MycorWeb Plant-Microbe Interactions
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The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimise parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analysed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.
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A long awaited genome! More rust genomes needed.

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Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life | Annual Review of Microbiology

As decomposers or plant pathogens, fungi deploy invasive growth and powerful carbohydrate active enzymes to reduce multicellular plant tissues to humus and simple sugars. Fungi are perhaps also the most important mutualistic symbionts in modern ecosystems, transporting poorly soluble mineral nutrients to plants and thus enhancing the growth of vegetation. However, at their origin over a billion years ago, fungus-like plants and animals were unicellular marine microbes. Like the other multicellular kingdoms, Fungi evolved increased size, complexity, and metabolic functioning. Interactions of fungi with plants changed terrestrial ecology and geology and modified the Earth’s atmosphere. In this review, we discuss the diversification and ecological roles of the fungi over their first 600 million years, from their origin through their colonization of land, drawing on phylogenomic evidence for their relationships and metabolic capabilities and on molecular dating, fossils, and modeling of Earth’s paleoclimate.
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Beyond nutrients: A meta-analysis of the diverse effects of arbuscular mycorrhizal fungi on plants and soils.

Beyond nutrients: A meta-analysis of the diverse effects of arbuscular mycorrhizal fungi on plants and soils. | MycorWeb Plant-Microbe Interactions | Scoop.it
Arbuscular mycorrhizal fungi (AMF) can increase plant fitness under certain environmental conditions. Among the mechanisms that may drive this mutualism, the most studied is provisioning of nutrients by AMF in exchange for carbon from plant hosts. However, AMF may also provide a suite of non-nutritional benefits to plants including improved water uptake, disease resistance, plant chemical defense, soil aggregation, and allelochemical transport and protection. Here, we use a meta-analysis of 93 studies to assess the relative effect of AMF on nutritional and non-nutritional factors that may influence plant fitness. We find that the positive effects of AMF on soil aggregation, water flow and disease resistance are equal to the effect of AMF on plant nitrogen and phosphorus uptake. However, AMF had no effect on the uptake of other nutrients, plant water content, allelopathic transport or production of chemical defense compounds. We suggest future research directions, including experimentally assessing the relative contribution on plant fitness of AMF interactions by untangling the independence of alternative benefits of AMF from an increase in nutrient uptake. This will lead to a more holistic view of the mycorrhizal-plant association and a more accurate picture of the net impact on the plant or plant community in question.

Via Jonathan Plett
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The energy expansions of evolution

The energy expansions of evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
The history of the life–Earth system can be divided into five ‘energetic’ epochs, each featuring the evolution of life forms that can exploit a new source of energy. These sources are: geochemical energy, sunlight, oxygen, flesh and fire. The first two were present at the start, but oxygen, flesh and fire are all consequences of evolutionary events. Since no category of energy source has disappeared, this has, over time, resulted in an expanding realm of the sources of energy available to living organisms and a concomitant increase in the diversity and complexity of ecosystems. These energy expansions have also mediated the transformation of key aspects of the planetary environment, which have in turn mediated the future course of evolutionary change. Using energy as a lens thus illuminates patterns in the entwined histories of life and Earth, and may also provide a framework for considering the potential trajectories of life–planet systems elsewhere.

Free energy is a universal requirement for life. It drives mechanical motion and chemical reactions—which in biology can change a cell or an organism1,2. Over the course of Earth history, the harnessing of free energy by organisms has had a dramatic impact on the planetary environment3,​4,​5,​6,​7. Yet the variety of free-energy sources available to living organisms has expanded over time. These expansions are consequences of events in the evolution of life, and they have mediated the transformation of the planet from an anoxic world that could support only microbial life, to one that boasts the rich geology and diversity of life present today. Here, I review these energy expansions, discuss how they map onto the biological and geological development of Earth, and consider what this could mean for the trajectories of life–planet systems elsewhere.
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Elevation alters ecosystem properties across temperate treelines globally : Nature

Elevation alters ecosystem properties across temperate treelines globally : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it

Temperature is a primary driver of the distribution of biodiversity as well as of ecosystem boundaries. Declining temperature with increasing elevation in montane systems has long been recognized as a major factor shaping plant community biodiversity, metabolic processes, and ecosystem dynamics. Elevational gradients, as thermoclines, also enable prediction of long-term ecological responses to climate warming. One of the most striking manifestations of increasing elevation is the abrupt transitions from forest to treeless alpine tundra. However, whether there are globally consistent above- and belowground responses to these transitions remains an open question. To disentangle the direct and indirect effects of temperature on ecosystem properties, here we evaluate replicate treeline ecotones in seven temperate regions of the world. We find that declining temperatures with increasing elevation did not affect tree leaf nutrient concentrations, but did reduce ground-layer community-weighted plant nitrogen, leading to the strong stoichiometric convergence of ground-layer plant community nitrogen to phosphorus ratios across all regions. Further, elevation-driven changes in plant nutrients were associated with changes in soil organic matter content and quality (carbon to nitrogen ratios) and microbial properties. Combined, our identification of direct and indirect temperature controls over plant communities and soil properties in seven contrasting regions suggests that future warming may disrupt the functional properties of montane ecosystems, particularly where plant community reorganization outpaces treeline advance.

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Advances in methods for identification and characterization of plant transporter function | Journal of Experimental Botany | Oxford Academic

Advances in methods for identification and characterization of plant transporter function | Journal of Experimental Botany | Oxford Academic | MycorWeb Plant-Microbe Interactions | Scoop.it
Transport proteins are crucial for cellular function at all levels. Numerous importers and exporters facilitate transport of a diverse array of metabolites and ions intra- and intercellularly. Identification of transporter function is essential for understanding biological processes at both the cellular and organismal level. Assignment of a functional role to individual transporter proteins or to identify a transporter with a given substrate specificity has notoriously been challenging. Recently, major advances have been achieved in function-driven screens, phenotype-driven screens, and in silico-based approaches. In this review, we highlight examples that illustrate how new technology and tools have advanced identification and characterization of plant transporter functions.
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Via Kevin Garcia
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Molecular basis of lipo-chitooligosaccharide recognition by the lysin motif receptor-like kinase LYR3 in legumes

Molecular basis of lipo-chitooligosaccharide recognition by the lysin motif receptor-like kinase LYR3 in legumes | MycorWeb Plant-Microbe Interactions | Scoop.it
LYR3 [LysM (lysin motif) receptor-like kinase 3] of Medicago truncatula is a high-affinity binding protein for symbiotic LCO (lipo-chitooligosaccharide) signals, produced by rhizobia bacteria and arbuscular mycorrhizal fungi. The present study shows that LYR3 from several other legumes, but not from two Lupinus species which are incapable of forming the mycorrhizal symbiosis, bind LCOs with high affinity and discriminate them from COs (chitooligosaccharides). The biodiversity of these proteins and the lack of binding to the Lupinus proteins were used to identify features required for high-affinity LCO binding. Swapping experiments between each of the three LysMs of the extracellular domain of the M. truncatula and Lupinus angustifolius LYR3 proteins revealed the crucial role of the third LysM in LCO binding. Site-directed mutagenesis identified a tyrosine residue, highly conserved in all LYR3 LCO-binding proteins, which is essential for high-affinity binding. Molecular modelling suggests that it may be part of a hydrophobic tunnel able to accommodate the LCO acyl chain. The lack of conservation of these features in the binding site of plant LysM proteins binding COs provides a mechanistic explanation of how LCO recognition might differ from CO perception by structurally related LysM receptors.


Via Jean-Michel Ané
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Puccinia striiformis f. sp. tritici microRNA-like RNA 1 (Pst-milR1), an important pathogenicity factor of Pst, impairs wheat resistance to Pst by suppressing the wheat pathogenesis-related 2 gene

Puccinia striiformis f. sp. tritici microRNA-like RNA 1 (Pst-milR1), an important pathogenicity factor of Pst, impairs wheat resistance to Pst by suppressing the wheat pathogenesis-related 2 gene | MycorWeb Plant-Microbe Interactions | Scoop.it
Small RNAs (sRNAs), an important type of pathogenicity factor, contribute to impairing host immune responses. However, little is known about sRNAs in Puccinia striiformis f. sp. tritici (Pst), one of the most destructive pathogens of wheat (Triticum aestivum L.). Here, the authors report a novel microRNA-like RNA (milRNA) from Pst termed microRNA-like RNA 1 (Pst- milR1), which suppresses wheat defenses during wheat–Pst interactions.  Pst-milR1 is identified as a novel milRNA in Pst. Biological prediction and co- transformation showed that Pst-milR1 takes part in cross-kingdom RNA interference (RNAi) events by binding the wheat pathogenesis-related 2 (PR2) gene. Silencing of the Pst-milR1 precursor resulted in increased wheat resistance to the virulent Pst isolate CYR31. PR2 knock-down plants increased the susceptibility of wheat to the avirulent Pst isolate CYR23. This suggests that Pst-milR1 represses the plant immune response by suppressing the expression of PR2.

Via Norwich Rust Group, Jonathan Plett
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uORF-mediated translation allows engineered plant disease resistance without fitness costs

uORF-mediated translation allows engineered plant disease resistance without fitness costs | MycorWeb Plant-Microbe Interactions | Scoop.it
Controlling plant disease has been a struggle for humankind since the advent of agriculture. Studies of plant immune mechanisms have led to strategies of engineering resistant crops through ectopic transcription of plants’ own defence genes, such as the master immune regulatory gene NPR1 (ref. 1). However, enhanced resistance obtained through such strategies is often associated with substantial penalties to fitness2, making the resulting products undesirable for agricultural applications. To remedy this problem, we sought more stringent mechanisms of expressing defence proteins. On the basis of our latest finding that translation of key immune regulators, such as TBF1 (ref. 3), is rapidly and transiently induced upon pathogen challenge (see accompanying paper4), we developed a ‘TBF1-cassette’ consisting of not only the immune-inducible promoter but also two pathogen-responsive upstream open reading frames (uORFsTBF1) of the TBF1 gene. Here we demonstrate that inclusion of uORFsTBF1-mediated translational control over the production of snc1-1 (an autoactivated immune receptor) in Arabidopsis thaliana and AtNPR1 in rice enables us to engineer broad-spectrum disease resistance without compromising plant fitness in the laboratory or in the field. This broadly applicable strategy may lead to decreased pesticide use and reduce the selective pressure for resistant pathogens.
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Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome | MycorWeb Plant-Microbe Interactions | Scoop.it
Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.
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The evolutionary significance of polyploidy : Nature Reviews Genetics : Nature Research

The evolutionary significance of polyploidy : Nature Reviews Genetics : Nature Research | MycorWeb Plant-Microbe Interactions | Scoop.it
Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity.
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The largest fungal genome discovered in Jafnea semitosta

The largest fungal genome discovered in Jafnea semitosta | MycorWeb Plant-Microbe Interactions | Scoop.it
Jafnea semitosta is an ascomycete (Pyronemataceae, Pezizales) originating from North America and spreading uncommonly in Europe. Its genome size was measured via flow cytometry of fruiting bodies from five localities in the Czech and Slovak Republic. The nuclear 1C DNA content was estimated at 3.706 ± 0.011 pg (~3.625 ± 0.011 Gbp) which represents the highest value ever reported for fungi and 100× higher than the average. Generally, the genome inflation in fungi appears to be driven mainly by proliferation of repetitive sequences, but polyploidy should also be considered in further studies on this greatly unexplored topic.
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Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch | MycorWeb Plant-Microbe Interactions | Scoop.it
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.
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Interspecies hormonal control of host root morphology by parasitic plants

Interspecies hormonal control of host root morphology by parasitic plants | MycorWeb Plant-Microbe Interactions | Scoop.it
Parasitic plants share a common anatomical feature, the haustorium. Haustoria enable both infection and nutrient transfer, which often leads to growth penalties for host plants and yield reduction in crop species. Haustoria also reciprocally transfer substances, such as RNA and proteins, from parasite to host, but the biological relevance for such movement remains unknown. Here, we studied such interspecies transport by using the hemiparasitic plant Phtheirospermum japonicum during infection of Arabidopsis thaliana. Tracer experiments revealed a rapid and efficient transfer of carboxyfluorescein diacetate (CFDA) from host to parasite upon formation of vascular connections. In addition, Phtheirospermum induced hypertrophy in host roots at the site of infection, a form of enhanced secondary growth that is commonly observed during various parasitic plant–host interactions. The plant hormone cytokinin is important for secondary growth, and we observed increases in cytokinin and its response during infection in both host and parasite. Phtheirospermum-induced host hypertrophy required cytokinin signaling genes (AHK3,4) but not cytokinin biosynthesis genes (IPT1,3,5,7) in the host. Furthermore, expression of a cytokinin-degrading enzyme in Phtheirospermum prevented host hypertrophy. Wild-type hosts with hypertrophy were smaller than ahk3,4 mutant hosts resistant to hypertrophy, suggesting hypertrophy improves the efficiency of parasitism. Taken together, these results demonstrate that the interspecies movement of a parasite-derived hormone modified both host root morphology and fitness. Several microbial and animal plant pathogens use cytokinins during infections, highlighting the central role of this growth hormone during the establishment of plant diseases and revealing a common strategy for parasite infections of plants.
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Ectomycorrhizal fungi and the enzymatic liberation of nitrogen from soil organic matter: why evolutionary history matters

Ectomycorrhizal fungi and the enzymatic liberation of nitrogen from soil organic matter: why evolutionary history matters | MycorWeb Plant-Microbe Interactions | Scoop.it
The view that ectomycorrhizal (ECM) fungi commonly participate in the enzymatic liberation of nitrogen (N) from soil organic matter (SOM) has recently been invoked as a key mechanism governing the biogeochemical cycles of forest ecosystems. Here, we provide evidence that not all evolutionary lineages of ECM have retained the genetic potential to produce extracellular enzymes that degrade SOM, calling into question the ubiquity of the proposed mechanism. Further, we discuss several untested conditions that must be empirically validated before it is certain that any lineage of ECM fungi actively expresses extracellular enzymes in order to degrade SOM and transfer N contained therein to its host plant.
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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

Via Loïc Lepiniec
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Phosphate scouting by root tips

Phosphate scouting by root tips | MycorWeb Plant-Microbe Interactions | Scoop.it

Highlights

• The two most abundant metals in soil, Fe and Al, limit phosphate bioavailability.
• Root tips sense phosphate together with Fe to locally inform root development.
• Low phosphate rapidly inhibits root cell elongation and, with delay, cell division.
• STOP1–ALMT1 and PDR2–LPR1 action mediate responses of root tips to low phosphate.
• Antagonistic interactions between phosphate, Fe and Al converge in phosphate sensing.



Chemistry assigns phosphate (Pi) dominant roles in metabolism; however, it also renders the macronutrient a genuinely limiting factor of plant productivity. Pi bioavailability is restricted by low Pi mobility in soil and antagonized by metallic toxicities, which force roots to actively seek and selectively acquire the vital element. During the past few years, a first conceptual outline has emerged of the sensory mechanisms at root tips, which monitor external Pi and transmit the edaphic cue to inform root development. This review highlights new aspects of the Pi acquisition strategy of Arabidopsis roots, as well as a framework of local Pi sensing in the context of antagonistic interactions between Pi and its major associated metallic cations, Fe3+ and Al3+.


Via Christophe Jacquet
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Temporal and Spatial Variability of Fungal Structures and Host Responses in an Incompatible Rust–Wheat Interaction

Temporal and Spatial Variability of Fungal Structures and Host Responses in an Incompatible Rust–Wheat Interaction | MycorWeb Plant-Microbe Interactions | Scoop.it

Information about temporal and spatial variability of fungal structures and host responses is scarce in comparison to the vast amount of genetic, biochemical, and physiological studies of host–pathogen interactions. In this study, the authors used avirulent wild type and virulent mutant isolates of Puccinia striiformis to characterize the interactions in wheat carrying yellow rust Yr2 resistance. Both conventional and advanced microscopic techniques were used for a detailed study of morphology and growth of fungal colonies and associated host cell responses. The growth of the wild type isolates was highly restricted due to hypersensitive response (HR, plant cell death) indicated by autofluorescence and change in the shape of the affected plant cells. The host response appeared post-haustorial, but large variation in the time and stage of arrest was observed for individual fungal colonies, probably due to a delay between detection and response. Some colonies were stopped right after the formation of the primary infection hyphae whereas others formed highly branched mycelia. HR was first observed in host cells in direct contact with fungal structures, after which the defense responses spread to adjacent host cells, and eventually led to encasement of the fungal colony. Several cells with HR contained haustoria, which were small and underdeveloped, but some cells contained normal sized haustoria without signs of hypersensitivity. The growth of the virulent mutants in the resistant plants was similar to the growth in plants without Yr2 resistance, which is a strong indication that the incompatible phenotype was associated with Yr2. The interaction between P. striiformis and wheat with Yr2 resistance was highly variable in time and space, which demonstrate that histological studies are important for a deeper understanding of host–pathogen interactions and plant defense mechanisms in general.


Via Norwich Rust Group, Steve Marek, Christophe Jacquet
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The RxLR Motif of the Host Targeting Effector AVR3a of Phytophthora infestans Is Cleaved Before Secretion

When plant-pathogenic oomycetes infect their hosts, they employ a large arsenal of effector proteins to establish a successful infection. Some effector proteins are secreted and are destined to be translocated and function inside host cells. The largest group of translocated proteins from oomycetes are the RxLR effectors, defined by their conserved N-terminal Arg-Xaa-Leu-Arg (RxLR) motif. However, the precise role of this motif in the host cell translocation process is unclear. Here detailed biochemical studies of the RxLR effector AVR3a from the potato pathogen Phytophthora infestans are presented. Mass spectrometric analysis revealed that the RxLR sequence of native AVR3a is cleaved off prior to secretion by the pathogen and the N-terminus of the mature effector was found likely to be acetylated. High-resolution NMR structure analysis of AVR3a indicates that the RxLR motif is well accessible to potential processing enzymes. Processing and modification of AVR3a is to some extent similar to events occurring with the export element (PEXEL) found in malaria effector proteins from Plasmodium falciparum. These findings imply a role for the RxLR motif in the secretion of AVR3a by the pathogen, rather than a direct role in the host cell entry process itself.
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Nat. Commun.: Sequencing and de novo assembly of a near complete indica rice genome (2017)

Nat. Commun.: Sequencing and de novo assembly of a near complete indica rice genome (2017) | MycorWeb Plant-Microbe Interactions | Scoop.it
A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism. Here we report the de novo assembly of an indica rice genome Shuhui498 (R498) through the integration of single-molecule sequencing and mapping data, genetic map and fosmid sequence tags. The 390.3 Mb assembly is estimated to cover more than 99% of the R498 genome and is more continuous than the current reference genomes of japonica rice Nipponbare (MSU7) and Arabidopsis thaliana (TAIR10). We annotate high-quality protein-coding genes in R498 and identify genetic variations between R498 and Nipponbare and presence/absence variations by comparing them to 17 draft genomes in cultivated rice and its closest wild relatives. Our results demonstrate how to de novo assemble a highly contiguous and near-complete plant genome through an integrative strategy. The R498 genome will serve as a reference for the discovery of genes and structural variations in rice.

Via Nicolas Denancé
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Trees in eastern US head west as climate changes

Trees in eastern US head west as climate changes | MycorWeb Plant-Microbe Interactions | Scoop.it

Ecologists have long predicted that climate change will send plants and animals uphill and towards the poles in search of familiar temperatures. Such movements have increasingly been documented around the world. But a study now shows that changing rainfall patterns may be driving some tree species in the eastern United States west, not north.

Songlin Fei, a forest ecologist at Purdue University in West Lafayette, Indiana, and his colleagues tracked the shifting distributions of 86 types of trees using data collected by the US Forest Service’s Forest Inventory and Analysis Program during two periods: from 1980 to 1995 and between 2013 and 2015 for all states. They found more species heading west than north, probably partly because of changing precipitation patterns, the team reported on 17 May in Science Advances1. “That was a huge surprise for us,” says Fei.

This study suggests that, in the near-term, trees are responding to changes in water availability more than to temperature changes, he says.

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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change | MycorWeb Plant-Microbe Interactions | Scoop.it
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
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Exocytosis for endosymbiosis: membrane trafficking pathways for development of symbiotic membrane compartments

During endosymbiosis with arbuscular mycorrhizal fungi or rhizobial bacteria, the microbial symbionts are housed within membrane-bound compartments in root cortex or nodule cells respectively. Their development involves polarized deposition of membrane around the symbionts as they enter the cells and the membranes show functional specialization, including transporters that mediate nutrient transfer between host and symbiont. The cellular changes associated with development of these compartments point to membrane deposition via exocytosis and over the past few years, researchers have uncovered several proteins within the exocytotic pathway that are required for development of endosymbiotic membrane compartments. The emerging theme is that unique membrane trafficking homologs or splice variants have evolved to enable exocytosis during endosymbiosis.

Via Pierre-Marc Delaux
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Rescooped by Francis Martin from Plant immunity and legume symbiosis
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Nitrogen sensing in legumes | Journal of Experimental Botany | Oxford Academic

Nitrogen sensing in legumes | Journal of Experimental Botany | Oxford Academic | MycorWeb Plant-Microbe Interactions | Scoop.it
Legumes fix atmospheric nitrogen (N) in a symbiotic relationship with bacteria. For this reason, although legume crops can be low yielding and less profitable when compared with cereals, they are frequently included in crop rotations. Grain legumes form only a minor part of most human diets, and legume crops are greatly underutilized. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. One limitation for the use of legumes as a source of N input into agricultural systems is the fact that the formation of N-fixing nodules is suppressed when soils are replete with n. In this review, we report what is known about this process and how soil N supply might be sensed and feed back to regulate nodulation.

Via Christophe Jacquet
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Widespread adenine N6-methylation of active genes in fungi

Widespread adenine N6-methylation of active genes in fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes1, 2, 3, 4, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages5. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.
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Ustilago maydis effectors and their impact on virulence : Nature Reviews Microbiology

Ustilago maydis effectors and their impact on virulence : Nature Reviews Microbiology | MycorWeb Plant-Microbe Interactions | Scoop.it
Biotrophic fungal plant pathogens establish an intimate relationship with their host to support the infection process. Central to this strategy is the secretion of a range of protein effectors that enable the pathogen to evade plant immune defences and modulate host metabolism to meet its needs. In this Review, using the smut fungus Ustilago maydis as an example, we discuss new insights into the effector repertoire of smut fungi that have been gained from comparative genomics and discuss the molecular mechanisms by which U. maydis effectors change processes in the plant host. Finally, we examine how the expression of effector genes and effector secretion are coordinated with fungal development in the host.
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