Emerging Research in Plant Cell Biology
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Rescooped by Jennifer Mach from Plant Biology Teaching Resources (Higher Education)
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Arctic Apples Developer Neal Carter's TEDx talk "Biotech and the hungry planet"

Arctic Apples Developer Neal Carter's TEDx talk "Biotech and the hungry planet" | Emerging Research in Plant Cell Biology | Scoop.it

Useful 12 min overview of the benefits of ag biotech. Here's how he describes the talk,

 

"I am convinced of the benefits biotechnology provides our global population, including saving lives. I have a unique perspective from working around the world as a bioresource engineer for nearly three decades, in addition to my experience as an orchardist and as the founder of Okanagan Specialty Fruits. My presentation covers the history and future of biotech crops, why they’re still controversial and the importance of public education in furthering the discussion"


Via Mary Williams
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Marybeth Shea's curator insight, December 17, 2012 8:28 AM

Genetic biodiversity:  a kind of insurance for us all, if preserved and studied.

Emerging Research in Plant Cell Biology
A science editor's take on what's new and interesting in the plant kingdom.
Curated by Jennifer Mach
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Effects of Bt cabbage pollen on the honeybee Apis mellifera L

Effects of Bt cabbage pollen on the honeybee Apis mellifera L | Emerging Research in Plant Cell Biology | Scoop.it

Honeybees may be exposed to insecticidal proteins from transgenic plants via pollen during their foraging activity. Assessing effects of such exposures on honeybees is an essential part of the risk assessment process for transgenic Bacillus thuringiensis (Bt) cabbage. Feeding trials were conducted in a laboratory setting to test for possible effects of Cry1Ba3 cabbage pollen on Italian-derived honeybees Apis mellifera L. Newly emerged A. mellifera were fed transgenic pollen, activated Cry1Ba3 toxin, pure sugar syrup (60% w/v sucrose solution), and non-transgenic cabbage pollen, respectively. Then the effects on survival, pollen consumption, weight, detoxification enzyme activity and midgut enzyme activity of A. mellifera were monitored. The results showed that there were no significant differences in survival, pollen consumption, weight, detoxification enzyme activity among all treatments. No significant differences in the activities of total proteolytic enzyme, active alkaline trypsin-like enzyme and weak alkaline trypsin-like enzyme were observed among all treatments. These results indicate that the side-effects of the Cry1Ba3 cabbage pollen on A. mellifera L. are unlikely.

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Rescooped by Jennifer Mach from How microbes emerge
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The quest for durable resistance

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

Via Pierre Gladieux, Niklaus Grunwald
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Rescooped by Jennifer Mach from Plant pathogens and pests
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Nature's genetic screens: using genome‐wide association studies for effector discovery

Nature's genetic screens: using genome‐wide association studies for effector discovery | Emerging Research in Plant Cell Biology | Scoop.it
Understanding the biology of infections requires knowledge about the intricate molecular dialogue between plants and pathogens. Some components of this molecular dialogue are well-conserved across taxa and the interacting molecules can often be inferred by homology. Yet in all specialized plant-pathogen interactions, a substantial portion of the molecular dialogue is based on proteins that are unique to the pathosystem (e.g. most effector proteins). Identifying these proteins is very challenging because the pathogen often gained the genes encoding these proteins in the recent past and the proteins often share only minor similarities among pathogens. Yet the speed of pathogen evolution can be exploited to identify these crucial components of the molecular dialogue. Pathogen populations often harbor both virulent and avirulent strains, because the adaptation to exploit a new host genotype is not yet fixed within the species. Hence, genomic analyses can point to the genetic differences between the evolved (i.e. virulent) and the ancestral (i.e. avirulent) genotypes. The complication is though that most genetic differences between such groups of strains are unrelated to the actual gain in virulence. A technique that was recently invented to identify the mutations responsible for human genetic diseases provides a solution to this dilemma.

Via Christophe Jacquet
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Rescooped by Jennifer Mach from Host-Microbe Interactions. Plant Biology.
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A role for small RNA in regulating innate immunity during plant growth

A role for small RNA in regulating innate immunity during plant growth | Emerging Research in Plant Cell Biology | Scoop.it
Author summary In plants, nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLR) mediate pathogen-specific effector triggered immunity and are widely used in breeding to generate pathogen-resistant crops. However, dysregulation of NLR expression can inhibit plant growth and how NLR expression and function are regulated in different stages of plant growth is poorly understood. Using a high-throughput sequencing and bioinformatics approach, we found an overall increase in NLR expression, but expression of NLR-targeting sRNA during plant growth was decreased. We also used resistance to tobacco mosaic virus (TMV) mediated by the resistance gene N as a model system to study the biological significance of growth regulation of NLR by miRNAs. We found that N-mediated TMV immunity strengthened and N transcript levels increased during plant maturation. Using genetic analysis, we showed that up-regulation of N was due to transcriptional down-regulation of the N-targeting miR6019/6020 cluster during plant growth. We also showed that sRNA-mediated growth regulation of N expression and function was conserved between tobacco and tomato plants. This study therefore reveals a role for miRNAs in regulating innate immunity during plant growth.

Via Yogesh Gupta, Tatsuya Nobori
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Rescooped by Jennifer Mach from Host-Microbe Interactions. Plant Biology.
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Stochastic gene expression in Arabidopsis thaliana

Stochastic gene expression in Arabidopsis thaliana | Emerging Research in Plant Cell Biology | Scoop.it
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Via Tatsuya Nobori
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Rescooped by Jennifer Mach from Plant pathogenic fungi
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nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing

nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing | Emerging Research in Plant Cell Biology | Scoop.it
Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model. nQuire handles large genomes at high coverage efficiently and uses standard input file formats. We demonstrate the utility of nQuire analyzing individual samples of the pathogenic oomycete Phytophthora infestans and the Baker's yeast Saccharomyces cerevisiae. Using these organisms we show the dependence between reliability of the ploidy assignment and sequencing depth. Additionally, we employ normalized maximized log-likelihoods generated by nQuire to ascertain ploidy level in a population of samples with ploidy heterogeneity. Using these normalized values we cluster samples in three dimensions using multivariate Gaussian mixtures. The cluster assignments retrieved from a S. cerevisiae population recovered the true ploidy level in over 96% of samples. Finally, we show that nQuire can be used regionally to identify chromosomal aneuploidies. nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at github.com/clwgg/nQuire under the MIT license.

Via IPM Lab, Steve Marek
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Rescooped by Jennifer Mach from Plant immunity and legume symbiosis
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Balancing Immunity and Yield in Crop Plants - ScienceDirect

Balancing Immunity and Yield in Crop Plants - ScienceDirect | Emerging Research in Plant Cell Biology | Scoop.it
Crop diseases cause enormous yield losses and threaten global food[ED1] security. The use of highly resistant cultivars can effectively control plant diseases, but in crops, genetic immunity to disease often comes with an unintended reduction in growth and yield. Here, we review recent advances in understanding how nucleotide-binding domain, leucine-rich repeat (NLR) receptors and cell wall-associated kinase (WAK) proteins function in balancing immunity and yield. We also discuss the role of plant hormones and transcription factors in regulating the trade-offs between plant growth and immunity. Finally, we describe how a novel mechanism of translational control of defense proteins can enhance immunity without the reduction in fitness.

Via Christophe Jacquet
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Rescooped by Jennifer Mach from Microbiome and plant immunity
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A plant effector‐triggered immunity signaling sector is inhibited by pattern‐triggered immunity

A plant effector‐triggered immunity signaling sector is inhibited by pattern‐triggered immunity | Emerging Research in Plant Cell Biology | Scoop.it
Since signaling machineries for two modes of plant‐induced immunity, pattern‐triggered immunity (PTI) and effector‐triggered immunity (ETI), extensively overlap, PTI and ETI signaling likely interact. In an Arabidopsis quadruple mutant, in which four major sectors of the signaling network, jasmonate, ethylene, PAD4, and salicylate, are disabled, the hypersensitive response (HR) typical of ETI is abolished when the Pseudomonas syringae effector AvrRpt2 is bacterially delivered but is intact when AvrRpt2 is directly expressed in planta. These observations led us to discovery of a network‐buffered signaling mechanism that mediates HR signaling and is strongly inhibited by PTI signaling. We named this mechanism the ETI‐Mediating and PTI‐Inhibited Sector (EMPIS). The signaling kinetics of EMPIS explain apparently different plant genetic requirements for ETI triggered by different effectors without postulating different signaling machineries. The properties of EMPIS suggest that information about efficacy of the early immune response is fed back to the immune signaling network, modulating its activity and limiting the fitness cost of unnecessary immune responses.

Via Christophe Jacquet, Yogesh Gupta, Steve Marek, Giannis Stringlis
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Rescooped by Jennifer Mach from Microbes, plant immunity, and crop science
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New Phytol.: Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases

New Phytol.: Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases | Emerging Research in Plant Cell Biology | Scoop.it
Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security. Rapid gene isolation enables their efficient deployment through marker-assisted selection and transgenic technology. Together with innovations in genome editing and progress in pathogen virulence studies, this creates further opportunities to engineer long-lasting resistance. These approaches will speed progress towards a future of farming using fewer pesticides.

Via Nicolas Denancé
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Rescooped by Jennifer Mach from Plants & Evolution
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The effect of artificial selection on phenotypic plasticity in maize

The effect of artificial selection on phenotypic plasticity in maize | Emerging Research in Plant Cell Biology | Scoop.it

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0–5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements.


Via Pierre-Marc Delaux
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Rescooped by Jennifer Mach from Plant pathogenic fungi
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Autophagy as a mediator of life and death in plants

Autophagy as a mediator of life and death in plants | Emerging Research in Plant Cell Biology | Scoop.it
Autophagy is a major pathway for degradation and recycling of cytoplasmic material, including individual proteins, aggregates, and entire organelles. Autophagic processes serve mainly survival functions in cellular homeostasis, stress adaptation and immune responses but can also have death-promoting activities in different eukaryotic organisms. In plants, the role of autophagy in the regulation of programmed cell death (PCD) remained elusive and a subject of debate. More recent evidence, however, has resulted in the consensus that autophagy can either promote or restrict different forms of PCD. Here, we present latest advances in understanding the molecular mechanisms and functions of plant autophagy and discuss their implications for life and death decisions in the context of developmental and pathogen-induced PCD.

Via Suayib Üstün, Steve Marek
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Rescooped by Jennifer Mach from Plant-Microbe Symbiosis
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Lotus japonicus alters in planta fitness of Mesorhizobium loti dependent on symbiotic nitrogen fixation

Lotus japonicus alters in planta fitness of Mesorhizobium loti dependent on symbiotic nitrogen fixation | Emerging Research in Plant Cell Biology | Scoop.it
Rhizobial bacteria are known for their capacity to fix nitrogen for legume hosts. However ineffective rhizobial genotypes exist and can trigger the formation of nodules but fix little if any nitrogen for hosts. Legumes must employ mechanisms to minimize exploitation by the ineffective rhizobial genotypes to limit fitness costs and stabilize the symbiosis. Here we address two key questions about these host mechanisms. What stages of the interaction are controlled by the host, and can hosts detect subtle differences in nitrogen fixation? We provide the first explicit evidence for adaptive host control in the interaction between Lotus japonicus and Mesorhizobium loti. In both single inoculation and co-inoculation experiments, less effective rhizobial strains exhibited reduced in planta fitness relative to the wildtype M. loti. We uncovered evidence of host control during nodule formation and during post-infection proliferation of symbionts within nodules. We found a linear relationship between rhizobial fitness and symbiotic effectiveness. Our results suggest that L. japonicus can adaptively modulate the fitness of symbionts as a continuous response to symbiotic nitrogen fixation.


Via Jean-Michel Ané
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Plant microRNAs in larval food regulate honeybee caste development

Plant microRNAs in larval food regulate honeybee caste development | Emerging Research in Plant Cell Biology | Scoop.it

How caste has formed in honeybees is an enduring puzzle. The prevailing view is that royal jelly stimulates the differentiation of larvae into queen. Here, we uncover a new mechanism that plant miRNAs in worker bee’s food postpone larval development, thereby inducing sterile worker bees. Thus, the theories about honeybee caste formation need to be re-examined from a new angle besides the traditional focus on royal jelly and its components. Furthermore, since miRNAs are transmitted between species of different kingdoms and can contribute to the phenotype regulation, this new model of horizontal miRNA transfer may open up a new avenue to further study the molecular mechanisms underlying cross-kingdom interaction and co-evolution.

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Rescooped by Jennifer Mach from Plants & Evolution
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An extracellular network of Arabidopsis leucine-rich repeat receptor kinases

The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation1,2. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability3,4. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions5. The largest of these families in Arabidopsis thaliana consists of 225 evolutionarily related leucine-rich repeat receptor kinases (LRR-RKs)5, which function in the sensing of microorganisms, cell expansion, stomata development and stem-cell maintenance6,7,8,9. Although the principles that govern LRR-RK signalling activation are emerging1,10, the systems-level organization of this family of proteins is unknown. Here, to address this, we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay3, and produced an LRR-based cell surface interaction network (CSILRR) that consists of 567 interactions. To demonstrate the power of CSILRR for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity. In addition, we show that CSILRR operates as a unified regulatory network in which the LRR-RKs most crucial for its overall structure are required to prevent the aberrant signalling of receptors that are several network-steps away. Thus, plants have evolved LRR-RK networks to process extracellular signals into carefully balanced responses.


Via Pierre-Marc Delaux
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Extracellular ATP Acts on Jasmonate Signaling to Reinforce Plant Defense

Extracellular ATP Acts on Jasmonate Signaling to Reinforce Plant Defense | Emerging Research in Plant Cell Biology | Scoop.it
Damaged cells send various signals to stimulate defense responses. Recent identification and genetic studies of the plant purinoceptor, P2K1 (also known as DORN1), have demonstrated that extracellular ATP is a signal involved in plant stress responses, including wounding, perhaps to evoke plant defense. However, it remains largely unknown how extracellular ATP induces plant defense responses. Here, we demonstrate that extracellular ATP induces plant defense mediated through activation of the intracellular signaling of jasmonate (JA), a well-characterized defense hormone. In Arabidopsis ( Arabidopsis thaliana ) leaves, ATP pretreatment induced resistance against the necrotrophic fungus, Botrytis cinerea . The induced resistance was enhanced in the P2K1 receptor overexpression line, but reduced in the receptor mutant, dorn1 - 3 . Mining the transcriptome data revealed that ATP induces a set of JA-induced genes. In addition, the P2K1-associated coexpression network contains defense-related genes, including those encoding jasmonate ZIM-domain (JAZ) proteins, which play key roles as repressors of JA signaling. We examined whether extracellular ATP impacts the stability of JAZ1 in Arabidopsis. The results showed that the JAZ1 stability decreased in response to ATP addition in a proteasome-dependent manner. This reduction required intracellular signaling via second messengers—cytosolic calcium, reactive oxygen species, and nitric oxide. Interestingly, the ATP-induced JAZ1 degradation was attenuated in the JA receptor mutant, coi1 , but not in the JA biosynthesis mutant, aos , or upon addition of JA biosynthesis inhibitors. Immunoprecipitation analysis demonstrated that ATP increases the interaction between COI1 and JAZ1, suggesting direct cross talk between extracellular ATP and JA in intracellular signaling events. Taken together, these results suggest that extracellular ATP signaling directly impacts the JA signaling pathway to maximize plant defense responses.

Via Tatsuya Nobori
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Julio Retamales's curator insight, January 11, 8:05 AM
Novel interactions between ATP and JA signaling
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Speed breeding is a powerful tool to accelerate crop research and breeding

Speed breeding is a powerful tool to accelerate crop research and breeding | Emerging Research in Plant Cell Biology | Scoop.it

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand1. This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called ‘speed breeding’, which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2–3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement.

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Rescooped by Jennifer Mach from microbial pathogenesis and plant immunity
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Extracellular ATP elicits DORN1-mediated RBOHD phosphorylation to regulate stomatal aperture

Extracellular ATP elicits DORN1-mediated RBOHD phosphorylation to regulate stomatal aperture | Emerging Research in Plant Cell Biology | Scoop.it
In addition to acting as a cellular energy source, ATP can also act as a damage-associated molecular pattern in both animals and plants. Stomata are leaf pores that control gas exchange and, therefore, impact critical functions such as photosynthesis, drought tolerance, and also are the preferred entry point for pathogens. Here we show the addition of ATP leads to the rapid closure of leaf stomata and enhanced resistance to the bacterial pathogen Psuedomonas syringae. This response is mediated by ATP recognition by the receptor DORN1, followed by direct phosphorylation of the NADPH oxidase RBOHD, resulting in elevated production of reactive oxygen species and stomatal closure. Mutation of DORN1 phosphorylation sites on RBOHD eliminates the ability of ATP to induce stomatal closure. The data implicate purinergic signaling via DORN1 in the control of stomatal aperture with important implications for the control of plant photosynthesis, water homeostasis, pathogen resistance, and ultimately yield.

Via Suayib Üstün, Tatsuya Nobori, Jim Alfano
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Sharing resources for mutual benefit: crosstalk between disciplines deepens the understanding of mycorrhizal symbioses across scales

Sharing resources for mutual benefit: crosstalk between disciplines deepens the understanding of mycorrhizal symbioses across scales | Emerging Research in Plant Cell Biology | Scoop.it
Mycorrhizal scientists from 53 countries gathered in the city of Prague from 30 July until 4 August 2017 for the 9th International Conference on Mycorrhiza (ICOM9). They came to discuss an ancient symbiosis based on the exchange of resources between plant and fungal partners, with many impacts on plant health (van der Heijden et al., 2015). Much like this mutualistic interaction, delegates from disparate disciplines united with a strong focus on integration and sharing of resources for mutual benefit. By exchanging knowledge among researchers from the fields of molecular biology, physiology and ecology, the participants of ICOM9 made a leap forward in our understanding of symbiotic structure and function at multiple scales (Fig. 1).


Via Jean-Michel Ané
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Bob Reeves's curator insight, December 14, 2017 2:49 PM
Would have loved to have been a fly on the wall at this conference. So may great insights become possible when the various science disciplines mingle and share their findings. Symbiosis?
Rescooped by Jennifer Mach from Plant-Microbe Symbiosis
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The P. patens chromosome‐scale assembly reveals moss genome structure and evolution

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2,000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.


Via Jean-Michel Ané
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Rescooped by Jennifer Mach from Plant immunity and legume symbiosis
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The Structural Basis of Ligand Perception and Signal Activation by Receptor Kinases | Annual Review of Plant Biology

The Structural Basis of Ligand Perception and Signal Activation by Receptor Kinases | Annual Review of Plant Biology | Emerging Research in Plant Cell Biology | Scoop.it
Plants have evolved a family of unique membrane receptor kinases to orchestrate the growth and development of their cells, tissues, and organs. Receptor kinases also form the first line of defense of the plant immune system and allow plants to engage in symbiotic interactions. Here, we discuss recent advances in understanding, at the molecular level, how receptor kinases with lysin-motif or leucine-rich-repeat ectodomains have evolved to sense a broad spectrum of ligands. We summarize and compare the established receptor activation mechanisms for plant receptor kinases and dissect how ligand binding at the cell surface leads to activation of cytoplasmic signaling cascades. Our review highlights that one family of plant membrane receptors has diversified structurally to fulfill very different signaling tasks.

Via Christophe Jacquet
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Rescooped by Jennifer Mach from Plants & Evolution
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Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1. Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.


Via Pierre-Marc Delaux
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Rescooped by Jennifer Mach from Plant Sciences
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Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients

Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients | Emerging Research in Plant Cell Biology | Scoop.it
Highlights
•Mobile small RNAs generate sharply defined domains of target gene expression
•Small RNA-to-target ratio instructs the threshold-based readout of mobility gradients
•Mobile small RNAs present a unique direct mechanism to relay positional information
•Readouts of opposing small RNA gradients specify robust developmental boundaries

Via Loïc Lepiniec, Saclay Plant Sciences
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WillistonPlantPath's comment, November 7, 2017 1:04 PM
Wow beautiful microscopy
Rescooped by Jennifer Mach from Plant Immunity And Microbial Effectors
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TomExpress, a unified tomato RNA‐Seq platform for visualization of expression data, clustering and correlation networks

TomExpress, a unified tomato RNA‐Seq platform for visualization of expression data, clustering and correlation networks | Emerging Research in Plant Cell Biology | Scoop.it
The TomExpress platform was developed to provide the tomato research community with a browser and integrated web tools for public RNA‐Seq data visualization and data mining. To avoid major biase

Via IPM Lab
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Rescooped by Jennifer Mach from Plant Gene Seeker -PGS
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Root hairs enable high transpiration rates in drying soils

Root hairs enable high transpiration rates in drying soils | Emerging Research in Plant Cell Biology | Scoop.it

Do root hairs help roots take up water from the soil? Despite the well-documented role of root hairs in phosphate uptake, their role in water extraction is controversial. We grew barley (Hordeum vulgare cv Pallas) and its root-hairless mutant brb in a root pressure chamber, whereby the transpiration rate could be varied whilst monitoring the suction in the xylem. The method provides accurate measurements of the dynamic relationship between the transpiration rate and xylem suction. The relationship between the transpiration rate and xylem suction was linear in wet soils and did not differ between genotypes. When the soil dried, the xylem suction increased rapidly and non-linearly at high transpiration rates. This response was much greater with the brb mutant, implying a reduced capacity to take up water. We conclude that root hairs facilitate the uptake of water by substantially reducing the drop in matric potential at the interface between root and soil in rapidly transpiring plants. The experiments also reinforce earlier observations that there is a marked hysteresis in the suction in the xylem when the transpiration rate is rising compared with when it is falling, and possible reasons for this behavior are discussed.


Via Andres Zurita
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Genome of wild olive and the evolution of oil biosynthesis

Genome of wild olive and the evolution of oil biosynthesis | Emerging Research in Plant Cell Biology | Scoop.it

Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.


Via Pierre-Marc Delaux
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