Microbes, plant immunity, and crop science
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Trends Ecol. Evol.: Integrating Biogeography with Contemporary Niche Theory (2017)

There is no consensus on when biotic interactions impact the range limits of species. Starting from MacArthur’s use of invasibility to understand how biotic interactions influence coexistence, here we examine how biotic interactions shape species distributions. Range limits emerge from how birth, death, and movement rates vary with the environment. We clarify some basic issues revolving around niche definitions, illustrated with simple resource–consumer theory. We then highlight two different avenues for linking community theory and range theory; the first based on calculating the effects of biotic interactions on range limits across scales and landscape configurations, and the second based on aggregate measures of diffuse interactions and network strength. We conclude with suggestions for a future research agenda.
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Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus

Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus | Microbes, plant immunity, and crop science | Scoop.it
Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales)—the first genomes available for Basidiomycota truffles—and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type A -locus as well as pheromone receptor and pheromone precursor homologs at the mating type B -locus. Comparison of Rhizopogon genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the A -locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the B -locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. Rhizopogon vinicolor possesses a greater number of B -locus pheromone receptor and precursor genes than R. vesiculosus , as well as a pair of isoprenyl cysteine methyltransferase genes flanking the B -locus compared to a single copy in R. vesiculosus . Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in R. vinicolor , consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with R. vinicolor possessing a B -locus region structure consistent with tetrapolar Boletales and R. vesiculosus possessing a B -locus region structure intermediate between bipolar and tetrapolar Boletales.

Via Francis Martin
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Plant Cell: The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies (2017)

Plant Cell: The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies (2017) | Microbes, plant immunity, and crop science | Scoop.it
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), which completes its life cycle in 9 weeks. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.
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Dorian Q Fuller's curator insight, July 14, 6:16 AM
fast moving genomics tools for rice!
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Recontres plantes-bactéries, 29/01-02/02/2018, Aussois

Recontres plantes-bactéries, 29/01-02/02/2018, Aussois | Microbes, plant immunity, and crop science | Scoop.it
- Huit thématiques sont proposées à l’appel à communication : *Structure et fonction du microbiome au sein du phytobiome *Programmes symbiotiques : composantes, contrôle, origine évolutive
*Réponses moléculaires et résistance des plantes
*Evolution, phylogénie et génomique comparative des bactéries *Métabolisme et métabolites des interactions
*Régulation et signalisation
*Gestion de la santé des plantes : diagnostic, biocontrôle et autres méthodes de lutte
*Emergence, épidémiologie, écologie et biologie des populations bactériennes associées aux plantes
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Mining microbes: Creating genomic tools to fight disease

Mining microbes: Creating genomic tools to fight disease | Microbes, plant immunity, and crop science | Scoop.it
In 2015, several patients in the intensive care unit of the Royal Brompton Hospital in London came down with an unexplained illness. Doctors suspected a fungal infection—but those can be difficult to diagnose, and culturing fungi from patient blood samples takes time.
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La Bibliothèque du Vivant : une référence génomique pour les espèces

La Bibliothèque du Vivant : une référence génomique pour les espèces | Microbes, plant immunity, and crop science | Scoop.it
Bibliothèque du Vivant (BdV) est un appel à projets financé par le CNRS, l'INRA et le MNHN de 2011 et 2013 et qui a bénéficié du support technique du Génoscope pour le séquençage massif de l’ADN. BdV avait pour objectif de soutenir et d’accompagner cent équipes françaises portant des projets d’étude de la biodiversité. Il voulait accélérer le séquençage massif de gènes, ou partie de gènes d’organismes pluricellulaires appartenant à différents groupes taxinomiques (plantes, champignons, vertébrés, insectes etc.) pour compléter une bibliothèque de codes-barres ADN de référence pour le vivant et ainsi accéder à phylogénie moléculaires de ces organismes. Des travaux issus de ce programme font l’objet d’un volume spécial "DNA library of life" (2017) publié dans la revue European Journal of Taxonomy.

 

CNRS - Institut écologie et environnement - Actualités de l'institut, 05.05.2017


Via Bernadette Cassel
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DocBiodiv's curator insight, May 17, 10:04 AM
A noter : 4ème Colloque de Génomique Environnementale 13615/09 à Marseille  http://gdr3692.wixsite.com/gdrge/4e-colloque-genomique-environnement
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Is There an Upper Limit to Genome Size?

Is There an Upper Limit to Genome Size? | Microbes, plant immunity, and crop science | Scoop.it

At 50-fold the size of the human genome (3 Gb), the staggeringly huge genome of 147.3 Gb recently discovered in the fern Tmesipteris obliqua is comparable in size to those of the other plant and animal record-holders (i.e., Paris japonica, a flowering plant with a genome size of 148.8 Gb, and Protopterus aethiopicus, a lungfish with a genome of 130 Gb). The synthesis of available information on giant genomes suggests that the biological limit to genome size expansion in eukaryotes may have been reached. We propose several explanations for why the genomes of ferns, flowering plants, and lungfish, all of which have independently undergone dramatic increases in genome size through a variety of mechanisms, do not exceed 150 Gb.


Via Pierre-Marc Delaux
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Curr. Biol.: Phylogenetic comparative methods (2017)

Curr. Biol.: Phylogenetic comparative methods (2017) | Microbes, plant immunity, and crop science | Scoop.it
Phylogenetic comparative methods (PCMs) enable us to study the history of organismal evolution and diversification. PCMs comprise a collection of statistical methods for inferring history from piecemeal information, primarily combining two types of data: first, an estimate of species relatedness, usually based on their genes, and second, contemporary trait values of extant organisms. Some PCMs also incorporate information from geological records, especially fossils, but also other gradual and episodic events in the Earth’s history (for example, trait data from fossils or the global oxygen concentration as an independent variable). It is important to note at the outset that PCMs are not concerned with reconstructing the evolutionary relationships among species; this has to do with estimating the phylogeny from genetic, fossil and other data, and a separate set of methods for this process makes up the field of phylogenetics. PCMs as a set of methods are distinct from, but are not completely independent of, phylogenetics. PCMs are used to address the questions: how did the characteristics of organisms evolve through time and what factors influenced speciation and extinction?
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Plant J.: Advances on plant–pathogen interactions from molecular toward systems biology perspectives (2017)

Plant J.: Advances on plant–pathogen interactions from molecular toward systems biology perspectives (2017) | Microbes, plant immunity, and crop science | Scoop.it
In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant–pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant–pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant–pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future.
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Mol. Plant: Effector–Decoy Pairs: Another Countermeasure Emerging during Host–Microbe Co-evolutionary Arms Races? (2017)

Mol. Plant: Effector–Decoy Pairs: Another Countermeasure Emerging during Host–Microbe Co-evolutionary Arms Races? (2017) | Microbes, plant immunity, and crop science | Scoop.it
Plant pathogenic microbes pose a significant threat to food production, collectively affecting all cultivated crops. Given the impact of these pathogens on food security, there continues to be an urgent need to understand and exploit the biology of pathogenesis, plant susceptibility, and immunity in crop systems. Consequently, intense research efforts have helped define the molecular and evolutionary events that underpin plant-microbe interactions.
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TiPS: RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

TiPS: RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome | Microbes, plant immunity, and crop science | Scoop.it
RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.
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Nat. Commun: Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce (2017)

Nat. Commun: Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce (2017) | Microbes, plant immunity, and crop science | Scoop.it
Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.
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Mol. Ecol. Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution (2017)

Mol. Ecol. Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution (2017) | Microbes, plant immunity, and crop science | Scoop.it
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Plant Cell: Direct and Indirect Visualization of Bacterial Effector Delivery into Diverse Plant Cell Types During Infection (2017)

Plant Cell: Direct and Indirect Visualization of Bacterial Effector Delivery into Diverse Plant Cell Types During Infection (2017) | Microbes, plant immunity, and crop science | Scoop.it
To cause disease, diverse pathogens deliver effector proteins into host cells. Pathogen effectors can inhibit defense responses, alter host physiology, and represent important cellular probes to investigate plant biology. However, effector function and localization have primarily been investigated after overexpression in planta. Visualizing effector delivery during infection is challenging due to the plant cell wall, autofluorescence, and low effector abundance. Here, we utilized a GFP strand system to directly visualize bacterial effectors delivered into plant cells through the Type III secretion system. GFP is a beta barrel that can be divided into 11 strands. We generated transgenic Arabidopsis thaliana plants expressing GFP1-10 (strands 1 to 10). Multiple bacterial effectors tagged with the complementary strand 11 epitope retained their biological function in Arabidopsis and tomato (Solanum lycopersicum). Infection of plants expressing GFP1-10 with bacteria delivering GFP11-tagged effectors enabled direct effector detection in planta. We investigated the temporal and spatial delivery of GFP11-tagged effectors during infection with the foliar pathogen Pseudomonas syringae and the vascular pathogen Ralstonia solanacearum. Thus, the GFP strand system can be broadly used to investigate effector biology in planta.
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Nature Genetics: High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
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Laboratoire d'Innovation Territorial (LIT) Ouest Territoires d'Elevage

LIT Ouest Territoires d’Elevage, L’élevage à vivre ensemble.
Un consortium d’acteurs des 3 régions Bretagne, Normandie et Pays de la Loire, et des filières agricoles et agroalimentaires du Grand Ouest (GO) de la France se sont saisis de cette opportunité pour travailler à la construction du Laboratoire d’Innovation Territorial « Ouest Territoires d’Élevage ». Il comporte: 3 coopératives polyvalentes et multi-espèces animales de l’Ouest : Agrial, Terrena et Triskalia, le pôle de compétitivité Valorial, les 3 Chambres Régionales d’Agriculture de Bretagne, de Normandie et des Pays de la Loire, les 3 instituts techniques agricoles (ITAs) du domaine animal :Ifip pour le porc, Itavi pour la volaille, Idele pour les ruminants, et des acteurs de la recherche et de l’enseignement supérieur agronomique et vétérinaire implantés dans l’Ouest :Inra, Irstea , Agrocampus Ouest, Oniris. Le LIT Ouest Territoires d’Elevage porte sur le développement d’élevages répondant mieux aux attentes des consommateurs, des citoyens et des politiques en matière de conditions d’élevage, plus spécifiquement en matière d’amélioration du bien-être des animaux d’élevage et de moindre recours aux médicaments en élevage.
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NAture: The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution (2017)

NAture: The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution (2017) | Microbes, plant immunity, and crop science | Scoop.it
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.
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Nat. Commun.: Sequencing and de novo assembly of a near complete indica rice genome (2017)

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

We analyzed tissue-specific transcriptomes of Arabidopsis thaliana and identified 66 gene families with a high frequency of “gradient genes” - genes showing a significant expression gradient between tissues. Gradient gene families include many with roles in hormone and peptide signaling, cell wall synthesis and remodeling, secondary metabolism, transcriptional regulation, and transport between cells. We compared the size of the gradient gene families among the genomes of four plant species with radically different body plans – a single-celled algae, a moss, a eudicot, and a monocot – and found that most of the gradient gene families (58/66) expanded in parallel with the evolution of morphological complexity. A novel measure of tissue diversity was used to show that members of any one gradient gene family tend not to be clustered in a single tissue, but are rather apportioned evenly across the tissues studied. Considered together, our results suggest that the diversification of these gene families supported the diversification of tissue types and the evolution of body plan complexity in plants.
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BMC Genomics: Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host rang...

BMC Genomics: Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host rang... | Microbes, plant immunity, and crop science | Scoop.it
Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia, with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.
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Plant Methods: A novel hairpin library-based approach to identify NBS–LRR genes required for effector-triggered hypersensitive response in Nicotiana benthamiana (2017)

Plant Methods: A novel hairpin library-based approach to identify NBS–LRR genes required for effector-triggered hypersensitive response in Nicotiana benthamiana (2017) | Microbes, plant immunity, and crop science | Scoop.it
PTI and ETI are the two major defence mechanisms in plants. ETI is triggered by the detection of pathogen effectors, or their activity, in the plant cell and most of the time involves internal receptors known as resistance (R) genes. An increasing number of R genes responsible for recognition of specific effectors have been characterised over the years; however, methods to identify R genes are often challenging and cannot always be translated to crop plants. We present a novel method to identify R genes responsible for the recognition of specific effectors that trigger a hypersensitive response (HR) in Nicotiana benthamiana. This method is based on the genome-wide identification of most of the potential R genes of N. benthamiana and a systematic silencing of these potential R genes in a simple transient expression assay. A hairpin-RNAi library was constructed covering 345 R gene candidates of N. benthamiana. This library was then validated using several previously described R genes. Our approach indeed confirmed that Prf, NRC2a/b and NRC3 are required for the HR that is mediated in N. benthamiana by Pto/avrPto (prf, NRC2a/b and NRC3) and by Cf4/avr4 (NRC2a/b and NRC3). We also confirmed that NRG1, in association with N, is required for the Tobacco Mosaic Virus (TMV)-mediated HR in N. benthamiana. We present a novel approach combining bioinformatics, multiple-gene silencing and transient expression assay screening to rapidly identify one-to-one relationships between pathogen effectors and host R genes in N. benthamiana. This approach allowed the identification of previously described R genes responsible for detection of avirulence determinants from Pseudomonas, Cladosporium and TMV, demonstrating that the method could be applied to any effectors/proteins originating from a broad range of plant pathogens that trigger an HR in N. benthamiana. Moreover, with the increasing availability of genome sequences from model and crop plants and pathogens, this approach could be implemented in other plants, accelerating the process of identification and characterization of novel resistance genes.
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Mol. Plant.: Emerging Jasmonate Transporters (2017)

Mol. Plant.: Emerging Jasmonate Transporters (2017) | Microbes, plant immunity, and crop science | Scoop.it
Empty descriJasmonic acid (JA) and methyl jasmonate (MeJA) are highly mobile and, when applied to intact plants, these compounds powerfully modulate gene expression. Moreover, activation of jasmonate-responsive genes usually occurs in tissues distal to the treatments. It therefore comes as no surprise that there are jasmonate transporters; these proteins are only now emerging and their discovery is important for a number of reasons. Firstly, biologically active jasmonates such as jasmonoyl-isoleucine (JA-Ile) are potent regulators that are made in small quantities and that need to be delivered to the correct cellular and subcellular sites. Secondly, jasmonates act to redirect resources from growth to defense. For example, when shoots are wounded, jasmonates help to coordinate the appropriate growth of roots so that organ growth rates are balanced even when a distal part of the plant is damaged. Moreover, some plants (Arabidopsis is an example) produce large quantities of the JA-Ile precursor JA upon wounding. JA and/or its immediate precursor can be transported from cell to cell and even from shoot to root (Gasperini et al., 2015; Figure 1A–1C ). The mechanisms underlying this transport need to be identified. However, a difficulty for the jasmonate field is that many studies of JA/JA-Ile transport have used exogenous jasmonates applied at sometimes non-physiological levels to plant tissues. These studies can be difficult to interpret, so the discovery of jasmonate transporter mutants represents a welcome breakthrough. Among these is the newly reported jasmonate transporter (JAT1) from Arabidopsis (Li et al., 2017).ption
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Phytopathol.: Characterization of the Xanthomonas translucens Complex Using Draft Genomes, Comparative Genomics, Phylogenetic Analysis, and Diagnostic LAMP Assays

Prevalence of Xanthomonas translucens, which causes cereal leaf streak (CLS) in cereal crops and bacterial wilt in forage and turfgrass species, has increased in many regions in recent years. Because the pathogen is seedborne in economically important cereals, it is a concern for international and interstate germplasm exchange and, thus, reliable and robust protocols for its detection in seed are needed. However, historical confusion surrounding the taxonomy within the species has complicated the development of accurate and reliable diagnostic tools for X. translucens. Therefore, we sequenced genomes of 15 X. translucens strains representing six different pathovars and compared them with additional publicly available X. translucens genome sequences to obtain a genome-based phylogeny for robust classification of this species. Our results reveal three main clusters: one consisting of pv. cerealis, one consisting of pvs. undulosa and translucens, and a third consisting of pvs. arrhenatheri, graminis, phlei, and poae. Based on genomic differences, diagnostic loop-mediated isothermal amplification (LAMP) primers were developed that clearly distinguish strains that cause disease on cereals, such as pvs. undulosa, translucens, hordei, and secalis, from strains that cause disease on noncereal hosts, such as pvs. arrhenatheri, cerealis, graminis, phlei, and poae. Additional LAMP assays were developed that selectively amplify strains belonging to pvs. cerealis and poae, distinguishing them from other pathovars. These primers will be instrumental in diagnostics when implementing quarantine regulations to limit further geographic spread of X. translucens pathovars.
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MPMI: mlo-Based Resistance: An Apparently Universal “Weapon” to Defeat Powdery Mildew Disease (2017)

MPMI: mlo-Based Resistance: An Apparently Universal “Weapon” to Defeat Powdery Mildew Disease (2017) | Microbes, plant immunity, and crop science | Scoop.it
Loss-of-function mutations of one or more of the appropriate Mildew resistance locus o (Mlo) genes are an apparently reliable “weapon” to protect plants from infection by powdery mildew fungi, as they confer durable broad-spectrum resistance. Originally detected as a natural mutation in an Ethiopian barley landrace, this so-called mlo-based resistance has been successfully employed in European barley agriculture for nearly four decades. More recently, mlo-mediated resistance was discovered to be inducible in virtually every plant species of economic or scientific relevance. By now, mlo resistance has been found (as natural mutants) or generated (by induced mutagenesis, gene silencing, and targeted or nontargeted gene knock-out) in a broad range of monocotyledonous and dicotyledonous plant species. Here, we review features of mlo resistance in barley, discuss approaches to identify the appropriate Mlo gene targets to induce mlo-based resistance, and consider the issue of pleiotropic effects often associated with mlo-mediated immunity, which can harm plant yield and quality. We portray mlo-based resistance as an apparently universal and effective weapon to defeat powdery mildew disease in a multitude of plant species.
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Curr. Biol.: Activation of a Plant NLR Complex through Heteromeric Association with an Autoimmune Risk Variant of Another NLR (2017)

Curr. Biol.: Activation of a Plant NLR Complex through Heteromeric Association with an Autoimmune Risk Variant of Another NLR (2017) | Microbes, plant immunity, and crop science | Scoop.it
When independently evolved immune receptor variants meet in hybrid plants, they can activate immune signaling in the absence of non-self recognition. Such autoimmune risk alleles have recurrently evolved at the DANGEROUS MIX2 (DM2) nucleotide-binding domain and leucine-rich repeat (NLR)-encoding locus in A. thaliana. One of these activates signaling in the presence of a particular variant encoded at another NLR locus, DM1. We show that the risk variants of DM1 and DM2d NLRs signal through the same pathway that is activated when plant NLRs recognize non-self elicitors. This requires the P loops of each protein and Toll/interleukin-1 receptor (TIR)-domain-mediated heteromeric association of DM1 and DM2d. DM1 and DM2d each resides in a multimeric complex in the absence of signaling, with the DM1 complex shifting to higher molecular weight when heteromerizing DM2 variants are present. The activation of the DM1 complex appears to be sensitive to the conformation of the heteromerizing DM2 variant. Autoimmunity triggered by interaction of this NLR pair thus suggests that activity of heteromeric NLR signaling complexes depends on the sum of activation potentials of partner NLRs.
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