MycorWeb Plant-Microbe Interactions
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MycorWeb Plant-Microbe Interactions
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De Novo Whole-Genome Sequencing of the Wood Rot Fungus Polyporus brumalis, Which Exhibits Potential Terpenoid Metabolism

Polyporus brumalis is able to synthesize several sesquiterpenes during fungal growth. Using a single-molecule real-time sequencing platform, we present the 53-Mb draft genome of P. brumalis, which contains 6,231 protein-coding genes. Gene annotation and isolation support genetic information, which can increase the understanding of sesquiterpene metabolism in P. brumalis.
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Fungi associated with mesophotic macroalgae from the ‘Au‘au Channel, west Maui are differentiated by host and overlap terrestrial communities

Fungi associated with mesophotic macroalgae from the ‘Au‘au Channel, west Maui are differentiated by host and overlap terrestrial communities | MycorWeb Plant-Microbe Interactions | Scoop.it
Mesophotic coral ecosystems are an almost entirely unexplored and undocumented environment that likely contains vast reservoirs of undescribed biodiversity. Twenty-four macroalgae samples, representing four genera, were collected from a Hawaiian mesophotic reef at water depths between 65 and 86 m in the ‘Au‘au Channel, Maui, Hawai‘i. Algal tissues were surveyed for the presence and diversity of fungi by sequencing the ITS1 gene using Illumina technology. Fungi from these algae were then compared to previous fungal surveys conducted in Hawaiian terrestrial ecosystems. Twenty-seven percent of the OTUs present on the mesophotic coral ecosystem samples were shared between the marine and terrestrial environment. Subsequent analyses indicated that host species of algae significantly differentiate fungal community composition. This work demonstrates yet another understudied habitat with a moderate diversity of fungi that should be considered when estimating global fungal diversity.
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Arabidopsis JASMONATE-INDUCED OXYGENASES down-regulate plant immunity by hydroxylation and inactivation of the hormone jasmonic acid

Arabidopsis JASMONATE-INDUCED OXYGENASES down-regulate plant immunity by hydroxylation and inactivation of the hormone jasmonic acid | MycorWeb Plant-Microbe Interactions | Scoop.it

In plants the hormone jasmonic acid (JA) is synthesized in response to attack by pathogens and herbivores, leading to activation of defense responses. Rapidly following JA accumulation the hormone is metabolized, presumably to prevent inhibitive effects of high JA levels on growth and development. The enzymes that directly inactivate JA were so far unknown. Here, we identify four jasmonate-induced oxygenases (JOXs) in Arabidopsis that hydroxylate jasmonic acid to form inactive 12-OH-JA. A mutant that no longer produces the four enzymes hyperaccumulates JA, exhibits reduced growth, and is highly resistant to attackers that are sensitive to JA-dependent defense. The JOX enzymes thus play an important role in determining the amplitude and duration of JA responses to balance the growth–defense trade-off.


Via Jonathan Plett
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Epigenetic regulation of development and pathogenesis in fungal plant pathogens

Epigenetic regulation of development and pathogenesis in fungal plant pathogens | MycorWeb Plant-Microbe Interactions | Scoop.it
Evidently, epigenetics is at forefront in explaining the mechanisms underlying the success of human pathogens and in the identification of pathogen-induced modifications within host plants. However, there is a lack of studies highlighting the role of epigenetics in the modulation of the growth and pathogenicity of fungal plant pathogens. In this review, we attempt to highlight and discuss the role of epigenetics in the regulation of the growth and pathogenicity of fungal phytopathogens using Magnaporthe oryzae, a devastating fungal plant pathogen, as a model system. With the perspective of wide application in the understanding of the development, pathogenesis and control of other fungal pathogens, we attempt to provide a synthesized view of the epigenetic studies conducted on M. oryzae to date. First, we discuss the mechanisms of epigenetic modifications in M. oryzae and their impact on fungal development and pathogenicity. Second, we highlight the unexplored epigenetic mechanisms and areas of research that should be considered in the near future to construct a holistic view of epigenetic functioning in M. oryzae and other fungal plant pathogens. Importantly, the development of a complete understanding of the modulation of epigenetic regulation in fungal pathogens can help in the identification of target points to combat fungal pathogenesis
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Population genomics of picophytoplankton unveils novel chromosome hypervariability

Population genomics of picophytoplankton unveils novel chromosome hypervariability | MycorWeb Plant-Microbe Interactions | Scoop.it
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.
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New technologies boost genome quality

New technologies boost genome quality | MycorWeb Plant-Microbe Interactions | Scoop.it
Three years ago, Erich Jarvis helped mastermind a massive DNA sequencing effort that netted genomes for more than 40 bird species and produced a better avian family tree. But when he tried to compare the avian genomes to those of other species to learn about the evolution and function of several key brain genes, he was stymied. His team found that gene sequences from most of the comparison species—even humans—were incomplete, missing, or misplaced in the larger genome. The group had to resequence sections of several genomes to get the needed data, delaying their project many months.

“The genome quality makes a huge difference in the type of science we can do,” says Jarvis, a neuroscientist at The Rockefeller University in New York City. So he and many other genomics experts are launching a quiet revolution aimed at building better genomes, one made possible by newer sequencing technologies, novel methods for locating sequences on chromosomes, and improved software for piecing DNA together. In the past 6 months, these approaches have led to a flood of high-quality animal and plant genomes in preprints and published papers.
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Evolution of the wheat blast fungus through functional losses in a host specificity determinant

Evolution of the wheat blast fungus through functional losses in a host specificity determinant | MycorWeb Plant-Microbe Interactions | Scoop.it

In the 1980s, wheat crops began to fall to the fungal pathogen that causes blast disease. First seen in Brazil, wheat blast last year caused devastating crop losses in Bangladesh. Inoue et al. tracked down the shifting genetics that have allowed the emergence of this potentially global threat to wheat crops (see the Perspective by Maekawa and Schulze-Lefert). Wheat varieties with a disabled resistance gene were susceptible to pathogen strains that affected oat and ryegrass crops. Subsequent genetic changes in the pathogen amped up the virulence in wheat.

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Regulation of growth–defense balance by the JASMONATE ZIM-DOMAIN (JAZ)-MYC transcriptional module

Regulation of growth–defense balance by the JASMONATE ZIM-DOMAIN (JAZ)-MYC transcriptional module | MycorWeb Plant-Microbe Interactions | Scoop.it
The plant hormone jasmonate (JA) promotes the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins to relieve repression on diverse transcription factors (TFs) that execute JA responses. However, little is known about how combinatorial complexity among JAZ–TF interactions maintains control over myriad aspects of growth, development, reproduction, and immunity.
We used loss-of-function mutations to define epistatic interactions within the core JA signaling pathway and to investigate the contribution of MYC TFs to JA responses in Arabidopsis thaliana.
Constitutive JA signaling in a jaz quintuple mutant (jazQ) was largely eliminated by mutations that block JA synthesis or perception. Comparison of jazQ and a jazQ myc2 myc3 myc4 octuple mutant validated known functions of MYC2/3/4 in root growth, chlorophyll degradation, and susceptibility to the pathogen Pseudomonas syringae. We found that MYC TFs also control both the enhanced resistance of jazQ leaves to insect herbivory and restricted leaf growth of jazQ. Epistatic transcriptional profiles mirrored these phenotypes and further showed that triterpenoid biosynthetic and glucosinolate catabolic genes are up-regulated in jazQ independently of MYC TFs.
Our study highlights the utility of genetic epistasis to unravel the complexities of JAZ–TF interactions and demonstrates that MYC TFs exert master control over a JAZ-repressible transcriptional hierarchy that governs growth–defense balance.
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Mycorrhizal fungi as drivers and modulators of terrestrial ecosystem processes

Mycorrhizal fungi as drivers and modulators of terrestrial ecosystem processes | MycorWeb Plant-Microbe Interactions | Scoop.it
Over 30 years have passed since David Read's observation that biome-level patterns in mycorrhizal dominance parallel distinct gradients in soil organic matter and nitrogen availability (Read, 1984). Read (1984) hypothesized these patterns emerged because arbuscular mycorrhizal (AM), ectomycorrhizal (ECM) and ericoid mycorrhizal (ERM) plants evolved unique functional traits in response to particular sets of environmental, and especially soil, conditions. Most intriguingly, Read suggested that mycorrhizal traits themselves modulate and stabilize this broad geographic pattern (Read, 1984; Read & Perez-Moreno, 2003), which raises a question that we still ponder today – do the functional traits of mycorrhizal fungi confer ecosystem properties that cannot be explained by climate, soils or plant composition alone? Within the last 5 years, there have been a number of key studies expanding upon Read's ideas, deepening our conceptual understanding of the ecosystem-level consequences of mycorrhizal fungi. In a cross-biome analysis, Averill et al. (2014) reported that soil carbon (C) per unit of soil nitrogen (N) is greater in temperate and boreal forests dominated by ECM and ERM plants compared to grasslands and tropical forests dominated by AM plants. Orwin et al. (2011) incorporated mycorrhizal fungi into biogeochemical models, and found that when inorganic N is scarce, the capacity for ECM and ERM fungi to take up organic N may increase soil C pools because it facilitates greater plant productivity and imposes N limitation on decomposers. To further understand the mechanism behind the accumulation of C in boreal forests, Clemmensen et al. (2013) analyzed bomb 14C to demonstrate that a substantial fraction of soil C is derived from roots and mycorrhizal fungi and thus, that ECM and ERM fungi play an important role in the development of soil C stocks. Together, these findings support the idea that mycorrhizal associations contribute to the emergence of patterns across ecosystems and provide the grounds for new predictive frameworks for C and nutrient cycling (e.g. Phillips et al., 2013). These new perspectives motivated our organized oral session at the Ecological Society of America's 2016 meeting, but several critical questions remain.
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Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of Saccharomyces cerevisiae

Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of Saccharomyces cerevisiae | MycorWeb Plant-Microbe Interactions | Scoop.it
The yeast Saccharomyces cerevisiae has emerged as a superior model organism. Selection of distinct laboratory strains of S. cerevisiae with unique phenotypic properties, such as superior mating or sporulation efficiencies, has facilitated advancements in research. W303 is one such laboratory strain that is closely related to the first completely sequenced yeast strain, S288C. In this work, we provide a high-quality, annotated genome sequence for W303 for utilization in comparative analyses and genome-wide studies. Approximately 9500 variations exist between S288C and W303, affecting the protein sequences of ∼700 genes. A listing of the polymorphisms and divergent genes is provided for researchers interested in identifying the genetic basis for phenotypic differences between W303 and S288C. Several divergent functional gene families were identified, including flocculation and sporulation genes, likely representing selection for desirable laboratory phenotypes. Interestingly, remnants of ancestor wine strains were found on several chromosomes. Finally, as a test of the utility of the high-quality reference genome, variant mapping revealed more accurate identification of accumulated mutations in passaged mismatch repair-defective strains.
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Distributions of fungal melanin across species and soils

Distributions of fungal melanin across species and soils | MycorWeb Plant-Microbe Interactions | Scoop.it
Soil is one of Earth's largest carbon (C) sinks, and the diverse community of fungi it houses may affect soil C storage through the biosynthesis of recalcitrant cell wall polymers like melanin. We tested the hypotheses that (1) specific biological features of fungi - evolutionary history, functional guild, growth rate, and functional gene abundance in fungal genomes - predict fungal melanin content across species and (2) the abundance of melanin-producing fungi in soil is related to soil C storage and oxidative enzyme activity by colorimetrically assaying melanin in hyphal tissue of 62 fungal species. We found no phylogenetic signal for melanin content across the species used in our study. Instead, hyphal melanin content varied across fungal species, correlating with 177 protein domains encoded in fungal genomes. Melanin concentrations were positively correlated with protein domains involved in biosynthesis of phenolic melanin precursors, as well as primary and secondary metabolite biosynthesis, cell signaling, and oxidation-reduction reactions. By contrast, hyphal melanin content was negatively correlated with protein domains involved in DNA replication processes and stress response, as well as hyphal growth rate, suggesting a physiological tradeoff between melanin biosynthesis and cellular growth. Estimated melanin content of soil was positively correlated with total soil C and soil peroxidase activity, suggesting that fungal melanin may influence soil C cycling processes.
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A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance

A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance | MycorWeb Plant-Microbe Interactions | Scoop.it

Rice feeds half the world’s population, and rice blast is often a destructive disease that results in significant crop loss. Non-race-specific resistance has been more effective in controlling crop diseases than race-specific resistance because of its broad spectrum and durability. Through a genome-wide association study, we report the identification of a natural allele of a C2H2-type transcription factor in rice that confers non-race-specific resistance to blast. A survey of 3,000 sequenced rice genomes reveals that this allele exists in 10% of rice, suggesting that this favorable trait has been selected through breeding. This allele causes a single nucleotide change in the promoter of the bsr-d1 gene, which results in reduced expression of the gene through the binding of the repressive MYB transcription factor and, consequently, an inhibition of H2O2 degradation and enhanced disease resistance. Our discovery highlights this novel allele as a strategy for breeding durable resistance in rice.


Via Pierre-Marc Delaux
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The emerging science of linked plant–fungal invasions

Invasions of alien plants are typically studied as invasions of individual species, yet interactions between plants and symbiotic fungi (mutualists and potential pathogens) affect plant survival, physiological traits, and reproduction and hence invasion success. Studies show that plant–fungal associations are frequently key drivers of plant invasion success and impact, but clear conceptual frameworks and integration across studies are needed to move beyond a series of case studies towards a more predictive understanding. Here, we consider linked plant–fungal invasions from the perspective of plant and fungal origin, simplified to the least complex representations or ‘motifs’. By characterizing these interaction motifs, parallels in invasion processes between pathogen and mutualist fungi become clear, although the outcomes are often opposite in effect. These interaction motifs provide hypotheses for fungal-driven dynamics behind observed plant invasion trajectories. In some situations, the effects of plant–fungal interactions are inconsistent or negligible. Variability in when and where different interaction motifs matter may be driven by specificity in the plant–fungal interaction, the size of the effect of the symbiosis (negative to positive) on plants and the dependence (obligate to facultative) of the plant−fungal interaction. Linked plant–fungal invasions can transform communities and ecosystem function, with potential for persistent legacies preventing ecosystem restoration.
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Biodiversité, combien de millions d’espèces ?

Biodiversité, combien de millions d’espèces ? | MycorWeb Plant-Microbe Interactions | Scoop.it
Après des siècles d’études, on pensait avoir au moins une idée approximative du nombre des différentes espèces vivant sur Terre. L’utilité d’un tel recensement est d’autant plus urgent que la biodiversité disparaît à une vitesse grandissante en raison des activités humaines. Des espèces vont s’éteindre avant même qu’on ne les découvre.

Les scientifiques ont répertorié près de 2 millions d’espèces, mais on estime le nombre total entre à 3 à 100 millions. Le consensus s’est fixé récemment au bas de la fourchette, avec une étude très popularisée qui a proposé un chiffre précis de 8,7 millions d’espèces (à l’exception des bactéries, trop compliquées à compter).

Si c’est bien le cas, on a accompli des progrès considérables en cataloguant la biodiversité de la planète en ayant effectué 20 % peut-être du travail.

Mais dans une correspondance publiée dans la revue Nature, nous estimons que ce consensus sous-estime la biodiversité terrestre d’un facteur dix. Auquel cas, la tâche de décrire et de comprendre la biodiversité s’avère plus herculéenne qu’on n’aurait jamais pu l’imaginer.

Depuis 300 ans que le naturaliste suédois Carolus Linnaeus s’est illustré comme pionnier en matière de classification scientifique, nous pourrions avoir désigné seulement 2 % de la biodiversité terrestre.
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Exposure to the leaf litter microbiome of healthy adults protects seedlings from pathogen damage

Exposure to the leaf litter microbiome of healthy adults protects seedlings from pathogen damage | MycorWeb Plant-Microbe Interactions | Scoop.it
It is increasingly recognized that microbiota affect host health and physiology. However, it is unclear what factors shape microbiome community assembly in nature, and how microbiome assembly can be manipulated to improve host health. All plant leaves host foliar endophytic fungi, which make up a diverse, environmentally acquired fungal microbiota. Here, we experimentally manipulated assembly of the cacao tree ( Theobroma cacao ) fungal microbiome in nature and tested the effect of assembly outcome on host health. Using next-generation sequencing, as well as culture-based methods coupled with Sanger sequencing, we found that manipulating leaf litter exposure and location within the forest canopy significantly altered microbiome composition in cacao. Exposing cacao seedlings to leaf litter from healthy conspecific adults enriched the seedling microbiome with Colletotrichum tropicale , a fungal endophyte known to enhance pathogen resistance of cacao seedlings by upregulating host defensive pathways. As a result, seedlings exposed to healthy conspecific litter experienced reduced pathogen damage. Our results link processes that affect the assembly and composition of microbiome communities to their functional consequences for host success, and have broad implications for understanding plant–microbe interactions. Deliberate manipulation of the plant–fungal microbiome also has potentially important applications for cacao production and other agricultural systems in general.

Via Stéphane Hacquard
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Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides

Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides | MycorWeb Plant-Microbe Interactions | Scoop.it
In this article, we describe the presence of genes encoding close homologues of an endogenous plant peptide, rapid alkalinization factor (RALF), within the genomes of 26 species of phytopathogenic fungi. Members of the RALF family are key growth factors in plants, and the sequence of the RALF active region is well conserved between plant and fungal proteins. RALF1-like sequences were observed in most cases; however, RALF27-like sequences were present in the Sphaerulina musiva and Septoria populicola genomes. These two species are pathogens of poplar and, interestingly, the closest relative to their respective RALF genes is a poplar RALF27-like sequence. RALF peptides control cellular expansion during plant development, but were originally defined on the basis of their ability to induce rapid alkalinization in tobacco cell cultures. To test whether the fungal RALF peptides were biologically active in plants, we synthesized RALF peptides corresponding to those encoded by two sequenced genomes of the tomato pathogen Fusarium oxysporum f. sp. lycopersici. One of these peptides inhibited the growth of tomato seedlings and elicited responses in tomato and Nicotiana benthamiana typical of endogenous plant RALF peptides (reactive oxygen species burst, induced alkalinization and mitogen-activated protein kinase activation). Gene expression analysis confirmed that a RALF-encoding gene in F. oxysporum f. sp. lycopersici was expressed during infection on tomato. However, a subsequent reverse genetics approach revealed that the RALF peptide was not required by F. oxysporum f. sp. lycopersici for infection on tomato roots. This study has demonstrated the presence of functionally active RALF peptides encoded within phytopathogens that harbour an as yet undetermined role in plant–pathogen interactions.
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Antifungal activities of wood extractives

Antifungal activities of wood extractives | MycorWeb Plant-Microbe Interactions | Scoop.it
Extractives are non-structural wood molecules that represent a minor fraction in wood. However, they are source of diverse molecules putatively bioactive. Inhibition of fungal growth is one of the most interesting properties of wood extractives in a context of wood preservation, crop protection or medical treatments. The antifungal effect of molecules isolated from wood extractives has been mainly attributed to various mechanisms such as metal and free radical scavenging activity, direct interaction with enzymes, disruption of membrane integrity and perturbation of ionic homeostasis. Lignolytic fungi, which are microorganisms adapted to wood substrates, have developed various strategies to protect themselves against this toxicity. A better knowledge of these strategies could help both developing new systems for extractive removal in biomass valorization processes and using these molecules as antifungal agents.


Via Steve Marek
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Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication | MycorWeb Plant-Microbe Interactions | Scoop.it
Modern wheat, which underlies the diet of many across the globe, has a long history of selection and crosses among different species. Avni et al. used the Hi-C method of genome confirmation capture to assemble and annotate the wild allotetraploid wheat ( Triticum turgidum ). They then identified the putative causal mutations in genes controlling shattering (a key domestication trait among cereal crops). They also performed an exome capture–based analysis of domestication among wild and domesticated genotypes of emmer wheat. The findings present a compelling overview of the emmer wheat genome and its usefulness in an agricultural context for understanding traits in modern bread wheat.

Science , this issue p. [93][1]

[1]: /lookup/doi/10.1126/science.aan0032
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Caught in the jump

Caught in the jump | MycorWeb Plant-Microbe Interactions | Scoop.it
Microbial pathogens of plants typically cause disease on a limited number of host species. In nature, pathogens rarely become pathogenic to a new host. The underlying mechanisms of such host jumps are poorly understood but are thought to be linked to the capacity of the pathogen to undermine immunity of the former nonhost species (1). On page 80 of this issue, Inoue et al. (2) report a host jump mechanism of a notorious pathogenic fungus, Pyricularia oryzae, which causes blast disease in cereals.

The immune system of plants consists of two branches. First, surface-resident pattern recognition receptors (PRRs) detect microbial epitopes that are often conserved among many microbial taxa. Second, intracellular nucleotide-binding and leucinerich repeat proteins (NLRs) detect the actions of polymorphic pathogen-delivered and virulence-promoting proteins, called effectors. Recognized effectors are denoted avirulence genes (AVRs). Pathogen effectors often work by subverting signaling initiated by PRRs, facilitating host colonization and disease. The effector arsenal varies between strains of a pathogen species and is a major determinant for adaptation to specific hosts.
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Dorian Q Fuller's curator insight, July 14, 6:18 AM
One of the poorly understood strands of the origins and spread of agriculture,is the origins of crop diseases, which must have be facilitated by the spread to new environments and the diversification of crop packages.
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Book: Fortress Plant- How to survive when everything wants to eat you (2017)

Book: Fortress Plant- How to survive when everything wants to eat you (2017) | MycorWeb Plant-Microbe Interactions | Scoop.it

The survival of plants on our planet is nothing short of miraculous. They are virtually stationary packages of food, providing sustenance for a vast array of organisms, ranging from bacteria and fungi, through to insects, and even other plants. But plants are master survivors, having coped with changing environments and evolving predators over much of the history of life on earth.

 

Looks at how plants defend themselves against a wide variety of attackers, such as big animals, tiny insects, fungi, and bacteria, using an arsenal of weaponsExplores the evolution of plant defences, showing how they have resulted from an arms race with attackers that has been raging for millions of yearsDescribes the approaches by which scientists learn about plant defencesConsiders how we can use our knowledge of plant defences to help protect our food crops and forests

Via Kamoun Lab @ TSL, Tofazzal Islam's Research Group, Elsa Ballini
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Novel soil-inhabiting clades fill gaps in the fungal tree of life

Novel soil-inhabiting clades fill gaps in the fungal tree of life | MycorWeb Plant-Microbe Interactions | Scoop.it

Background
Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water.
Results
We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH.
Conclusions
This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.


Via Steve Marek
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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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Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure

Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure | MycorWeb Plant-Microbe Interactions | Scoop.it
Extremophilic organisms demonstrate the flexibility and adaptability of basic biological processes by highlighting how cell physiology adapts to environmental extremes. Few eukaryotic extremophiles have been well studied and only a small number are amenable to laboratory cultivation and manipulation. A detailed characterization of the genome architecture of such organisms is important to illuminate how they adapt to environmental stresses. One excellent example of a fungal extremophile is the halophile Hortaea werneckii (Pezizomycotina, Dothideomycetes, Capnodiales), a yeast-like fungus able to thrive at near-saturating concentrations of sodium chloride and which is also tolerant to both UV irradiation and desiccation. Given its unique lifestyle and its remarkably recent whole genome duplication, H. werneckii provides opportunities for testing the role of genome duplications and adaptability to extreme environments. We previously assembled the genome of H. werneckii using short-read sequencing technology and found a remarkable degree of gene duplication. Technology limitations, however, precluded high-confidence annotation of the entire genome. We therefore revisited the H. wernickii genome using long-read, single-molecule sequencing and provide an improved genome assembly which, combined with transcriptome and nucleosome analysis, provides a useful resource for fungal halophile genomics. Remarkably, the ∼50 Mb H. wernickii genome contains 15,974 genes of which 95% (7608) are duplicates formed by a recent whole genome duplication (WGD), with an average of 5% protein sequence divergence between them. We found that the WGD is extraordinarily recent, and compared to Saccharomyces cerevisiae , the majority of the genome’s ohnologs have not diverged at the level of gene expression of chromatin structure.
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evolution of hydrophobic cell wall biopolymers: from algae to angiosperms 

The transition from an aquatic ancestral condition to a terrestrial environment exposed the first land plants to the desiccating effects of air and potentially large fluctuations in temperature and light intensity. To be successful, this transition necessitated metabolic, physiological, and morphological modifications, among which one of the most important was the capacity to synthesize hydrophobic extracellular biopolymers such as those found in the cuticular membrane, suberin, lignin, and sporopollenin, which collectively reduce the loss of water, provide barriers to pathogens, protect against harmful levels of UV radiation, and rigidify targeted cell walls. Here, we review phylogenetic and molecular data from extant members of the green plant clade (Chlorobionta) and show that the capacity to synthesize the monomeric precursors of all four biopolymers is ancestral and extends in some cases to unicellular plants (e.g. Chlamydomonas). We also review evidence from extant algae, bryophytes, and early-divergent tracheophytes and show that gene duplication, subsequent neo-functionalization, and the co-option of fundamental and ancestral metabolic pathways contributed to the early evolutionary success of the land plants.

Via Pierre-Marc Delaux
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Genome Analysis of a Zygomycete Fungus Choanephora cucurbitarum Elucidates Necrotrophic Features Including Bacterial Genes Related to Plant Colonization

Genome Analysis of a Zygomycete Fungus Choanephora cucurbitarum Elucidates Necrotrophic Features Including Bacterial Genes Related to Plant Colonization | MycorWeb Plant-Microbe Interactions | Scoop.it
A zygomycete fungus, Choanephora cucurbitarum is a plant pathogen that causes blossom rot in cucurbits and other plants. Here we report the genome sequence of Choanephora cucurbitarum KUS-F28377 isolated from squash. The assembled genome has a size of 29.1 Mbp and 11,977 protein-coding genes. The genome analysis indicated that C. cucurbitarum may employ a plant pathogenic mechanism similar to that of bacterial plant pathogens. The genome contained 11 genes with a Streptomyces subtilisin inhibitor-like domain, which plays an important role in the defense against plant immunity. This domain has been found only in bacterial genomes. Carbohydrate active enzyme analysis detected 312 CAZymes in this genome where carbohydrate esterase family 6, rarely found in dikaryotic fungal genomes, was comparatively enriched. The comparative genome analysis showed that the genes related to sexual communication such as the biosynthesis of β-carotene and trisporic acid were conserved and diverged during the evolution of zygomycete genomes. Overall, these findings will help us to understand how zygomycetes are associated with plants.
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