Adaptive Evolution and Speciation
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A single fungal MAP kinase controls plant cell-to-cell invasion by the rice blast fungus - Science

A single fungal MAP kinase controls plant cell-to-cell invasion by the rice blast fungus - Science | Adaptive Evolution and Speciation | Scoop.it
Blast disease destroys up to 30% of the rice crop annually and threatens global food security. The blast fungus Magnaporthe oryzae invades plant tissue with hyphae that proliferate and grow from cell to cell, often through pit fields, where plasmodesmata cluster. We showed that chemical genetic inhibition of a single fungal mitogen-activated protein (MAP) kinase, Pmk1, prevents M. oryzae from infecting adjacent plant cells, leaving the fungus trapped within a single plant cell. Pmk1 regulates expression of secreted fungal effector proteins implicated in suppression of host immune defenses, preventing reactive oxygen species generation and excessive callose deposition at plasmodesmata. Furthermore, Pmk1 controls the hyphal constriction required for fungal growth from one rice cell to the neighboring cell, enabling host tissue colonization and blast disease.

Via Francis Martin
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Genomic changes associated with the evolutionary transitions of Nostoc to a plant symbiont - MBE

Genomic changes associated with the evolutionary transitions of Nostoc to a plant symbiont - MBE | Adaptive Evolution and Speciation | Scoop.it

The cyanobacteria belonging to the genus Nostoc comprise free-living strains but also facultative plant-symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here we compared the genomes derived from eleven symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acid, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate L-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell-walls. These compounds could function as C sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 million years ago, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.

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Why did filamentous plant pathogens evolve the potential to secrete hundreds of effectors to enable disease? - Molecular Plant Pathology

Why did filamentous plant pathogens evolve the potential to secrete hundreds of effectors to enable disease? - Molecular Plant Pathology | Adaptive Evolution and Speciation | 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.
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STAG: Species Tree Inference from All Genes - biorxiv

STAG: Species Tree Inference from All Genes - biorxiv | Adaptive Evolution and Speciation | Scoop.it
Species tree inference is fundamental to our understanding of the evolution of life on earth. However, species tree inference from molecular sequence data is complicated by gene duplication events that limit the availably of suitable data for phylogenetic reconstruction. Here we propose a novel method for species tree inference called STAG that is specifically designed to leverage data from multi-copy gene families. By application to 12 real species datasets sampled from across the eukaryotic domain we demonstrate that species trees inferred from multi-copy gene families are comparable in accuracy to species trees inferred from single-copy orthologues. We further show that the ability to utilise data from multi-copy gene families increases the amount of data available for species tree inference by an average of 8 fold. We reveal that on real species datasets STAG has higher accuracy than other leading methods for species tree inference; including concatenated alignments of protein sequences, ASTRAL & NJst. Finally we show that STAG is fast, memory efficient and scalable and thus suitable for analysis of large multispecies datasets.
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Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life - Cell

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life - Cell | Adaptive Evolution and Speciation | 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, Steve Marek
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Exploring and exploiting the boundaries of host specificity using the cereal rust and mildew models - New Phytologist

Exploring and exploiting the boundaries of host specificity using the cereal rust and mildew models - New Phytologist | Adaptive Evolution and Speciation | Scoop.it
Individual plants encounter a vast number of microbes including bacteria, viruses, fungi, and oomycetes through their growth cycle, yet few of these pathogens are able to infect them.Plant species have diverged over millions of years, co-evolving with few specific pathogens.The host boundaries of most pathogen species can be clearly defined. In general, the greater the genetic divergence from the preferred host, the less likely that pathogen would be able to infect that plant species. Co-evolution and divergence also occur within pathogen species, leading to highly specialized subspecies with narrow host ranges. For example, cereal rust and mildew pathogens (Puccinia and Blumeria spp.) display high host specificity as a result of ongoing co-evolution with a narrow range of grass species. In rare cases, however, some plant species are in a transition from host to nonhost or are intermediate hosts (near nonhost). Barley was reported as a useful model for genetic and molecular studies of nonhost resistance due to rare susceptibility to numerous heterologous rust and mildew fungi. This review evaluates host specificity in numerous Puccinia/Blumeria–cereal pathosystems and discusses various approaches for transferring nonhost resistance (NHR) genes between crop species to reduce the impact of important diseases in food production
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Via Yogesh Gupta
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Influence of resistance breeding in common bean on rhizosphere microbiome composition and function - ISME

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function - ISME | Adaptive Evolution and Speciation | Scoop.it
The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.
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The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte - Current Biology

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte - Current Biology | Adaptive Evolution and Speciation | Scoop.it
The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, “Setaphyta,” as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes.
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Control fast or control smart: When should invading pathogens be controlled? - PLOS Comp. Biol.

Control fast or control smart: When should invading pathogens be controlled? - PLOS Comp. Biol. | Adaptive Evolution and Speciation | Scoop.it
The intuitive response to an invading pathogen is to start disease management as rapidly as possible, since this would be expected to minimise the future impacts of disease. However, since more spread data become available as an outbreak unfolds, processes underpinning pathogen transmission can almost always be characterised more precisely later in epidemics. This allows the future progression of any outbreak to be forecast more accurately, and so enables control interventions to be targeted more precisely. There is also the chance that the outbreak might die out without any intervention whatsoever, making prophylactic control unnecessary. Optimal decision-making involves continuously balancing these potential benefits of waiting against the possible costs of further spread. We introduce a generic, extensible data-driven algorithm based on parameter estimation and outbreak simulation for making decisions in real-time concerning when and how to control an invading pathogen. The Control Smart Algorithm (CSA) resolves the trade-off between the competing advantages of controlling as soon as possible and controlling later when more information has become available. We show–using a generic mathematical model representing the transmission of a pathogen of agricultural animals or plants through a population of farms or fields–how the CSA allows the timing and level of deployment of vaccination or chemical control to be optimised. In particular, the algorithm outperforms simpler strategies such as intervening when the outbreak size reaches a pre-specified threshold, or controlling when the outbreak has persisted for a threshold length of time. This remains the case even if the simpler methods are fully optimised in advance. Our work highlights the potential benefits of giving careful consideration to the question of when to start disease management during emerging outbreaks, and provides a concrete framework to allow policy-makers to make this decision.
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Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions - bioRxiv

Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions - bioRxiv | Adaptive Evolution and Speciation | Scoop.it

Filamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this "two-speed" genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.


Via Kamoun Lab @ TSL, Francis Martin
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Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome - BMC Biology

Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome - BMC Biology | Adaptive Evolution and Speciation | Scoop.it

Background. Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence.

 

Results. We constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes.

 

Conclusions. The pangenome construction of a highly polymorphic eukaryotic pathogen showed that a single reference genome significantly underestimates the gene space of a species. The substantial accessory genome provides a cradle for adaptive evolution.


Via Kamoun Lab @ TSL
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Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data - Bioinformatics

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data - Bioinformatics | Adaptive Evolution and Speciation | Scoop.it
Motivation: The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data.
Results: Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches.
Availability and implementation: Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/.
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Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution | Adaptive Evolution and Speciation | Scoop.it

Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial. We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation. Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil-based interpretations of angiosperm diversification may be a consequence of false precision on both sides. We reject a post-Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators.

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davidemms/OrthoFinder: Accurate inference of orthologous gene groups made easy. 

davidemms/OrthoFinder: Accurate inference of orthologous gene groups made easy.  | Adaptive Evolution and Speciation | Scoop.it
OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.

Via Jesper Svedberg
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Putative Late Ordovician land plants - New Phytologist

Putative Late Ordovician land plants - New Phytologist | Adaptive Evolution and Speciation | Scoop.it

The colonization of early terrestrial ecosystems by embryophytes (i.e. land plants) irreversibly changed global biogeochemical cycles (Berner & Kothavala, 2001; Berner et al., 2007; Song et al., 2012). However, when and how the process of plant terrestrialization took place is still intensely debated (Kenrick & Crane, 1997; Kenrick et al., 2012; Edwards et al., 2014; Edwards & Kenrick, 2015). Current knowledge suggests that the earliest land plants evolved from charophycean green algae (Karol et al., 2001) most probably during Early-Middle Ordovician times (Rubinstein et al., 2010; and references cited therein). They were represented by small nonvascular bryophyte-like organisms (Edwards & Wellman, 2001; Wellman et al., 2003; Kenrick et al., 2012). The oldest fossil evidence from dispersed spores of presumable bryophytic nature is known from a Middle Ordovician locality (c. 470 million years ago (Ma), Rubinstein et al., 2010; Fig. 1) from Argentina (Gondwana palaeocontinent). The dispersed spore fossil record also suggests that the first radiation of vascular plants probably occurred during Late Ordovician times (c. 450 Ma, Steemans et al., 2009). However, unequivocal macrofossils of vascular plants appear much later, during mid-Silurian (c. 430 Ma, Edwards et al., 1992). This macrofossil evidence comes from the fossil-genus Cooksonia, an early polysporangiophyte (i.e. a plant with bifurcating axes and more than one sporangium), which is considered the earliest vascular land plant (Edwards et al., 1992; Fig. 1). Further advances in knowledge about the origin and early dispersion of polysporangiophytes are needed for a better understanding of the initial plant diversification. Unfortunately, unravelling the initial steps of polysporangiophyte evolution is hindered by gaps in the fossil record of the earliest plants as well as by limitations of inference based on molecular clocks (Kenrick et al., 2012; Edwards & Kenrick, 2015).


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Tracing the role of human civilization in the globalization of plant pathogens - ISME

Tracing the role of human civilization in the globalization of plant pathogens - ISME | Adaptive Evolution and Speciation | Scoop.it
Co-evolution between plants and parasites, including herbivores and pathogens, has arguably generated much of Earth’s biological diversity. Within an ecosystem, co-evolution of plants and pathogens is a stepwise reciprocal evolutionary interaction: epidemics result in intense selection pressures on both host and pathogen populations, ultimately allowing long-term persistence and ecosystem stability. Historically, plants, and pathogens evolved in unique regional assemblages, largely isolated from other assemblages by geographical barriers. When barriers are broken, non-indigenous pathogenic organisms are introduced into new environments, potentially finding suitable hosts lacking resistance genes and environments favouring pathogenic behavior; this process may result in epidemics of newly emerging diseases. Biological invasions are tightly linked to human activities and have been a constant feature throughout human history. Several pathways enable pathogens to enter new environments, the great majority being human mediated.
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Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora - PLOS One

Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora - PLOS One | Adaptive Evolution and Speciation | Scoop.it
Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the “subgeneric” clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.
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Genomic features of bacterial adaptation to plants - Nature Genetics

Genomic features of bacterial adaptation to plants - Nature Genetics | Adaptive Evolution and Speciation | 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.
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The Soil-Borne Legacy - Cell

The Soil-Borne Legacy - Cell | Adaptive Evolution and Speciation | Scoop.it
Plants greatly rely on their root microbiome for uptake of nutrients and protection against stresses. Recent studies have uncovered the involvement of plant stress responses in the assembly of plant-beneficial microbiomes. To facilitate durable crop production, deciphering the driving forces that shape the microbiome is crucial.
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Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae - mBio

Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae - mBio | Adaptive Evolution and Speciation | Scoop.it
IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.

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Phyllosphere microbiology: at the interface between microbial individuals and the plant host - Remus-Emsermann - New Phytologist

Phyllosphere microbiology: at the interface between microbial individuals and the plant host - Remus-Emsermann - New Phytologist | Adaptive Evolution and Speciation | Scoop.it
Leaf surfaces are home to diverse bacterial communities. Within these communities, every individual cell perceives its unique environment and responds accordingly. In this insight article, the perspective of the bacterial individual is assumed in an attempt to describe how the spatially heterogeneous leaf surface determines the fate of bacteria. To investigate behaviour at scales relevant to bacteria, single-cell approaches are essential. Single-cell studies provide important lessons about how current ‘omics’ approaches fail to give an accurate picture of the behaviour of bacterial populations in heterogeneous environments. Upcoming techniques will soon allow us to combine the power of single-cell and omics approaches.
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Genome-Enhanced Detection and Identification (GEDI) of plant pathogens - PeerJ

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens - PeerJ | Adaptive Evolution and Speciation | Scoop.it
Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.

Via Steve Marek
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The role of water in plant–microbe interactions - The Plant Journal

The role of water in plant–microbe interactions - The Plant Journal | Adaptive Evolution and Speciation | Scoop.it
Throughout their life plants are associated with various microorganisms, including commensal, symbiotic and pathogenic microorganisms. Pathogens are genetically adapted to aggressively colonize and proliferate in host plants to cause disease. However, disease outbreaks occur only under permissive environmental conditions. The interplay between host, pathogen and environment is famously known as the ‘disease triangle’. Among the environmental factors, rainfall events, which often create a period of high atmospheric humidity, have repeatedly been shown to promote disease outbreaks in plants, suggesting that the availability of water is crucial for pathogenesis. During pathogen infection, water-soaking spots are frequently observed on infected leaves as an early symptom of disease. Recent studies have shown that pathogenic bacteria dedicate specialized virulence proteins to create an aqueous habitat inside the leaf apoplast under high humidity. Water availability in the apoplastic environment, and probably other associated changes, can determine the success of potentially pathogenic microbes. These new findings reinforce the notion that the fight over water may be a major battleground between plants and pathogens. In this article, we will discuss the role of water availability in host–microbe interactions, with a focus on plant–bacterial interactions.
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Rescooped by Ronny Kellner from Plant Pathogenomics
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A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements - ISME

A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements - ISME | Adaptive Evolution and Speciation | Scoop.it

Fungal pathogens can rapidly evolve virulence towards resistant crops in agricultural ecosystems. Gains in virulence are often mediated by the mutation or deletion of a gene encoding a protein recognized by the plant immune system. However, the loci and the mechanisms of genome evolution enabling rapid virulence evolution are poorly understood. We performed genome-wide association mapping on a global collection of 106 strains of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe, to identify polymorphisms linked to virulence on two wheat varieties. We found 25 distinct genomic loci associated with reproductive success of the pathogen. However, no locus was shared between the host genotypes, suggesting host specialization. The main locus associated with virulence encoded a highly expressed, small secreted protein. Population genomic analyses showed that the gain in virulence was explained by a segregating gene deletion polymorphism. The deletion was likely adaptive by preventing detection of the encoded protein. Comparative genomics of closely related species showed that the locus emerged de novo since speciation. A large cluster of transposable elements in direct proximity to the locus generated extensive rearrangements leading to multiple independent gene losses. Our study demonstrates that rapid turnover in the chromosomal structure of a pathogen can drive host specialization.


Via Kamoun Lab @ TSL
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Rescooped by Ronny Kellner from Host Microbe Interactions
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Soil commensal rhizobia promote Rhizobium etli nodulation efficiency through CinR-mediated quorum sensing

Soil commensal rhizobia promote Rhizobium etli nodulation efficiency through CinR-mediated quorum sensing | Adaptive Evolution and Speciation | Scoop.it
The rhizosphere microbiome is composed of diverse microorganisms directly interacting with plants and each other. We sought to achieve a better understanding of how rhizobia interact with other soil bacteria during the initial symbiosis period. In this study, we investigated how soil commensals, particularly other rhizobia, affect Rhizobium etli–Phaseolus vulgaris interactions. We found that R. etli formed significantly more nodules on beans grown in unsterilized soil than those in sterilized soil. Furthermore, a strain identified as Rhizobium fabae, isolated from unsterilized soil, was found to affect R. etli nodulation. Interestingly, we found that the key quorum sensing regulator CinR is important for R. etli nodulation efficiency when it is co-inoculated with R. fabae. Moreover, we found that quorum sensing signals produced by R. fabae promoted CinR-mediated gene expression in R. etli. These data suggest that the effects of R. fabae on R. etli symbiosis may act through multispecies bacterial cell–cell communication.

Via Ryohei Thomas Nakano
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