented these hypotheses from being tested. Therefore, the evolutionary history of Epirixanthes remains largely unknown.

• Methods: We reconstructed the phylogenetic relationships of Epirixanthesbased on nuclear ITS and plastid matK data. Divergence times were inferred using a Bayesian relaxed clock approach, and we phylogenetically analyzed its mycorrhizal symbionts. We furthermore assigned these symbionts to operational taxonomic units, compared them with symbionts of other Polygalaceae, and measured their phylogenetic diversity.

• Key results: We found that Epirixanthes is placed in tribe Polygaleae as sister to Salomonia. Epirixanthes has a Miocene-Oligocene stem age and grows exclusively in symbiosis with fungi of Glomeraceae. Salomonia and somePolygala species are linked to both Glomeraceae and Acaulosporaceae, resulting in higher phylogenetic diversity values. The majority of the symbionts of Epirixanthes are not found in Salomonia or Polygala, although a few shared fungal taxa are found.

• Conclusions: Epirixanthes forms a relatively young mycoheterotrophic lineage. The Oligocene-Miocene origin suggests its evolution was influenced by the environmental dynamics in Southeast Asia during this time. Although comparison of fungi from Epirixanthes with those from Salomonia and Polygalasuggests some specialization, many other mycoheterotrophic plants are linked to a more narrow set of Glomeraceae.


Via Pierre-Marc Delaux
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