MycorWeb Plant-Microbe Interactions
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The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties

The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties | MycorWeb Plant-Microbe Interactions | Scoop.it
The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden or Tiger milk mushroom (Polyporales, Basidiomycota) is a valuable folk medicine for indigenous peoples in Southeast Asia. Despite the increasing interest in this ethnobotanical mushroom, very little is known about the molecular and genetic basis of its medicinal and nutraceutical properties.
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Le climat se réchauffe, les Alpes verdissent

Le climat se réchauffe, les Alpes verdissent | MycorWeb Plant-Microbe Interactions | Scoop.it
Le climat se réchauffe, les Alpes verdissent

Une étude menée au Laboratoire d’Ecologie Alpine en partenariat avec le Parc National des Ecrins montre que les hautes montagnes de l’Oisans sont aujourd’hui davantage recouvertes de végétation qu’elles ne l’étaient il y a trente ans. C’est l’utilisation d’images satellites de haute résolution qui a permis de déceler cette tendance au verdissement dans les secteurs d’altitude du parc national. On connaissait déjà le verdissement de la zone arctique mais c’est la première fois qu’une étude détaillée indique qu’un phénomène semblable est à l’œuvre dans les Alpes françaises.
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BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017)

BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017) | MycorWeb Plant-Microbe Interactions | Scoop.it

Background. Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches’ broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S. graminicola.

 

Results. Sequence reads were generated from S. graminicola using an Illumina sequencing platform and assembled de novo into a draft genome sequence comprising approximately 360 Mbp. Of this sequence, 73% comprised repetitive elements, and a total of 16,736 genes were predicted from the RNA-seq data. The predicted genes included those encoding effector-like proteins with high sequence similarity to those previously identified in other oomycete pathogens. Genes encoding jacalin-like lectin-domain-containing secreted proteins were enriched in S. graminicola compared to other oomycetes. Of a total of 1220 genes encoding putative secreted proteins, 91 significantly changed their expression levels during the infection of plant tissues compared to the sporangia and zoospore stages of the S. graminicola lifecycle.

 

Conclusions. We established the draft genome sequence of a downy mildew pathogen that infects Gramineae plants. Based on this sequence and our transcriptome analysis, we generated a catalog of in planta-induced candidate effector genes, providing a solid foundation from which to identify the effectors causing phyllody.


Via Kamoun Lab @ TSL
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Glomeromycotina: what is a species and why should we care?

Glomeromycotina: what is a species and why should we care? | MycorWeb Plant-Microbe Interactions | Scoop.it

A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi including sexual or clonal reproduction, similarity or dissimilarity of nuclei within an individual, and species boundaries need to be re-examined and scrutinized with current techniques.


Via Pierre-Marc Delaux
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Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales | MycorWeb Plant-Microbe Interactions | Scoop.it

Background
Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size.


Results
In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years.


Conclusions
Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species.

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Trade-Offs in Arbuscular Mycorrhizal Symbiosis: Disease Resistance, Growth Responses and Perspectives for Crop Breeding

Trade-Offs in Arbuscular Mycorrhizal Symbiosis: Disease Resistance, Growth Responses and Perspectives for Crop Breeding | MycorWeb Plant-Microbe Interactions | Scoop.it
There is an increasing need to develop high-yielding, disease-resistant crops and reduce fertilizer usage. Combining disease resistance with efficient nutrient assimilation through improved associations with symbiotic microorganisms would help to address this. Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with most terrestrial plants, resulting in nutritional benefits and the enhancement of stress tolerance and disease resistance. Despite these advantages, arbuscular mycorrhizal (AM) interactions are not normally directly considered in plant breeding. Much of our understanding of the mechanisms of AM symbiosis comes from model plants, which typically exhibit positive growth responses. However, applying this knowledge to crops has not been straightforward. In many crop plants, phosphate uptake and growth responses in AM-colonized plants are variable, with AM plants exhibiting sometimes zero or negative growth responses and lower levels of phosphate acquisition. Host plants must also balance the ability to host AMF with the ability to resist pathogens. Advances in understanding the plant immune system have revealed similarities between pathogen infection and AM colonization that may lead to trade-offs between symbiosis and disease resistance. This review considers the potential trade-offs between AM colonization, agronomic traits and disease resistance and highlights the need for translational research to apply fundamental knowledge to crop improvement.

Via Jonathan Plett
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Frontiers | Differential Signaling and Sugar Exchanges in Response to Avirulent Pathogen- and Symbiont-Derived Molecules in Tobacco Cells | Microbiology 

Frontiers | Differential Signaling and Sugar Exchanges in Response to Avirulent Pathogen- and Symbiont-Derived Molecules in Tobacco Cells | Microbiology  | MycorWeb Plant-Microbe Interactions | Scoop.it

Plants interact with microbes whose ultimate aim is to exploit plant carbohydrates for their reproduction. Plant-microbe interactions (PMIs) are classified according to the nature of their trophic exchanges: while mutualistic microbes trade nutrients with plants, pathogens unilaterally divert carbohydrates. The early responses following microbe recognition and the subsequent control of plant sugar distribution are still poorly understood. To further decipher PMI functionality, we used tobacco cells treated with microbial molecules mimicking pathogenic or mutualistic PMIs, namely cryptogein, a defense elicitor, and chitotetrasaccharide (CO4), which is secreted by mycorrhizal fungi. CO4 was perceived by tobacco cells and triggered widespread transient signaling components such as a sharp cytosolic Ca2+ elevation, NtrbohD-dependent H2O2 production, and MAP kinase activation. These CO4-induced events differed from those induced by cryptogein, i.e. sustained events leading to cell death. Furthermore, cryptogein treatment inhibited glucose and sucrose uptake but not fructose uptake, and promoted the expression of NtSUT and NtSWEET sugar transporters, whereas CO4 had no effect on sugar uptake and only a slight effect on NtSWEET2B expression. Our results suggest that microbial molecules induce different signaling responses that reflect microbial lifestyle and the subsequent outcome of the interaction.

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Via Kevin Garcia
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Comparative modeling and molecular docking analysis of white, brown and soft rot fungal laccases using lignin model compounds for understanding the structural and functional properties of laccases ...

Comparative modeling and molecular docking analysis of white, brown and soft rot fungal laccases using lignin model compounds for understanding the structural and functional properties of laccases ... | MycorWeb Plant-Microbe Interactions | Scoop.it
Extrinsic catalytic properties of laccase enable it to oxidize a wide range of aromatic (phenolic and non-phenolic) compounds which makes it commercially an important enzyme. In this study, we have extensively compared and analyzed the physico-chemical, structural and functional properties of white, brown and soft rot fungal laccases using standard protein analysis software. We have computationally predicted the three-dimensional comparative models of these laccases and later performed the molecular docking studies using the lignin model compounds. We also report a customizable rapid and reliable protein modelling and docking pipeline for developing structurally and functionally stable protein structures. We have observed that soft rot fungal laccases exhibited comparatively higher structural variation (higher random coil) when compared to brown and white rot fungal laccases. White and brown rot fungal laccase sequences exhibited higher similarity for conserved domains of Trametes versicolor laccase, whereas soft rot fungal laccases shared higher similarity towards conserved domains of Melanocarpus albomyces laccase. Results obtained from molecular docking studies showed that aminoacids PRO, PHE, LEU, LYS and GLN were commonly found to interact with the ligands. We have also observed that white and brown rot fungal laccases showed similar docking patterns (topologically monomer, dimer and trimer bind at same pocket location and tetramer binds at another pocket location) when compared to soft rot fungal laccases. Finally, the binding efficiencies of white and brown rot fungal laccases with lignin model compounds were higher compared to the soft rot fungi. These findings can be further applied in developing genetically efficient laccases which can be applied in growing biofuel and bioremediation industries.
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Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species | MycorWeb Plant-Microbe Interactions | Scoop.it
Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here, we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed 5 general types of variation in SM gene clusters: nonfunctional gene polymorphisms; gene gain and loss polymorphisms; whole cluster gain and loss polymorphisms; allelic polymorphisms, in which different alleles corresponded to distinct, nonhomologous clusters; and location polymorphisms, in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms, the detection of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and nonhomologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, and genomic deletion and insertion events as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.
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Labex ARBRE | Recherches Avancées sur la Biologie de l’Arbre et les Ecosystèmes Forestiers

Labex ARBRE | Recherches Avancées sur la Biologie de l’Arbre et les Ecosystèmes Forestiers | MycorWeb Plant-Microbe Interactions | Scoop.it
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A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus

A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus | MycorWeb Plant-Microbe Interactions | Scoop.it
Small secreted proteins (SSPs), along with lignocellulose degrading enzymes, are integral components of the secretome of Pleurotus ostreatus, a white rot fungus. In this study, we identified 3 genes (ssp1, 2 and 3) encoding proteins that are annotated as SSPs and that exhibited of ~4,500- fold expression, 24 hr following exposure to the toxic compound 5-hydroxymethylfurfural (HMF). Homologues to genes encoding these SSPs are present in the genomes of other basidiomycete fungi, however the role of SSPs is not yet understood. SSPs, aryl-alcohol oxidases (AAO) and the intracellular aryl-alcohol dehydrogenases (AAD) were also produced after exposure to other aryl-alcohols, known substrates and inducers of AAOs, and during idiophase (after the onset of secondary metabolism). A knockdown strain of ssp1 exhibited reduced production of AAO-and AAD-encoding genes after HMF exposure. Conversely, a strain overexpressing ssp1 exhibited elevated expression of genes encoding AAOs and ADD, resulting in a 3-fold increase in enzymatic activity of AAOs, as well as increased expression and protein abundance of versatile peroxidase 1, which directly degrades lignin. We propose that in addition to symbionts and pathogens, SSPs also have roles in saprophytes and function in P. ostreatus as components of the ligninolytic system.
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Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels

Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels | MycorWeb Plant-Microbe Interactions | Scoop.it
Roots grow in highly dynamic and heterogeneous environments. Biological activity as well as uneven nutrient availability or localized stress factors result in diverse microenvironments. Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip, a microfluidic platform for asymmetric perfusion of Arabidopsis roots to investigate root–environment interactions under simulated environmental heterogeneity. Applications range from investigating physiology, root hair development and calcium signalling upon selective exposure to environmental stresses to tracing molecular uptake, performing selective drug treatments and localized inoculations with microbes. Using the dual-flow-RootChip, we revealed cell-autonomous adaption of root hair development under asymmetric phosphate (Pi) perfusion, with unexpected repression in root hair growth on the side exposed to low Pi and rapid tip-growth upregulation when Pi concentrations increased. The asymmetric root environment further resulted in an asymmetric gene expression of RSL4, a key transcriptional regulator of root hair growth. Our findings demonstrate that roots possess the capability to locally adapt to heterogeneous conditions in their environment at the physiological and transcriptional levels. Being able to generate asymmetric microenvironments for roots will help further elucidate decision-making processes in root–environment interactions.
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Rescooped by Francis Martin from Life Sciences Université Paris-Saclay
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Le Prix Recherche de la Société Française d’Écologie et d’Évolution (SFE²) 2017 attribué à Tatiana Giraud

Le Prix Recherche de la Société Française d’Écologie et d’Évolution (SFE²) 2017 attribué à Tatiana Giraud | MycorWeb Plant-Microbe Interactions | Scoop.it

Le Prix Recherche de la SFE² est destiné à récompenser une ou un écologue/évolutionniste en début ou milieu de carrière pour l’originalité et l’ampleur de ses travaux scientifiques. Il est attribué tous les ans depuis 2013. Une tribune libre est également offerte au lauréat sur le site de la SFE². En 2017, le Prix Recherche a été attribué à Tatiana Giraud, Directrice de recherches au CNRS, Chargée de cours à l’école Polytechnique et directrice adjointe du laboratoire Ecologie, Systématique et Evolution (ESE) à Orsay.


Toutes nos félicitations !


Via Life Sciences UPSaclay
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A nonnative and a native fungal plant pathogen similarly stimulate ectomycorrhizal development but are perceived differently by a fungal symbiont

A nonnative and a native fungal plant pathogen similarly stimulate ectomycorrhizal development but are perceived differently by a fungal symbiont | MycorWeb Plant-Microbe Interactions | Scoop.it

The effects of plant symbionts on host defence responses against pathogens have been extensively documented, but little is known about the impact of pathogens on the symbiosis and if such an impact may differ for nonnative and native pathogens. Here, this issue was addressed in a study of the model system comprising Pinus pinea, its ectomycorrhizal symbiont Tuber borchii, and the nonnative and native pathogens Heterobasidion irregulare and Heterobasidion annosum, respectively. In a 6-month inoculation experiment and using both in planta and gene expression analyses, we tested the hypothesis that H. irregulare has greater effects on the symbiosis than H. annosum. Although the two pathogens induced the same morphological reaction in the plant−symbiont complex, with mycorrhizal density increasing exponentially with pathogen colonization of the host, the number of target genes regulated in T. borchii in plants inoculated with the native pathogen (i.e. 67% of tested genes) was more than twice that in plants inoculated with the nonnative pathogen (i.e. 27% of genes). Although the two fungal pathogens did not differentially affect the amount of ectomycorrhizas, the fungal symbiont perceived their presence differently. The results may suggest that the symbiont has the ability to recognize a self/native and a nonself/nonnative pathogen, probably through host plant-mediated signal transduction.


Via Jonathan Plett
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Observed long-term greening of alpine vegetation—a case study in the French Alps

Observed long-term greening of alpine vegetation—a case study in the French Alps | MycorWeb Plant-Microbe Interactions | Scoop.it
We combined imagery from multiple sources (MODIS, Landsat-5, 7, 8) with land cover data to test for long-term (1984–2015) greening or browning trends of vegetation in a temperate alpine area, the Ecrins National Park, in the context of recent climate change and domestic grazing practices. We showed that over half (56%) of the Ecrins National Park displayed significant increases in peak normalized difference vegetation index (NDVImax) over the last 16 years (2000–2015). Importantly, the highest proportional increases in NDVImax occurred in rocky habitats at high elevations (> 2500 m a.s.l.). While spatial agreement in the direction of change in NDVImax as detected by MODIS and Landsat was high (76% overlap), correlations between log-response ratio values were of moderate strength (approx. 0.3). In the context of above treeline habitats, we found that proportional increases in NDVImax were higher between 1984 and 2000 than between 2000 and 2015, suggesting a slowing of greening dynamics during the recent decade. The timing of accelerated greening prior to 2000 coincided with a pronounced increase in the amount of snow-free growing degree-days that occurred during the 1980s and 1990s. In the case of grasslands and low-shrub habitats, we did not find evidence for a negative effect of grazing on greening trends, possibly due to the low grazing intensity typically found in the study area. We propose that the emergence of a longer and warmer growing season enabled high-elevation plant communities to produce more biomass, and also allowed for plant colonization of habitats previously characterized by long-lasting snow cover. Increasing plant productivity in an alpine context has potential implications for biodiversity trajectories and for ecosystem services in mountain landscapes. The presented evidence for long-term greening trends in a representative region of the European Alps provides the basis for further research on mechanisms of greening in alpine landscapes.
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Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics

Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics | MycorWeb Plant-Microbe Interactions | Scoop.it

Background
Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes.

Results
Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Conclusions
Synima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.


Via Ronny Kellner, Matt Agler, Jessie Uehling
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Symbiosis and cell evolution: Lynn Margulis and the origin of eukaryotes

Symbiosis and cell evolution: Lynn Margulis and the origin of eukaryotes | MycorWeb Plant-Microbe Interactions | Scoop.it
Although that for a long-time symbiosis was considered to be quite exceptional and restricted to few classical textbooks examples like lichens, American biologist Lynn Margulis (1938-2011) devoted most of her professional life to demonstrate that it is in fact a pervasive mechanism uniting what would otherwise would appear as isolated biological species and lineages. Starting with her seminal assay, “On the origin of mitosing cells,” published in the Journal of Theoretical Biology in 1967 (authored as Lynn Sagan), her lifelong work on eukaryogenesis and the role of symbiosis in evolution stands as a valid and authoritative contribution to science.

She was not the first to discuss the significance of symbiosis to explain the origin of mitochondria and chloroplasts, but no one else had done it to her extent and depth, nor had anyone provided a variety of testable hypotheses by making specific predictions on the chimeric nature of genomes and the mosaicism of metabolic pathways in eukaryotic cells.
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New Phytologist: Multiple strategies for pathogen perception by plant immune receptors (2017)

New Phytologist: Multiple strategies for pathogen perception by plant immune receptors (2017) | MycorWeb Plant-Microbe Interactions | Scoop.it

Plants have evolved a complex immune system to protect themselves against phytopathogens. A major class of plant immune receptors called nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) is ubiquitous in plants and is widely used for crop disease protection, making these proteins critical contributors to global food security. Until recently, NLRs were thought to be conserved in their modular architecture and functional features. Investigation of their biochemical, functional and structural properties has revealed fascinating mechanisms that enable these proteins to perceive a wide range of pathogens. Here, I review recent insights demonstrating that NLRs are more mechanistically and structurally diverse than previously thought. I also discuss how these findings provide exciting future prospects to improve plant disease resistance.


Via Kamoun Lab @ TSL, Bridget Barker
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Bridget Barker's curator insight, November 21, 9:22 AM
Always thinking about links between animal and plant pathogens
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A new promising phylogenetic marker to study the diversity of fungal communities: The Glycoside Hydrolase 63 gene

A new promising phylogenetic marker to study the diversity of fungal communities: The Glycoside Hydrolase 63 gene | MycorWeb Plant-Microbe Interactions | Scoop.it
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.
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The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus | MycorWeb Plant-Microbe Interactions | Scoop.it
Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high-quality 313.4-Mb genome sequence of a bottle gourd inbred line, USVL1VR-Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome-level syntenic relationships between bottle gourd and other cucurbits, as well as lineage-specific gene family expansions in bottle gourd. We reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which revealed that the ancestral Cucurbitaceae karyotypes consisted of 12 protochromosomes with 18 534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The 11 bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ring-spot virus (PRSV) resistance in bottle gourd, to a 317.8-kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker-assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high-quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement.
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New Phytologist: Effectors involved in fungal–fungal interaction lead to a rare phenomenon of hyperbiotrophy in the tritrophic system biocontrol agent–powdery mildew–plant (2017)

New Phytologist: Effectors involved in fungal–fungal interaction lead to a rare phenomenon of hyperbiotrophy in the tritrophic system biocontrol agent–powdery mildew–plant (2017) | MycorWeb Plant-Microbe Interactions | Scoop.it
Tritrophic interactions involving a biocontrol agent, a pathogen and a plant have been analyzed predominantly from the perspective of the biocontrol agent. We have conducted the first comprehensive transcriptomic analysis of all three organisms in an effort to understand the elusive properties of Pseudozyma flocculosa in the context of its biocontrol activity against Blumeria graminis f.sp. hordei as it parasitizes Hordeum vulgare.After inoculation of P. flocculosa, the tripartite interaction was monitored over time and samples collected for scanning electron microscopy and RNA sequencing.Based on our observations, P. flocculosa indirectly parasitizes barley, albeit transiently, by diverting nutrients extracted by B. graminis from barley leaves through a process involving unique effectors. This brings novel evidence that such molecules can also influence fungal–fungal interactions. Their release is synchronized with a higher expression of powdery mildew haustorial effectors, a sharp decline in the photosynthetic machinery of barley and a developmental peak in P. flocculosa. The interaction culminates with a collapse of B. graminis haustoria, thereby stopping P. flocculosa growth, as barley plants show higher metabolic activity.To conclude, our study has uncovered a complex and intricate phenomenon, described here as hyperbiotrophy, only achievable through the conjugated action of the three protagonists.
Via Kamoun Lab @ TSL, Nicolas Denancé, Jim Alfano
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Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities | MycorWeb Plant-Microbe Interactions | Scoop.it
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
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Mineral-surface-reactive metabolites secreted during fungal decomposition contribute to the formation of soil organic matter

Mineral-surface-reactive metabolites secreted during fungal decomposition contribute to the formation of soil organic matter | MycorWeb Plant-Microbe Interactions | Scoop.it
Soil organic matter (SOM) constitutes the largest terrestrial C pool. An emerging, untested, view is that oxidation and depolymerization of SOM by microorganisms promote the formation of SOM-mineral associations that is critical for SOM stabilization. To test this hypothesis we performed laboratory-scale experiments involving one ectomycorrhizal and one saprotrophic fungus that represent the two major functional groups of microbial decomposers in the boreal forest soils. Fungal decomposition enhanced the retention of SOM on goethite, partly because of oxidative modifications of organic matter (OM) by the fungi. Moreover, both fungi secreted substantial amounts (>10% new biomass C) of aromatic metabolites that also contributed to an enhanced mineral retention of OM. Our study demonstrates that soil fungi can form mineral-stabilized SOM not only by oxidative conversion of the SOM but also by synthesizing mineral surface-reactive metabolites. Metabolites produced by fungal decomposers can play a yet overlooked role in the formation and stabilization of SOM.
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Source and sink mechanisms of nitrogen transport and use 

Source and sink mechanisms of nitrogen transport and use  | MycorWeb Plant-Microbe Interactions | Scoop.it
Nitrogen is an essential nutrient for plant growth. World-wide, large quantities of nitrogenous fertilizer are applied to ensure maximum crop productivity. However, nitrogen fertilizer application is expensive and negatively affects the environment, and subsequently human health. A strategy to address this problem is the development of crops that are efficient in acquiring and using nitrogen and that can achieve high seed yields with reduced nitrogen input. This review integrates the current knowledge regarding inorganic and organic nitrogen management at the whole-plant level, spanning from nitrogen uptake to remobilization and utilization in source and sink organs. Plant partitioning and transient storage of inorganic and organic nitrogen forms are evaluated, as is how they affect nitrogen availability, metabolism and mobilization. Essential functions of nitrogen transporters in source and sink organs and their importance in regulating nitrogen movement in support of metabolism, and vegetative and reproductive growth are assessed. Finally, we discuss recent advances in plant engineering, demonstrating that nitrogen transporters are effective targets to improve crop productivity and nitrogen use efficiency. While inorganic and organic nitrogen transporters were examined separately in these studies, they provide valuable clues about how to successfully combine approaches for future crop engineering.
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Jean-Michel Ané's curator insight, November 14, 9:29 AM

Fantastic review!

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Multiple strategies for pathogen perception by plant immune receptors

Multiple strategies for pathogen perception by plant immune receptors | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants have evolved a complex immune system to protect themselves against phytopathogens. A major class of plant immune receptors called nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) is ubiquitous in plants and is widely used for crop disease protection, making these proteins critical contributors to global food security. Until recently, NLRs were thought to be conserved in their modular architecture and functional features. Investigation of their biochemical, functional and structural properties has revealed fascinating mechanisms that enable these proteins to perceive a wide range of pathogens. Here, I review recent insights demonstrating that NLRs are more mechanistically and structurally diverse than previously thought. I also discuss how these findings provide exciting future prospects to improve plant disease resistance.
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Rescooped by Francis Martin from Host:microbe Interactions
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Ecosystem responses to elevated CO2 governed by plant–soil interactions and the cost of nitrogen acquisition

Land ecosystems sequester on average about a quarter of anthropogenic CO2 emissions. It has been proposed that nitrogen (N) availability will exert an increasingly limiting effect on plants’ ability to store additional carbon (C) under rising CO2, but these mechanisms are not well understood. Here, we review findings from elevated CO2 experiments using a plant economics framework, highlighting how ecosystem responses to elevated CO2 may depend on the costs and benefits of plant interactions with mycorrhizal fungi and symbiotic N-fixing microbes. We found that N-acquisition efficiency is positively correlated with leaf-level photosynthetic capacity and plant growth, and negatively with soil C storage. Plants that associate with ectomycorrhizal fungi and N-fixers may acquire N at a lower cost than plants associated with arbuscular mycorrhizal fungi. However, the additional growth in ectomycorrhizal plants is partly offset by decreases in soil C pools via priming. Collectively, our results indicate that predictive models aimed at quantifying C cycle feedbacks to global change may be improved by treating N as a resource that can be acquired by plants in exchange for energy, with different costs depending on plant interactions with microbial symbionts.


Via Jonathan Plett
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