Microbes, plant immunity, and crop science
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BMC Genomics: Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels (2012)

BMC Genomics: Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels (2012) | Microbes, plant immunity, and crop science | Scoop.it

Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic X. albilineans strain GPE PC73 focused exclusively on distinctive genomic features shared with Xylella fastidiosa---another xylem-limited Xanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of X. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity. Comparative genomic analyses showed that most of the known pathogenicity factors from other Xanthomonas species are conserved in X. albilineans, with the notable absence of two major determinants of the "artillery" of other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific to X. albilineans that may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, none genes potentially involved in any offensive or counter-defensive mechanism specific to X. albilineans were identified, supposing that X. albilineans has a reduced artillery compared to other pathogenic Xanthomonas species. Particular attention has therefore been given to genomic features specific to X. albilineans making it more capable of evading sugarcane surveillance systems or resisting sugarcane defense systems. This study confirms that X. albilineans is a highly distinctive species within the genus Xanthomonas, and opens new perpectives towards a greater understanding of the pathogenicity of this destructive sugarcane pathogen.

 

Isabelle Pieretti, Monique Royer, Valérie Barbe, Sébastien Carrere, Ralf Koebnik, Arnaud Couloux, Armelle Darrasse, Jérôme Gouzy, Marie-Agnès Jacques, Emmanuelle Lauber, Charles Manceau, Sophie Mangenot, Stéphane Poussier, Béatrice Segurens, Boris Szurek, Valérie Verdier, Matthieu Arlat, Dean W Gabriel, Philippe Rott and Stéphane Cociancich

 

 

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Rescooped by Nicolas Denancé from The Plant Microbiome
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The multilayer nature of ecological networks

The multilayer nature of ecological networks | Microbes, plant immunity, and crop science | Scoop.it

Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems such as networks of networks. The emergent field of ‘multilayer networks’ provides a natural framework for extending analyses of ecological systems to include such multiple layers of complexity, as it specifically allows one to differentiate and model ‘intralayer’ and ‘interlayer’ connectivity. The framework provides a set of concepts and tools that can be adapted and applied to ecology, facilitating research on high-dimensional, heterogeneous systems in nature. Here, we formally define ecological multilayer networks based on a review of previous, related approaches; illustrate their application and potential with analyses of existing data; and discuss limitations, challenges, and future applications. The integration of multilayer network theory into ecology offers largely untapped potential to investigate ecological complexity and provide new theoretical and empirical insights into the architecture and dynamics of ecological systems.


Via Stéphane Hacquard
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Rescooped by Nicolas Denancé from Plant immunity and legume symbiosis
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Plant Immunity Inducer Development and Application | Molecular Plant-Microbe Interactions

Plant Immunity Inducer Development and Application | Molecular Plant-Microbe Interactions | Microbes, plant immunity, and crop science | Scoop.it
Plant immunity inducers represent a new and rapidly developing field in plant protection research. In this paper, we discuss recent research on plant immunity inducers and their development and applications in China. Plant immunity inducers include plant immunity-inducing proteins, chitosan oligosaccharides, and microbial inducers. These compounds and microorganisms can trigger defense responses and confer disease resistance in plants. We also describe the mechanisms of plant immunity inducers and how they promote plant health. Furthermore, we summarize the current situation in plant immunity inducer development in China and the global marketplace. Finally, we also deeply analyze the development trends and application prospects of plant immunity inducers in environmental protection and food safety.

Via Christophe Jacquet
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Rescooped by Nicolas Denancé from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Genomic history of the origin and domestication of common bean unveils its closest sister species

Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

Via Pierre Gladieux
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Front. Plant Sci.: Effector Mimics and Integrated Decoys, the Never-Ending Arms Race between Rice and Xanthomonas oryzae (2017)

Front. Plant Sci.: Effector Mimics and Integrated Decoys, the Never-Ending Arms Race between Rice and Xanthomonas oryzae (2017) | Microbes, plant immunity, and crop science | Scoop.it
Plants are constantly challenged by a wide range of pathogens and have therefore evolved an array of mechanisms to defend against them. In response to these defense systems, pathogens have evolved strategies to avoid recognition and suppress plant defenses (Brown & Tellier 2011). Three recent reports dealing with the resistance of rice to Xanthomonas oryzae have added a new twist to our understanding of this fascinating co-evolutionary arms race (Ji et al. 2016; Read et al. 2016 and Triplett et al. 2016). They show that pathogens also develop sophisticated effector mimics to trick recognition.
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Rescooped by Nicolas Denancé from Forêt, Bois, Milieux naturels : politique, législation et réglementation
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L’ONF fait le plein de projets avec l’IGN, l’INRA et AgroParisTech

L’ONF fait le plein de projets avec l’IGN, l’INRA et AgroParisTech | Microbes, plant immunity, and crop science | Scoop.it
Télédétection, portail Web, cartographie, renouvellement des peuplements forestiers, sont au programme de partenariats impliquant plusieurs acteurs publics.

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Rescooped by Nicolas Denancé from Emerging Research in Plant Cell Biology
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New phytol.: Diverse mechanisms of resistance to Pseudomonas syringae in a thousand natural accessions of Arabidopsis thaliana (2017)

New phytol.: Diverse mechanisms of resistance to Pseudomonas syringae in a thousand natural accessions of Arabidopsis thaliana (2017) | Microbes, plant immunity, and crop science | Scoop.it

Plants are continuously threatened by pathogen attack and, as such, they have evolved mechanisms to evade, escape and defend themselves against pathogens. However, it is not known what types of defense mechanisms a plant would already possess to defend against a potential pathogen that has not co-evolved with the plant. We addressed this important question in a comprehensive manner by studying the responses of 1041 accessions of Arabidopsis thaliana to the foliar pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. We characterized the interaction using a variety of established methods, including different inoculation techniques, bacterial mutant strains, and assays for the hypersensitive response, salicylic acid (SA) accumulation and reactive oxygen species production . Fourteen accessions showed resistance to infection by Pst DC3000. Of these, two accessions had a surface-based mechanism of resistance, six showed a hypersensitive-like response while three had elevated SA levels. Interestingly, A. thaliana was discovered to have a recognition system for the effector AvrPto, and HopAM1 was found to modulate Pst DC3000 resistance in two accessions. Our comprehensive study has significant implications for the understanding of natural disease resistance mechanisms at the species level and for the ecology and evolution of plant–pathogen interactions.


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Rescooped by Nicolas Denancé from Emerging Research in Plant Cell Biology
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Plant physiol.: Hierarchically aligning 10 legume genomes establishes a family-level genomics platform (2017)

Plant physiol.: Hierarchically aligning 10 legume genomes establishes a family-level genomics platform (2017) | Microbes, plant immunity, and crop science | Scoop.it
Mainly due to their economic importance, genomes of 10 legumes, including soybean, wild peanuts, barrel medic, etc, have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by wide-spread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported a likely autopolypoidy nature of its tetraploid ancestor. Moreover, though mostly gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes, and by performing Ks correction, re-dated major evolutionary events during their expansion. The present effort laid a solid foundation further genomics exploration in the legume research community and beyond. We described only a tiny fraction of legume comparative genomics analysis that we performed, and more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org).

Via Jennifer Mach
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Front. Plant Sci.: Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii (2017)

Front. Plant Sci.: Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii (2017) | Microbes, plant immunity, and crop science | Scoop.it
Bacterial wilt of potatoes—also called brown rot—is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.
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Rescooped by Nicolas Denancé from Plant and Seed Biology
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Genomic innovation for crop improvement : Nature : Nature Research

Genomic innovation for crop improvement : Nature : Nature Research | Microbes, plant immunity, and crop science | Scoop.it
Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genomes and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access the large and complex genomes of crops and their wild relatives. These have helped to identify a wide spectrum of genetic variation and permitted the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems.

Via Loïc Lepiniec
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Rescooped by Nicolas Denancé from Plants & Evolution
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Reconstructing the genome of the most recent common ancestor of flowering plants

We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of 22,899 ancestral genes conserved in present-day crops. The MRCA provides a starting point for deciphering the reticulated evolutionary plasticity between species (rapidly versus slowly evolving lineages), subgenomes (pre- versus post-duplication blocks), genomic compartments (stable versus labile loci), genes (ancestral versus species-specific genes) and functions (gained versus lost ontologies), the key mutational forces driving the success of polyploidy in crops. The estimation of the timing of angiosperm evolution, based on MRCA genes, suggested that this group emerged 214 million years ago during the late Triassic era, before the oldest recorded fossil. Finally, the MRCA constitutes a unique resource for scientists to dissect major agronomic traits in translational genomics studies extending from model species to crops.

Via Pierre-Marc Delaux
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Rescooped by Nicolas Denancé from Innovation Agro-activités et Bio-industries
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INRA - Dossier : les mondes microbiens

INRA - Dossier : les mondes microbiens | Microbes, plant immunity, and crop science | Scoop.it

Dossier : "Les mondes microbiens"


Via AgroParisTech DOC IST
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eLife: Codon optimization underpins generalist parasitism in fungi (2017)

eLife: Codon optimization underpins generalist parasitism in fungi (2017) | Microbes, plant immunity, and crop science | Scoop.it
The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.
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Mol. Mic.: The Processive Kinetics of Gene Conversion in Bacteria (2017)

Mol. Mic.: The Processive Kinetics of Gene Conversion in Bacteria (2017) | Microbes, plant immunity, and crop science | Scoop.it
Gene conversion, non-reciprocal transfer from one homologous sequence to another, is a major force in evolutionary dynamics, promoting co-evolution in gene families, and maintaining similarities between repeated genes. However, the properties of the transfer – where it initiates, how far it proceeds, and how the resulting conversion tracts are affected by mismatch repair – are not well understood. Here we use the duplicate tuf genes in Salmonella as a quantitatively tractable model system for gene conversion. We selected for conversion in multiple different positions of tuf, and examined the resulting distributions of conversion tracts in mismatch repair-deficient and mismatch repair-proficient strains. A simple stochastic model accounting for the essential steps of conversion showed excellent agreement with the data for all selection points using the same value of the conversion processivity, which is the only kinetic parameter of the model. The analysis suggests that gene conversion effectively initiates uniformly at any position within a tuf gene, and proceeds with an effectively uniform conversion processivity in either direction limited by the bounds of the gene.
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Rescooped by Nicolas Denancé from Systems Biology of Plants & Microbes Interactions
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The plant perceptron connects
environment to development | Nature

The plant perceptron connects <br/>environment to development | Nature | Microbes, plant immunity, and crop science | Scoop.it
"Plants cope with the environment in a variety of ways, and ecological analyses attempt to capture this through life-history strategies or trait-based categorization. These approaches are limited because they treat the trade-off mechanisms that underlie plant responses as a black box. Approaches that involve the molecular or physiological analysis of plant responses to the environment have elucidated intricate connections between developmental and environmental signals, but in only a few well-studied model species. By considering diversity in the plant response to the environment as the adaptation of an information-processing network, new directions can be found for the study of life-history strategies, trade-offs and evolution in plants."

Via Peyraud Rémi
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Rescooped by Nicolas Denancé from Plant Biology Teaching Resources (Higher Education)
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CRISPR, microbes and more are joining the war against crop killers

CRISPR, microbes and more are joining the war against crop killers | Microbes, plant immunity, and crop science | Scoop.it
Agricultural scientists look beyond synthetic chemistry to battle pesticide resistance.

Via Mary Williams
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Rescooped by Nicolas Denancé from ECOLOGIE BIODIVERSITE PAYSAGE
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Oser le génie végétal en rivière de montagne – Retour d'expérience sur les ouvrages Géni'Alp | Sciences Eaux & Territoires, la revue d'Irstea

Oser le génie végétal en rivière de montagne – Retour d'expérience sur les ouvrages Géni'Alp  | Sciences Eaux & Territoires, la revue d'Irstea | Microbes, plant immunity, and crop science | Scoop.it
Encore peu utilisées sur les cours d'eau dynamiques comme les rivières de montagne, les techniques de génie végétal représentent pourtant une solution écologique et économique pour la protection des berges. En s'appuyant sur le retour d'expérience de plusieurs chantiers pilotes en France et en Suisse, cet article s'intéresse à la capacité des techniques de génie végétal à résister sur des rivières de montagne associant contraintes climatiques, végétation et hydrologie particulière avec d'importantes contraintes physiques liées à l'eau et au transport solide.
Auteurs :  EVETTE, André ; FROSSARD, Pierre-André ; VALÉ, Nicolas ; LEBLOIS, Solange ; RECKING, Alain
Crédit photo : L'ouvrage de génie végétal Géni'Alp sur le Bens à Saint-Hugon : pendant les travaux. © A. Matringe

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Rescooped by Nicolas Denancé from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks

Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks | Microbes, plant immunity, and crop science | Scoop.it
Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.

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GMR: Mapping and validation of Xanthomonas citri subsp citri genes regulated by putative plant-inducible promoter box (PIP-box) (2016)

Citrus canker, caused by the Gram-negative bacterium Xanthomonas citri subsp citri (Xac), is a major disease affecting citriculture worldwide, because of the susceptibility of the host and the lack of efficient control methods. Previous studies have reported that some genes of phytopathogenic bacteria possess a consensus nucleotide sequence (TTCGC...N15...TTCGC) designated the “plant-inducible-promoter box” (PIP box) located in the promoter region, which is responsible for activating the expression of pathogenicity and virulence factors when the pathogen is in contact with the host plant. In this study, we mapped and investigated the expression of 104 Xac genes associated with the PIP box sequences using a macroarray analysis. Xac gene expression was observed during in vitro (Xac grown for 12 or 20 h in XAM1 induction medium) or in vivo (bacteria grown in orange leaves for 3 to 5 days) infection conditions. Xac grown in non-induction NB liquid medium was used as the control. cDNA was isolated from bacteria grown under the different conditions and hybridized to the macroarray, and 32 genes differentially expressed during the infection period (in vitro or in vivo induction) were identified. The macroarray results were validated for some of the genes through semi-quantitative RT-PCR, and the functionality of the PIP box-containing promoter was demonstrated by activating b-glucuronidase reporter gene activity by the PIP box-containing promoter region during Xac-citrus host interaction. Citrus canker, caused by the Gram-negative bacterium Xanthomonas citri subsp citri (Xac), is a major disease affecting citriculture worldwide, because of the susceptibility of the host and the lack of efficient control methods. Previous studies have reported that some genes of phytopathogenic bacteria possess a consensus nucleotide sequence (TTCGC...N15...TTCGC) designated the “plant-inducible-promoter box” (PIP box) located in the promoter region, which is responsible for activating the expression of pathogenicity and virulence factors when the pathogen is in contact with the host plant. In this study, we mapped and investigated the expression of 104 Xac genes associated with the PIP box sequences using a macroarray analysis. Xac gene expression was observed during in vitro (Xac grown for 12 or 20 h in XAM1 induction medium) or in vivo (bacteria grown in orange leaves for 3 to 5 days) infection conditions. Xac grown in non-induction NB liquid medium was used as the control. cDNA was isolated from bacteria grown under the different conditions and hybridized to the macroarray, and 32 genes differentially expressed during the infection period (in vitro or in vivo induction) were identified. The macroarray results were validated for some of the genes through semi-quantitative RT-PCR, and the functionality of the PIP box-containing promoter was demonstrated by activating b-glucuronidase reporter gene activity by the PIP box-containing promoter region during Xac-citrus host interaction.
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Plant signalling in symbiosis and immunity 

Plant signalling in symbiosis and immunity  | Microbes, plant immunity, and crop science | Scoop.it
Plants encounter a myriad of microorganisms, particularly at the root–soil interface, that can invade with detrimental or beneficial outcomes. Prevalent beneficial associations between plants and microorganisms include those that promote plant growth by facilitating the acquisition of limiting nutrients such as nitrogen and phosphorus. But while promoting such symbiotic relationships, plants must restrict the formation of pathogenic associations. Achieving this balance requires the perception of potential invading microorganisms through the signals that they produce, followed by the activation of either symbiotic responses that promote microbial colonization or immune responses that limit it.


Via Jean-Michel Ané
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Very good review

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Very good review

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Rescooped by Nicolas Denancé from TAL effector science
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Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations

Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations | Microbes, plant immunity, and crop science | Scoop.it

Streubel et al, 2017

Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators.


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Nat. Commun.: Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration (2017)

Nat. Commun.: Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration (2017) | Microbes, plant immunity, and crop science | Scoop.it
Maize is the highest yielding cereal crop grown worldwide. Here Sunet al. show that maize growth can be further enhanced by prolonging the duration of leaf elongation by targeted ectopic expression of the PLASTOCHRON1gene and show that this leads to increased yield in field trials.
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Expanded type III effector recognition by the ZAR1 NLR protein using ZED1-related kinases

Expanded type III effector recognition by the ZAR1 NLR protein using ZED1-related kinases | Microbes, plant immunity, and crop science | Scoop.it
Nucleotide-binding domain and leucine-rich repeat domain-containing (NLR) proteins are sentinels of plant immunity that monitor host proteins for perturbations induced by pathogenic effector proteins. Here we show that the Arabidopsis ZAR1 NLR protein requires the ZRK3 kinase to recognize the Pseudomonas syringae type III effector (T3E) HopF2a. These results support the hypothesis that ZAR1 associates with an expanded ZRK protein family to broaden its effector recognition spectrum.

Via Christophe Jacquet
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TiPS: Accelerating the Domestication of New Crops: Feasibility and Approaches (2017)

TiPS: Accelerating the Domestication of New Crops: Feasibility and Approaches (2017) | Microbes, plant immunity, and crop science | Scoop.it
The domestication of new crops would promote agricultural diversity and could provide a solution to many of the problems associated with intensive agriculture. We suggest here that genome editing can be used as a new tool by breeders to accelerate the domestication of semi-domesticated or even wild plants, building a more varied foundation for the sustainable provision of food and fodder in the future. We examine the feasibility of such plants from biological, social, ethical, economic, and legal perspectives.

A second wave of the green revolution is underway that focuses on environmental sustainability, low input, and increased nutritional value. Of the more than 300 000 plant species that exist, less than 200 are commercially important, and three species – rice, wheat, and maize – account for the major part of the plant-derived nutrients that humans consume. Plants with desirable traits, such as perennials with extensive root systems and nitrogen-fixing plants, are currently being domesticated as new crops. Recent years have given rise to the use of CRISPR/Cas9 for genome editing in plants. The method allows mutations to be generated at precise locations in genes that can lead to knockout or knockdown of protein activity. Several traits in crops that were crucial for their domestication are caused by mutations that can be reproduced by genome-editing techniques such as CRISPR/Cas9, offering the potential for accelerated domestication of new crops.
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Rescooped by Nicolas Denancé from Plant pathogens and pests
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Profiling the extended phenotype of plant pathogens

Profiling the extended phenotype of plant pathogens | Microbes, plant immunity, and crop science | Scoop.it
One of the most fundamental questions in plant pathology is what determines whether a pathogen grows within a plant? This question is frequently studied in terms of the role of elicitors and pathogenicity factors in the triggering or overcoming of host defences. However, this focus fails to address the basic question of how the environment in host tissues acts to support or restrict pathogen growth. Efforts to understand this aspect of host–pathogen interactions are commonly confounded by several issues, including the complexity of the plant environment, the artificial nature of many experimental infection systems and the fact that the physiological properties of a pathogen growing in association with a plant can be very different from the properties of the pathogen in culture. It is also important to recognize that the phenotype and evolution of pathogen and host are inextricably linked through their interactions, such that the environment experienced by a pathogen within a host, and its phenotype within the host, is a product of both its interaction with its host and its evolutionary history, including its co-evolution with host plants. As the phenotypic properties of a pathogen within a host cannot be defined in isolation from the host, it may be appropriate to think of pathogens as having an ‘extended phenotype’ that is the product of their genotype, host interactions and population structure within the host environment. This article reflects on the challenge of defining and studying this extended phenotype, in relation to the questions posed below, and considers how knowledge of the phenotype of pathogens in the host environment could be used to improve disease control.

What determines whether a pathogen grows within a plant?

What aspects of pathogen biology should be considered in describing the extended phenotype of a pathogen within a host?

How can we study the extended phenotype in ways that provide insights into the phenotypic properties of pathogens during natural infections?

Via Christophe Jacquet
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Cell host Microbes: MAP Kinase Signaling Pathways: A Hub of Plant-Microbe Interactions (2017)

Cell host Microbes: MAP Kinase Signaling Pathways: A Hub of Plant-Microbe Interactions (2017) | Microbes, plant immunity, and crop science | Scoop.it
In 2007, we reported that a phytopathogen effector directly inhibits a MAP kinase cascade. In the decade since, many more effectors have been found to inhibit MAP kinase cascades, providing not only a mechanistic understanding of pathogenesis and immunity in plants, but also the identification of previously unknown enzymes.
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