How microbes emerge
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Diagnosing plant diseases is ‘a detective task’

Diagnosing plant diseases is ‘a detective task’ | How microbes emerge | Scoop.it
Sherlock Holmes would feel at home, deducing plant diseases at an Oregon State University clinic.
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Rescooped by Niklaus Grunwald from Plant pathogenic fungi
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Out of Water: The Origin and Early Diversification of Plant R-Genes

Out of Water: The Origin and Early Diversification of Plant R-Genes | How microbes emerge | Scoop.it
During plant-pathogen interactions, plants use intracellular proteins with nucleotide-binding site and leucine-rich repeat (NBS-LRR) domains to detect pathogens. NBS-LRR proteins represent a major class of plant disease resistance genes (R-genes). Whereas R-genes have been well characterized in angiosperms, little is known about their origin and early diversification. Here we perform comprehensive evolutionary analyses of R-genes in plants and report the identification of R-genes in basal-branching streptophytes, including charophytes, liverworts, and mosses. Phylogenetic analyses suggest that plant R-genes originated in charophytes and R-proteins diversified into TIR-NBS-LRR proteins (TNLs) and non-TIR-NBS-LRR proteins (nTNLs) in charophytes. Moreover, we show that plant R-proteins evolved in a modular fashion through frequent gain or loss of protein domains. Most of the R-genes in basal-branching streptophytes underwent adaptive evolution, indicating an ancient involvement of R-genes in plant-pathogen interactions. Our findings provide novel insights into the origin and evolution of R-genes and the mechanisms underlying colonization of terrestrial environments by plants.

Via Pierre-Marc Delaux, Francis Martin, Steve Marek
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Rescooped by Niklaus Grunwald from Microbes and Microbiomes
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Disease-induced assemblage of a plant-beneficial bacterial consortium

Disease-induced assemblage of a plant-beneficial bacterial consortium | How microbes emerge | Scoop.it
Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate that Arabidopsis thaliana specifically promotes three bacterial species in the rhizosphere upon foliar defense activation by the downy mildew pathogen Hyaloperonospora arabidopsidis. The promoted bacteria were isolated and found to interact synergistically in biofilm formation in vitro. Although separately these bacteria did not affect the plant significantly, together they induced systemic resistance against downy mildew and promoted growth of the plant. Moreover, we show that the soil-mediated legacy of a primary population of downy mildew infected plants confers enhanced protection against this pathogen in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance of survival of their offspring that will grow in the same soil.

Via Matt Agler
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Rescooped by Niklaus Grunwald from Forest microbiome
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Ericoid plant species and Pinus sylvestris shape fungal communities in their roots and surrounding soil

Ericoid plant species and Pinus sylvestris shape fungal communities in their roots and surrounding soil | How microbes emerge | Scoop.it

Root-colonizing fungi can form mycorrhizal or endophytic associations with plant roots, the type of association depending on the host. We investigated the differences and similarities of the fungal communities of three boreal ericoid plants and one coniferous tree, and identified the community structure of fungi utilizing photosynthates from the plants studied. The fungal communities of roots and soils of Vaccinium myrtillus, Vaccinium vitis-idaea, Calluna vulgaris and Pinus sylvestris were studied in an 18-month-long experiment where the plants were grown individually in natural substrate. Photosynthates utilizing fungi were detected with DNA stable-isotope probing using 13CO2 (13C-DNA-SIP). The results indicated that the plants studied provide different ecological niches preferred by different fungal species. Those fungi which dominated the community in washed roots had also the highest 13C-uptake. In addition, a common root endophyte without confirmed mycorrhizal status also obtained 13C from all the plants, indicating close plant-association of this fungal species. We detect several fungal species inhabiting the roots of both ericoid mycorrhizal and ectomycorrhizal plants. Our results highlight that the ecological role of co-occurrence of fungi with different life styles (e.g. mycorrhizal or endophytic) in plant root systems should be further investigated.


Via Petr Baldrian
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Rescooped by Niklaus Grunwald from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens | How microbes emerge | Scoop.it

The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.


Via Pierre Gladieux
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Bridget Barker's curator insight, March 3, 10:11 AM
Very interesting approach
Rescooped by Niklaus Grunwald from Adaptive Evolution and Speciation
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Forward Genetics Approach Reveals Host Genotype-Dependent Importance of Accessory Chromosomes in the Fungal Wheat Pathogen Zymoseptoria tritici - mBio

Forward Genetics Approach Reveals Host Genotype-Dependent Importance of Accessory Chromosomes in the Fungal Wheat Pathogen Zymoseptoria tritici - mBio | How microbes emerge | Scoop.it
The fungal wheat pathogen Zymoseptoria tritici possesses a large complement of accessory chromosomes showing presence/absence polymorphism among isolates. These chromosomes encode hundreds of genes; however, their functional role and why the chromosomes have been maintained over long evolutionary times are so far not known. In this study, we addressed the functional relevance of eight accessory chromosomes in reference isolate IPO323. We induced chromosome losses by inhibiting the β-tubulin assembly during mitosis using carbendazim and generated several independent isogenic strains, each lacking one of the accessory chromosomes. We confirmed chromosome losses by electrophoretic karyotyping and whole-genome sequencing. To assess the importance of the individual chromosomes during host infection, we performed in planta assays comparing disease development results in wild-type and chromosome mutant strains. Loss of the accessory chromosomes 14, 16, 18, 19, and 21 resulted in increased virulence on wheat cultivar Runal but not on cultivars Obelisk, Titlis, and Riband. Moreover, some accessory chromosomes affected the switch from biotrophy to necrotrophy as strains lacking accessory chromosomes 14, 18, 19, and 21 showed a significantly earlier onset of necrosis than the wild type on the Runal cultivar. In general, we observed that the timing of the lifestyle switch affects the fitness of Z. tritici. Taking the results together, this study was the first to use a forward-genetics approach to demonstrate a cultivar-dependent functional relevance of the accessory chromosomes of Z. tritici during host infection.

Via Ronny Kellner
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Rescooped by Niklaus Grunwald from The Plant Microbiome
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Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming | How microbes emerge | Scoop.it
Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be manipulated through different cropping practices. Here, we investigated soil and wheat root microbial communities in a cropping system experiment consisting of conventional and organic managements, both with different tillage intensities. While microbial richness was marginally affected, we found pronounced cropping effects on community composition, which were specific for the respective microbiomes. Soil bacterial communities were primarily structured by tillage, whereas soil fungal communities responded mainly to management type with additional effects by tillage. In roots, management type was also the driving factor for bacteria but not for fungi, which were generally determined by changes in tillage intensity. To quantify an “effect size” for microbiota manipulation, we found that about 10% of variation in microbial communities was explained by the tested cropping practices. Cropping sensitive microbes were taxonomically diverse, and they responded in guilds of taxa to the specific practices. These microbes also included frequent community members or members co-occurring with many other microbes in the community, suggesting that cropping practices may allow manipulation of influential community members. Understanding the abundance patterns of cropping sensitive microbes presents the basis towards developing microbiota management strategies for smart farming. For future targeted microbiota management—e.g., to foster certain microbes with specific agricultural practices—a next step will be to identify the functional traits of the cropping sensitive microbes.

Via Stéphane Hacquard
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Jonathan Lapleau's curator insight, January 20, 5:50 AM
Combining cropping practices and soil microbes management = smart farming. We are at the beginning of big changes in agriculture.
Rescooped by Niklaus Grunwald from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Runs of homozygosity: windows into population history and trait architecture

Runs of homozygosity: windows into population history and trait architecture | How microbes emerge | Scoop.it

Long runs of homozygosity (ROH) arise when identical haplotypes are inherited from each parent and thus a long tract of genotypes is homozygous. Cousin marriage or inbreeding gives rise to such autozygosity; however, genome-wide data reveal that ROH are universally common in human genomes even among outbred individuals. The number and length of ROH reflect individual demographic history, while the homozygosity burden can be used to investigate the genetic architecture of complex disease. We discuss how to identify ROH in genome-wide microarray and sequence data, their distribution in human populations and their application to the understanding of inbreeding depression and disease risk.


Via Pierre Gladieux
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Rescooped by Niklaus Grunwald from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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The quest for durable resistance

The quest for durable resistance | How microbes emerge | Scoop.it
Agriculture transformed humans from hunter-gatherers into city dwellers. This was made possible through the domestication of crops, such as wheat and barley. Based on archaeological evidence ( 1 ), we know that our ancestors' crops were constantly plagued by disease, including rusts and mildews on cereals. During the 4th century BCE, Romans sacrificed red cattle, foxes, and dogs to the god Robigus in the belief that it would prevent epidemics of cereal rusts. Today, we understand that crop diseases are caused by plant pathogens. Cereal rusts are fungal pathogens that colonize foliar parts of the plant, such as the stem or leaf. The ability of these pathogens to infect a plant requires the suppression of the plant's immune system. The principal weapon used by pathogens to inhibit immunity are effectors, typically small secreted proteins. Plants recognize pathogens through immune receptors, including those that either directly or indirectly “perceive” pathogen effectors secreted into the plant ( 2 ). On pages 1604 and 1607 of this issue, Salcedo et al. ( 3 ) and Chen et al. ( 4 ), respectively, describe the identification of two effectors from the fungal pathogen Puccinia graminis f. sp. tritici , the causal agent of wheat stem rust. The discovery of these effectors represents a critical milestone for developing an approach to track and prevent the worldwide spread of the rusts of wheat ( 5 ) and improve our understanding of the biology of these devastating pathogens.

Via Pierre Gladieux
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Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management

Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management | How microbes emerge | Scoop.it
Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.
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Rescooped by Niklaus Grunwald from Plant Pathogenomics
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bioRxiv: Extremely flexible infection programs in a fungal plant pathogen (2017)

bioRxiv: Extremely flexible infection programs in a fungal plant pathogen (2017) | How microbes emerge | Scoop.it

Filamentous plant pathogens exhibit extraordinary levels of genomic variability that is proposed to facilitate rapid adaptation to changing host environments. However, the impact of genomic variation on phenotypic differentiation in pathogen populations is largely unknown. Here, we address the extent of variability in infection phenotypes of the hemibiotrophic wheat pathogen Zymoseptoria tritici by studying three field isolates collected in Denmark, Iran, and the Netherlands. These three isolates differ extensively in genome structure and gene content, but produce similar disease symptoms in the same susceptible wheat cultivar. Using advanced confocal microscopy, staining of reactive oxygen species, and comparative analyses of infection stage-specific RNA-seq data, we demonstrate considerable variation in the temporal and spatial course of infection of the three isolates. Based on microscopic observation, we determined four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction. Comparative analyses of the fungal transcriptomes, sequenced for every infection stage, revealed that the gene expression profiles of the isolates differed significantly, and 20% of the genes are differentially expressed between the three isolates during infection. The genes exhibiting isolate-specific expression patterns are enriched in genes encoding effector candidates that are small, secreted, cysteine-rich proteins and putative virulence determinants. Moreover, the differentially expressed genes were located significantly closer to transposable elements, which are enriched for the heterochromatin-associated histone marks H3K9me3 and H3K27me3 on the accessory chromosomes. This observation indicates that transposable elements and epigenetic regulation contribute to the infection-associated transcriptional variation between the isolates. Our findings illustrate how high genetic diversity in a pathogen population can result in highly differentiated infection and expression phenotypes that can support rapid adaptation in changing environments. Furthermore, our study reveals an exceptionally high extent of plasticity in the infection program of an important wheat pathogen and shows a substantial redundancy in infection-related gene expression.


Via Kamoun Lab @ TSL
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Rescooped by Niklaus Grunwald from MycorWeb Plant-Microbe Interactions
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Forward Genetics Approach Reveals Host Genotype-Dependent Importance of Accessory Chromosomes in the Fungal Wheat Pathogen Zymoseptoria tritici

Forward Genetics Approach Reveals Host Genotype-Dependent Importance of Accessory Chromosomes in the Fungal Wheat Pathogen Zymoseptoria tritici | How microbes emerge | Scoop.it
The fungal wheat pathogen Zymoseptoria tritici possesses a large complement of accessory chromosomes showing presence/absence polymorphism among isolates. These chromosomes encode hundreds of genes; however, their functional role and why the chromosomes have been maintained over long evolutionary times are so far not known. In this study, we addressed the functional relevance of eight accessory chromosomes in reference isolate IPO323. We induced chromosome losses by inhibiting the β-tubulin assembly during mitosis using carbendazim and generated several independent isogenic strains, each lacking one of the accessory chromosomes. We confirmed chromosome losses by electrophoretic karyotyping and whole-genome sequencing. To assess the importance of the individual chromosomes during host infection, we performed in planta assays comparing disease development results in wild-type and chromosome mutant strains. Loss of the accessory chromosomes 14, 16, 18, 19, and 21 resulted in increased virulence on wheat cultivar Runal but not on cultivars Obelisk, Titlis, and Riband. Moreover, some accessory chromosomes affected the switch from biotrophy to necrotrophy as strains lacking accessory chromosomes 14, 18, 19, and 21 showed a significantly earlier onset of necrosis than the wild type on the Runal cultivar. In general, we observed that the timing of the lifestyle switch affects the fitness of Z. tritici. Taking the results together, this study was the first to use a forward-genetics approach to demonstrate a cultivar-dependent functional relevance of the accessory chromosomes of Z. tritici during host infection.

Via Francis Martin
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fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks

fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks | How microbes emerge | Scoop.it
Public health related decisions often have to balance the cost of intervention strategies with the benefit of the reduction in disease burden. While the cost can often be inferred, forward modelling of the effect of different intervention options is complicated and disease specific. Here we introduce a package that is aimed to simplify this process. The package allows one to infer parameters using a Bayesian approach, perform forward modelling of the likely results of the proposed intervention and finally perform cost effectiveness analysis of the results. The package is based on a method previously used in the UK to inform vaccination strategies for influenza, with extensions to make it easily adaptable to other diseases and data sources.
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Rescooped by Niklaus Grunwald from MycorWeb Plant-Microbe Interactions
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Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems

Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems | How microbes emerge | Scoop.it
Why should fungi identify nonself?
Fungi colonize nearly all environments on Earth (reviewed in [4]), where they interact with every major organismal group: viruses, bacteria, protists, amoeba, plants, and animals. Many of these interactions lead to symbioses ranging from mutualism to pathogenesis (Fig 1) [4]. Examples include fungi that are targeted by pathogens and predators [5] or that become hosts for intracellular bacterial populations [6]. Some of these fungal endosymbiont interactions have coevolved over their 400 million year old [7] symbiosis and likely involve specific bidirectional recognition systems [8–10]. The evolutionary success of the kingdom Fungi and diversity of fungal biotic interactions suggest that, like plants and animals, fungi have developed the ability to accurately identify and respond to interacting organisms. However, mechanisms for such monitoring and response are just beginning to be understood [11]. An intriguing possibility is the involvement of NLR-based nonself recognition mechanisms in Fungi.

Via Francis Martin
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Rescooped by Niklaus Grunwald from Plant pathogens and pests
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Why did filamentous plant pathogens evolve the potential to secrete hundreds of effectors to enable disease? - Thordal-Christensen - 2018 - Molecular Plant Pathology -

Why did filamentous plant pathogens evolve the potential to secrete hundreds of effectors to enable disease? - Thordal-Christensen - 2018 - Molecular Plant Pathology - | How microbes emerge | Scoop.it
During the past decade, many genomes have been sequenced from fungal and oomycete pathogens that interact biotrophically with plants, i.e. they thrive at least initially on living plant tissue. This has revealed genomes that often encode hundreds of proteins predicted to be secreted on the basis of N-terminal signal peptides. Most of these proteins are unique or found only within restricted phylogenetic clades (Franceschetti et al., 2017). They are predicted to be ‘effectors’, i.e. proteins which, in some way, contribute to the virulence of the pathogen (see below). The fact that these filamentous microbes have hundreds of candidate effector genes is in stark contrast with bacterial pathogens, which typically have an order of magnitude fewer effector candidate genes. Although most of these hundreds of effectors currently lack evidence for significant roles in virulence, it is still striking that many of them appear to contribute measurably to virulence and that several of them seem to physically interact with numerous host proteins. In this Opinion Piece, we discuss these observations and attempt to address the apparent need for hundreds of effector candidate genes in these species. We suggest that this requirement reflects, in part, the need for effectors to target defence-unrelated susceptibility components. Many of these, in turn, may be monitored (‘guarded’) by resistance-triggering immune sensors. Potentially, pathogen success depends on additional sets of effectors dedicated to suppress this kind of surveillance.

Via Christophe Jacquet
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Rescooped by Niklaus Grunwald from Microbes and Microbiomes
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Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life | How microbes emerge | Scoop.it
The tree of life is arguably the most important organizing principle in biology and perhaps the most widely understood depiction of the evolutionary process. It explains to us how we are related to other organisms and where we may have come from. The tree has undergone some tremendous revolutions since the first version was sketched by Charles Darwin. A major innovation was the construction of phylogenetic trees using DNA sequence information, which opened the way for classification of microbial life. As implemented by Carl Woese and collaborators, this work enabled the definition of three domains: Bacteria, Archaea, and Eukaryotes (Woese and Fox, 1977, Woese et al., 1990). More recently, the three-domain topology has been questioned, and eukaryotes—our own branch of life—potentially relocated into the archael domain (Spang et al., 2015, Williams et al., 2013). Beyond this, and as described here, cultivation-independent genomic methods that access sequences from laboratory-intractable organisms have added many new lineages to the tree. Their inclusion completely clarifies the extreme minority of life’s diversity that is represented by macroscopic organisms and underscores that our place in biology is dwarfed by bacteria and archaea.

Via Matt Agler
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Rescooped by Niklaus Grunwald from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D | How microbes emerge | Scoop.it
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction. Assembly of the reads derived from all three technologies resulted in complete sequences for all 16 yeast chromosomes, as well as the mitochondrial chromosome, in one step. Further, we identified three types of DNA methylation (5mC, 4mC and 6mA). Comparison between the reference strain S288C and strain CEN.PK113-7D identified chromosomal rearrangements against a background of similar gene content between the two strains. We identified full-length transcripts through ONT direct RNA sequencing technology. This allows for the identification of transcriptional landscapes, including untranslated regions (UTRs) (5′ UTR and 3′ UTR) as well as differential gene expression quantification. About 91% of the predicted transcripts could be consistently detected across biological replicates grown either on glucose or ethanol. Direct RNA sequencing identified many polyadenylated non-coding RNAs, rRNAs, telomere-RNA, long non-coding RNA and antisense RNA. This work demonstrates a strategy to obtain complete genome sequences and transcriptional landscapes that can be applied to other eukaryal organisms.

Via Pierre Gladieux
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Rescooped by Niklaus Grunwald from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Factors driving metabolic diversity in the budding yeast subphylum

Factors driving metabolic diversity in the budding yeast subphylum | How microbes emerge | Scoop.it
Associations between traits are prevalent in nature, occurring across a diverse range of taxa and traits. Individual traits may co-evolve with one other, and these correlations can be driven by factors intrinsic or extrinsic to an organism. However, few studies, especially in microbes, have simultaneously investigated both across a broad taxonomic range. Here we quantify pairwise associations among 48 traits across 784 diverse yeast species of the ancient budding yeast subphylum Saccharomycotina, assessing the effects of phylogenetic history, genetics, and ecology. We find extensive negative (traits that tend to not occur together) and positive (traits that tend to co-occur) pairwise associations among traits, as well as between traits and environments. These associations can largely be explained by the biological properties of the traits, such as overlapping biochemical pathways. The isolation environments of the yeasts explain a minor but significant component of the variance, while phylogeny (the retention of ancestral traits in descendant species) plays an even more limited role. Positive correlations are pervasive among carbon utilization traits and track with chemical structures (e.g., glucosides and sugar alcohols) and metabolic pathways, suggesting a molecular basis for the presence of suites of traits. In several cases, characterized genes from model organisms suggest that enzyme promiscuity and overlapping biochemical pathways are likely mechanisms to explain these macroevolutionary trends. Interestingly, fermentation traits are negatively correlated with the utilization of pentose sugars, which are major components of the plant biomass degraded by fungi and present major bottlenecks to the production of cellulosic biofuels. Finally, we show that mammalian pathogenic and commensal yeasts have a suite of traits that includes growth at high temperature and, surprisingly, the utilization of a narrowed panel of carbon sources. These results demonstrate how both intrinsic physiological factors and extrinsic ecological factors drive the distribution of traits present in diverse organisms across macroevolutionary timescales.

Via Pierre Gladieux
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Rescooped by Niklaus Grunwald from Plant-Microbe Symbiosis
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Rhizobia: from saprophytes to endosymbionts

Rhizobia: from saprophytes to endosymbionts | How microbes emerge | Scoop.it
Rhizobia are some of the best-studied plant microbiota. These oligotrophic Alphaproteobacteria or Betaproteobacteria form symbioses with their legume hosts. Rhizobia must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids. These dramatic lifestyle and developmental changes are underpinned by large genomes and even more complex pan-genomes, which encompass the whole population and are subject to rapid genetic exchange. The ability to respond to plant signals and chemoattractants and to colonize nutrient-rich roots are crucial for the competitive success of these bacteria. The availability of a large body of genomic, physiological, biochemical and ecological studies makes rhizobia unique models for investigating community interactions and plant colonization.


Via Jean-Michel Ané
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Rescooped by Niklaus Grunwald from Adaptive Evolution and Speciation
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Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island - New Phytologist

Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island - New Phytologist | How microbes emerge | Scoop.it
Microbes can have profound effects on their hosts, driving natural selection, promoting speciation and determining species distributions. However, soil-dwelling microbes are rarely investigated as drivers of evolutionary change in plants.
We used metabarcoding and experimental manipulation of soil microbiomes to investigate the impact of soil and root microbes in a well-known case of sympatric speciation, the Howea palms of Lord Howe Island (Australia). Whereas H. forsteriana can grow on both calcareous and volcanic soils, H. belmoreana is restricted to, but more successful on, volcanic soil, indicating a trade-off in adaptation to the two soil types.
We suggest a novel explanation for this trade-off. Arbuscular mycorrhizal fungi (AMF) are significantly depleted in H. forsteriana on volcanic soil, relative to both H. belmoreana on volcanic soil and H. forsteriana on calcareous soil. This is mirrored by the results of survival experiments, where the sterilization of natural soil reduces Howea fitness in every soil–species combination except H. forsteriana on volcanic soil. Furthermore, AMF-associated genes exhibit evidence of divergent selection between Howea species.
These results show a mechanism by which divergent adaptation can have knock-on effects on host–microbe interactions, thereby reducing interspecific competition and promoting the coexistence of plant sister species.

Via Ronny Kellner
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Rescooped by Niklaus Grunwald from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Genomic features of bacterial adaptation to plants

Genomic features of bacterial adaptation to plants | How microbes emerge | Scoop.it
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe–microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant–microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.

Via Matt Agler, Pierre Gladieux
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Steve Marek's curator insight, December 19, 2017 10:30 AM
"identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes"
WillistonPlantPath's curator insight, December 20, 2017 2:43 PM
484 bacterial genomes. wow.
Rescooped by Niklaus Grunwald from MycorWeb Plant-Microbe Interactions
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Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum | How microbes emerge | Scoop.it

Background

Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2 V. longisporum field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed.

Results

The draft genomes of 2 Verticillium longisporum single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70 Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in V. dahliae and V. albo-atrum. Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the V. longisporum genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to V. dahliae. Presence of the mating-type genes MAT1–1-1 and MAT1–2-1 in the V. longisporum genomes were confirmed. However, the MAT genes in V. dahliae, V. albo-atrum and V. longisporum have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species.


Conclusions

The established draft genome of V. longisporum is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two V. longisporum genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to V. dahliae. Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.


Via Francis Martin
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Plant Pathology: Plasmid-powered evolutionary transitions

Plant Pathology: Plasmid-powered evolutionary transitions | How microbes emerge | Scoop.it
The acquisition of a virulence plasmid is sufficient to turn a beneficial strain of Rhodococcus bacteria into a pathogen.
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Scooped by Niklaus Grunwald
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Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean (Phaseolus vulgaris) in the United States

Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean (Phaseolus vulgaris) in the United States | How microbes emerge | Scoop.it
The ascomycete pathogen Sclerotinia sclerotiorum is a necrotrophic pathogen on over 400 known host plants, and is the causal agent of white mold on dry bean. Currently, there are no known cultivars of dry bean with complete resistance to white mold. For more than 20 years, bean breeders have been using white mold screening nurseries (wmn) with natural populations of S. sclerotiorum to screen new cultivars for resistance. It is thus important to know if the genetic diversity in populations of S. sclerotiorum within these nurseries (a) reflect the genetic diversity of the populations in the surrounding region and (b) are stable over time. Furthermore, previous studies have investigated the correlation between mycelial compatibility groups (MCG) and multilocus haplotypes (MLH), but none have formally tested these patterns. We genotyped 366 isolates of S. sclerotiorum from producer fields and wmn surveyed over 10 years in 2003–2012 representing 11 states in the United States of America, Australia, France, and Mexico at 11 microsatellite loci resulting in 165 MLHs. Populations were loosely structured over space and time based on analysis of molecular variance and discriminant analysis of principal components, but not by cultivar, aggressiveness, or field source. Of all the regions tested, only Mexico (n = 18) shared no MLHs with any other region. Using a bipartite network-based approach, we found no evidence that the MCGs accurately represent MLHs. Our study suggests that breeders should continue to test dry bean lines in several wmn across the United States to account for both the phenotypic and genotypic variation that exists across regions.
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Scooped by Niklaus Grunwald
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Estimating virus effective population size and selection without neutral markers

Estimating virus effective population size and selection without neutral markers | How microbes emerge | Scoop.it
Author summary A growing number of experimental evolution studies are using an “evolve-and-resequence” approach to observe the within-host dynamics of pathogen variants of biomedical or ecological interest. The resulting data are particularly appropriate for studying the effects of evolutionary forces, such as selection and genetic drift, on the emergence of new pathogen variants. However, it remains challenging to unravel the effects of selection and genetic drift in the absence of neutral markers, a situation frequently encountered for microbes, such as viruses, due to their small constrained genomes. Using such an approach on a plant virus, we observed that the same set of virus variants displayed highly diverse dynamics in closely related plant genotypes. We developed and validated a method that does not require neutral markers, for estimating selection coefficients and effective population sizes from these experimental evolution data. We found that the viruses experienced considerable diversity in genetic drift regimes, depending on host genotype. Importantly, genetic drift experienced by virus populations was shown to be a heritable plant trait. These findings pave the way for the breeding of plant varieties exposing viruses to strong genetic drift, thereby slowing virus adaptation.
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Rescooped by Niklaus Grunwald from MycorWeb Plant-Microbe Interactions
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A communal catalogue reveals Earth’s multiscale microbial diversity : Nature

A communal catalogue reveals Earth’s multiscale microbial diversity : Nature | How microbes emerge | Scoop.it
Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.

Via Francis Martin
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