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bioRxiv: Lessons in effector and NLR biology of plant-microbe systems (2017)

bioRxiv: Lessons in effector and NLR biology of plant-microbe systems (2017) | Publications | Scoop.it

A diversity of plant-associated organisms secrete effectors: proteins and metabolites that modulate plant physiology to favor host infection and colonization. However, effectors can also activate plant immune receptors, notably nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins, enabling plants to fight off invading organisms. This interplay between effectors, their host targets, and the matching immune receptors is shaped by intricate molecular mechanisms and exceptionally dynamic coevolution. In this article, we focus on three effectors, AVR-Pik, AVR-Pia, and AVR-Pii, from the rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae), and their corresponding rice NLR immune receptors, Pik, Pia, and Pii, to highlight general concepts of plant-microbe interactions. We draw 12 lessons in effector and NLR biology that have emerged from studying these three little effectors and are broadly applicable to other plant-microbe systems.

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Plantae: Taproot Episode 1, Season 1: Extreme Open Science and the Meaning of Scientific Impact (2017)

Plantae: Taproot Episode 1, Season 1: Extreme Open Science and the Meaning of Scientific Impact (2017) | Publications | Scoop.it

In this episode, the hosts and Sophien discuss a recent collaborative paper (Islam et al., 2016, BMC Biology) that really embodies the concepts of open science. It addresses the source and characterization of a newly discovered wheat blast in Bangladesh. Wheat blast is a fungal disease that affects grasses that are a huge threat to food security. The authors report the geographical distribution of this new disease, characterize the disease symptoms of affected plants, and isolate and validate the causal fungus. Most strikingly, they performed RNA sequencing on symptomatic and asymptomatic leaves and show that RNA from these infected leaves aligns to the genome of a Brazilian wheat blast strain. They conclude that the Bangladesh isolate of wheat blast is phylogenetically related to the Brazilian wheat blast, rather than an unknown or new lineage.

 

Listen to this episode to hear Sophien, Ivan, and Liz discuss the science in this paper, how the project started, and how it developed into a peer-reviewed publication. Also discussed is the importance of redefining what is meant by scientific “impact”, and new ways to do science in the plant pathology community and beyond.

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IS-MPMI Interactions: InterViews: Sophien Kamoun by Jixiang Kong (2017)

IS-MPMI Interactions: InterViews: Sophien Kamoun by Jixiang Kong (2017) | Publications | Scoop.it

This InterView with Sophien Kamoun, John Innes Centre, was performed by one of the 2016 IS-MPMI student travel awardees, Jixiang Kong, Gregor Mendel Institute.

 

JIXIANG KONG: What led you to study biology? More specifically plant-pathogen interactions.

 

SOPHIEN KAMOUN: I grew up with a passion for nature. As a teenager I collected insects and became fascinated by their incredible diversity. Later I took this “hobby” more seriously and I specialized in studying tiger beetles. I even published a few papers on this topic.

 

After high school in Tunisia, I went to Paris with the firm intention of studying biology and becoming an entomologist. However, I was disappointed by how badly taught zoology was—too much emphasis on taxonomy and little mechanistic thinking. Instead, I became drawn to the more rigorous methods and approaches of molecular biology, and I ended up majoring in genetics. I reconciled this major with my natural history interests by taking multiple modules in evolution and reading a lot on the subject.

 

Plant pathology came later when I moved from Paris to the University of California-Davis for my Ph.D. The fellowship I received stipulated that I should study plant biology. It wasn’t by choice but rather by accident. But I quickly became engrossed in molecular plant pathology and I really liked that this science involves interactions between multiple organisms. However, for many years I missed a direct connection between the lab work and the field.

 

JK: If you would not have chosen the topic of plant-pathogen interactions, what would you choose?

 

SK: Definitely, entomology. I’m still fascinated by insects, especially beetles. I feel we know so little about their biology, especially from a mechanistic angle. They are so diverse and yet most insect research focuses on a few species, such as Drosophila. There are so many fascinating questions, for example, about the evolution of insect behavior and the underlying genes. Also, insects can be important crop pests and disease vectors. This is a very fertile area of research that I highly recommend to early career scientists.

 

JK: How do you envision large-scale “omics” approaches in studying plant immunity?

 

SK: Omics are just another tool. They’re powerful tools but they’re still methods we use to answer questions. I advise everyone to frame their research based on questions and then look for the best methods to answer these questions.

 

This said, genomics has transformed biology in a fundamental way. It’s a new way of doing business. We now have catalogs of plant and pathogen genes, so the challenge is to link genes to function rather than discovering the genes per se. Another key aspect is that genomics is a great equalizer. Model systems are less important than in earlier days. One can make a lot of progress with a genome and a few functional assays. For example, consider the progress made in discovering effectors in obligate parasites. This would have been almost unthinkable in the pre-genomics age. This is why I wish to see more early career scientists explore the diversity of pathogen systems rather than working on established model systems.

 

JK: Social media is changing the way of communication rapidly. However, the scientific communication on social media is just emerging. How do you see the direction of social media in the future regarding the impact on science? Will social media replace or minimize some conventional communication such as conferences?

 

SK: Communication is an essential function of being a scientist. We’re not only in the business of producing new knowledge but it’s also our obligation to communicate knowledge to our peers and the public. These days social media became a major medium for communication in science. It’s an efficient way to filter through the incessant flow of information, stay up to date, and broadly broadcast new knowledge. It also enables us to expand our network way beyond traditional colleagues. I interact on Twitter with teachers, farmers, journalists, etc. I also use it, of course, to communicate with colleagues and share information and insights. I also find Twitter immensely entertaining. Scientists have a lot of humor.

 

I don’t think social media will replace the need for direct contact and interaction between peers. I think we still would want to break off our daily routine and meet in person with colleagues. However, I wish we could start rethinking the format of scientific conferences. Both the fairly detailed oral presentations and poster sessions could be improved if they were combined with some sort of Internet interaction. Twitter is already transforming how scientists interact at conferences but we could do better.

 

JK: What advice would you provide to young researchers who are in their early scientific career?

 

SK: Don't follow the herd. Take chances. Look beyond the current trends both in terms of experimental systems and questions, and ask provocative questions.

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CropLife International (2017)

CropLife International (2017) | Publications | Scoop.it

Why did you want to be a plant scientist?

I became a scientist because I grew up being extremely curious about the natural world. I wanted to know how living organisms function. How they became the way they are. Plant pathology came later after realized that I may as well study a field of biology that is important to the human condition. This inspires me to narrow the gap between fundamental and applied research. My aim is to perform cutting-edge research and significantly advance knowledge on economically important plant pathogen systems. In contrast, much research focuses on model systems and is therefore further steps away from practical applications.

Can you explain what your job involves?

As an academic scientist, I am in the business of knowledge. My job is to generate new knowledge to advance science, and to influence others to pursue new directions, generate more knowledge and apply it to address practical problems. My job is also to communicate scientific knowledge and discoveries to my peers and to a broader audience, including the general public.

 

What are the plant diseases that you are working on?

I work primarily on blight and blast diseases. Throughout my career, I have worked primarily on the Irish potato famine pathogen Phytophthora infestans. More recently, I was inspired by the sense of urgency brought upon by the February 2016 Bangladeshi wheat blast epidemic to expand my research to blast fungi. I aim to apply the concepts and ideas I developed throughout my career to a problem with an immediate impact on global food security.

Can you describe how damaging these diseases can be for farmers?

Plant diseases are a major constraint for achieving food security. Losses caused by fungal plant pathogens alone account for enough to feed several billion people. Magnaporthe oryzae, the causal agent of blast disease of cereals, is among the most destructive plant pathogens, causing losses in rice production that, if mitigated, could feed up to 740 million people. This pathogen has emerged since the 1980s as an important pathogen of wheat seriously limiting the potential for wheat production in South America. In 2016, wheat blast was detected for the first time in Asia with reports of a severe epidemic in Bangladesh. The outbreak is particularly worrisome because wheat blast has already spread further to India, and is threatening major wheat producing areas in neighboring South Asian countries. Global trade and a warming climate are contributing to the spread and establishment of blast diseases as a global problem for cereal production and a present and clear danger to food security.

Why is your profession important in the challenge to feed the world?

Plant pathology delivers science-driven solutions to plant diseases. In particular, genetic solutions through disease resistant crop varieties can be sustainable and environmentally friendly.

What inspires you about your job?

Knowledge and people. The thrill of learning something new every day is addictive. Sharing the experience with others –be they students, colleagues, stakeholders or members of the public – is priceless.

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BMC Biology: Can a biologist fix a smartphone?—Just hack it! (2017)

BMC Biology: Can a biologist fix a smartphone?—Just hack it! (2017) | Publications | Scoop.it

Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encoded in the genome sequence) and hardware (organism), genome editors can operate as software engineers to hack biological systems without any particularly deep understanding of the complexity of the systems.

 

This article was inspired by the influential and entertaining essay by Yuri Lazebnik who argued that there are fundamental flaws in how biologists approach problems [1]. Lazebnik proposed that the complexity of biological systems calls for a systems approach to the study of living systems using a radio as a colourful metaphor to illustrate his points [1]. He postulated that, conceptually, a radio functions similarly to a biological system by converting a signal from one form into another using a signal transduction pathway [1]. Here I argue that Lazebnik’s thesis is limited by two fundamental principles of biology. First, the clear-cut separation between the software code—the operating information for living systems as written in the genome sequence—and hardware, or the organism itself [2, 3]. Second, biological systems are not optimally designed but are shaped by historicity—the historical constraints that are integral to their evolution [4]. This limits the extent to which principles of design and engineering can be useful in understanding and manipulating the structures and functions of living organisms. In contrast, modern day biologists are starting to operate as software engineers to hack biological systems and write apps despite a somewhat superficial understanding of the underlying complexity of these systems.

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MPMI: Foundational and translational research opportunities to improve plant health (2017)

MPMI: Foundational and translational research opportunities to improve plant health (2017) | Publications | Scoop.it

This whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on non-sustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture. Specific findings: ● Genetic improvement of crops is the most reliable, least expensive management strategy when suitable genetic variation is available. Nonetheless, some interventions have not proved durable due to the evolution and global dispersal of virulent pathogens and pests as well as herbicide-resistant weeds. ● Additional strategies are becoming essential as multiple fungicides, nematicides, and herbicides become ineffective due to the evolution of resistance and/or are phased out due to registration withdrawals. ● Strategies are needed that maximize the evolutionary hurdles for pathogens, pests, and weeds to overcome control measures. Interventions need to evolve as fast as the biotic challenges. Moreover, deployments of interventions must be driven by knowledge of the evolutionary capacity of the biotic challenge. ● Considerable knowledge exists but more research into the mechanisms of plant immunity and other forms of resistance is needed as the foundation for translational applications. ● Several new technologies are increasing foundational knowledge and providing numerous opportunities for generating crops with durable resistance to pests and diseases as well as control of weeds and reduction of the environmental impact of agriculture. ● There are multiple strategies for counteracting biotic challenges involving canonical and non-canonical disease resistance genes, genes encoding susceptibility factors, small RNAs, or immunomodulators. Simultaneous deployment of disease resistance strategies with different modes of action, as well as the judicious use of fungicides, will enhance durability of control measures. ● Pathogen effectors provide tools for discovering resistance genes and susceptibility factors as well as for dissecting/manipulating plant biology and breeding plants for durable disease resistance. ● There are several, as yet little exploited, opportunities for leveraging beneficial interactions among plants, microbes, insects and other organisms in the phytobiome to enhance plant health and productivity as well as breeding plants to promote beneficial phytobiome communities. ● Global monitoring of plant health is feasible and desirable in order to anticipate and counter threats. ● Climate change increases the need for continual global monitoring of pathogens, pests, and weeds and adjusting of control strategies. ● There are numerous current and future opportunities for knowledge exchange and partnerships between developed and developing countries to foster improved local and global food security. ● Both genetically modified (GM) and non-GM strategies are needed to maximize plant health and food security. ● Significant, sustained financial support is required if the beneficial impacts of foundational and translational research on global food security are to be realized. The needs, opportunities, approaches, and deliverables for addressing biotic challenges to plant health are detailed in Table 1. These can be broadly classified as assessing variation, characterizing it in detail at a variety of scales, and deploying beneficial interventions. Immediate investments in global monitoring of pathogens/pests and in situ and ex-situ determination of what natural variation exists in crop plants for countering challenges and threats should be a high priority. Detailed investigations of the molecular basis of the various types of plant resistance and of the basis of pathogen/pest virulence are critical for providing the foundation for novel intervention strategies; these will be facilitated by development of high resolution structural and functional analytical techniques. Optimization of protocols for delivery of reagents for allele replacement and gene insertions into diverse major and minor crop plants should be a high priority. Monitoring and deployment should be a global endeavor involving multinational partnerships and knowledge exchanges in order to ensure that interventions are locally relevant and globally durable.

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BMC Biology: Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thalian...

BMC Biology: Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thalian... | Publications | Scoop.it
Plants are exposed to diverse pathogens and pests, yet most plants are resistant to most plant pathogens. Non-host resistance describes the ability of all members of a plant species to successfully prevent colonization by any given member of a pathogen species. White blister rust caused by Albugo species can overcome non-host resistance and enable secondary infection and reproduction of usually non-virulent pathogens, including the potato late blight pathogen Phytophthora infestans on Arabidopsis thaliana. However, the molecular basis of host defense suppression in this complex plant–microbe interaction is unclear. Here, we investigate specific defense mechanisms in Arabidopsis that are suppressed by Albugo infection.Empty description

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The Sainsbury Lab's curator insight, March 22, 8:01 AM
Plants are exposed to diverse pathogens and pests, yet most plants are resistant to most plant pathogens. Non-host resistance describes the ability of all members of a plant species to successfully prevent colonization by any given member of a pathogen species. White blister rust caused by Albugo species can overcome non-host resistance and enable secondary infection and reproduction of usually non-virulent pathogens, including the potato late blight pathogen Phytophthora infestans on Arabidopsis thaliana. However, the molecular basis of host defense suppression in this complex plant–microbe interaction is unclear. Here, we investigate specific defense mechanisms in Arabidopsis that are suppressed by Albugo infection.
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Microbiology Molecular Biology Reviews: Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity (2017)

Microbiology Molecular Biology Reviews: Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity (2017) | Publications | Scoop.it

Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.

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bioRxiv: Host autophagosomes are diverted to a plant-pathogen interface (2017)

bioRxiv: Host autophagosomes are diverted to a plant-pathogen interface (2017) | Publications | Scoop.it

Filamentous plant pathogens and symbionts invade their host cells but remain enveloped by host-derived membranes. The mechanisms underlying the biogenesis and functions of these host-microbe interfaces are poorly understood. Recently, we showed that PexRD54, an effector from the Irish potato famine pathogen Phytophthora infestans, binds host protein ATG8CL to stimulate autophagosome formation and deplete the selective autophagy receptor Joka2 from ATG8CL complexes. Here, we show that during P. infestans infection, ATG8CL autophagosomes are diverted to the pathogen interface. Our findings are consistent with the view that the pathogen coopts host selective autophagy for its own benefit.

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Plant Methods: Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana (2016)

Plant Methods: Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana (2016) | Publications | Scoop.it

CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas. A single construct was assembled using Golden Gate cloning. Two sgRNAs were used to introduce a precise 37 nt deletion early in the coding region of the urease gene. A high percentage of bi-allelic mutations (≤61.5%) were observed in clones with the CRISPR-Cas construct. Growth of bi-allelic mutants in urea led to a significant reduction in growth rate and cell size compared to growth in nitrate. CRISPR-Cas can precisely and efficiently edit the genome of T. pseudonana. The use of Golden Gate cloning to assemble CRISPR-Cas constructs gives additional flexibility to the CRISPR-Cas method and facilitates modifications to target alternative genes or species.

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Trends in Plant Science: ATG8 Expansion: A Driver of Selective Autophagy Diversification? (2016)

Trends in Plant Science: ATG8 Expansion: A Driver of Selective Autophagy Diversification? (2016) | Publications | Scoop.it

Selective autophagy is a conserved homeostatic pathway that involves engulfment of specific cargo molecules into specialized organelles called autophagosomes. The ubiquitin-like protein ATG8 is a central player of the autophagy network that decorates autophagosomes and binds to numerous cargo receptors. Although highly conserved across eukaryotes, ATG8 diversified from a single protein in algae to multiple isoforms in higher plants. We present a phylogenetic overview of 376 ATG8 proteins across the green plant lineage that revealed family-specific ATG8 clades. Because these clades differ in fixed amino acid polymorphisms, they provide a mechanistic framework to test whether distinct ATG8 clades are functionally specialized. We propose that ATG8 expansion may have contributed to the diversification of selective autophagy pathways in plants.

 

  • Selective autophagy is an ancient membrane-trafficking pathway that is essential for cellular homeostasis.
  • Selective autophagy involves engulfment of autophagic cargo within double-membrane vesicles called autophagosomes.
  • Autophagosomes are decorated by ATG8, a ubiquitin-like protein conserved across eukaryotes that is expanded in higher plants.
  • Selective cargo recruitment is mediated by autophagy receptors that interact with ATG8 via an ATG8 interaction motif (AIM). Specialization of autophagy receptors toward ATG8 variants contributes to selective autophagy.
  • Although selective autophagy plays important roles in development and stress tolerance, the molecular mechanisms underlying selectivity are currently elusive in plants.
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bioRxiv: NLR signaling network mediates immunity to diverse plant pathogens (2016)

bioRxiv: NLR signaling network mediates immunity to diverse plant pathogens (2016) | Publications | Scoop.it

Plant and animal nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins often function in pairs to mediate innate immunity to pathogens. However, the degree to which NLR proteins form signaling networks beyond genetically linked pairs is poorly understood. In this study, we discovered that a large NLR immune signaling network with a complex genetic architecture confers immunity to oomycetes, bacteria, viruses, nematodes, and insects. The network emerged over 100 million years ago from a linked NLR pair that diversified into up to one half of the NLR of asterid plants. We propose that this NLR network increases robustness of immune signaling to counteract rapidly evolving plant pathogens.

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New Phytologist: Nine things to know about elicitins (2016)

New Phytologist: Nine things to know about elicitins (2016) | Publications | Scoop.it

Elicitins are structurally conserved extracellular proteins in Phytophthora and Pythium oomycete pathogen species. They were first described in the late 1980s as abundant proteins in Phytophthora culture filtrates that have the capacity to elicit hypersensitive (HR) cell death and disease resistance in tobacco. Later, they became well-established as having features of microbe-associated molecular patterns (MAMPs) and to elicit defences in a variety of plant species. Research on elicitins culminated in the recent cloning of the elicitin response (ELR) cell surface receptor-like protein, from the wild potato Solanum microdontum, which mediates response to a broad range of elicitins. In this review, we provide an overview on elicitins and the plant responses they elicit. We summarize the state of the art by describing what we consider to be the nine most important features of elicitin biology.

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Blog: What’s up with preprints? And why I’m bothering with them (2017)

Blog: What’s up with preprints? And why I’m bothering with them (2017) | Publications | Scoop.it

What’s up with preprints? And why I’m bothering with them. A few answers to @hormiga post about why he’s not bothering with preprints.

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PNAS: NLR network mediates immunity to diverse plant pathogens (2017)

PNAS: NLR network mediates immunity to diverse plant pathogens (2017) | Publications | Scoop.it

Both plants and animals rely on nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins to respond to invading pathogens and activate immune responses. An emerging concept of NLR function is that “sensor” NLR proteins are paired with “helper” NLRs to mediate immune signaling. However, our fundamental knowledge of sensor/helper NLRs in plants remains limited. In this study, we discovered a complex NLR immune network in which helper NLRs in the NRC (NLR required for cell death) family are functionally redundant but display distinct specificities toward different sensor NLRs that confer immunity to oomycetes, bacteria, viruses, nematodes, and insects. The helper NLR NRC4 is required for the function of several sensor NLRs, including Rpi-blb2, Mi-1.2, and R1, whereas NRC2 and NRC3 are required for the function of the sensor NLR Prf. Interestingly, NRC2, NRC3, and NRC4 redundantly contribute to the immunity mediated by other sensor NLRs, including Rx, Bs2, R8, and Sw5. NRC family and NRC-dependent NLRs are phylogenetically related and cluster into a well-supported superclade. Using extensive phylogenetic analysis, we discovered that the NRC superclade probably emerged over 100 Mya from an NLR pair that diversified to constitute up to one-half of the NLRs of asterids. These findings reveal a complex genetic network of NLRs and point to a link between evolutionary history and the mechanism of immune signaling. We propose that this NLR network increases the robustness of immune signaling to counteract rapidly evolving plant pathogens.

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bioRxiv: nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing (2017)

bioRxiv: nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing (2017) | Publications | Scoop.it

nQuire is a statistical framework that distinguishes between diploids, triploids and tetraploids using next generation sequencing. 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. Availability and Implementation: The model is implemented as a stand-alone Linux command line tool in the C programming language and is available at github under the MIT licence. Please also refer to github.com/clwgg/nQuire for usage instructions.

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Horizon: Can CRISPR feed the world? (2017)

Horizon: Can CRISPR feed the world? (2017) | Publications | Scoop.it

Scientists want to edit the genes of potatoes and wheat.

 

As the world’s population rises, scientists want to edit the genes of potatoes and wheat to help them fight plant diseases that cause famine.

 

By 2040, there will be 9 billion people in the world. ‘That’s like adding another China onto today’s global population,’ said Professor Sophien Kamoun of the Sainsbury Laboratory in Norwich, UK.

 

Prof. Kamoun is one of a growing number of food scientists trying to figure out how to feed the world. As an expert in plant pathogens such as Phytophthora infestans – the fungus-like microbe responsible for potato blight – he wants to make crops more resistant to disease.

 

Potato blight sparked the Irish famine in the 19th century, causing a million people to starve to death and another million migrants to flee. European farmers now keep the fungus in check by using pesticides. However, in regions without access to chemical sprays, it continues to wipe out enough potatoes to feed hundreds of millions of people every year.

 

‘Potato blight is still a problem,’ said Prof. Kamoun. ‘In Europe, we use 12 chemical sprays per season to manage the pathogen that causes blight, but other parts of the world cannot afford this.’

 

Plants try to fight off the pathogens that cause disease but these are continuously changing to evade detection by the plant’s immune system.

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Wired: Who Wants Disease-Resistant GM Tomatoes? Probably Not Europe (2017)

Wired: Who Wants Disease-Resistant GM Tomatoes? Probably Not Europe (2017) | Publications | Scoop.it

ENGINEERING A TOMATO resistant to a pernicious fungal disease doesn’t seem like it’d be the easiest part of a plant pathologist’s job. But compared to getting that tomato to market? It’s a snap.


At least, that’s how Sophien Kamoun sees it. Kamoun studies plant diseases at the Sainsbury Laboratory in England, and in March his team published a paper describing a tomato they’d tweaked. Using the gene-editing technique Crispr/Cas9, Kamoun’s group snipped out a piece of a gene called Mildew Resistant Locus O, or Mlo. That deletion makes the tomato resistant to powdery mildew, a serious agricultural problem that takes a lot of chemicals to control.


Kamoun’s “Tomelo” actually looks a lot like a naturally occurring tomato, a mutant with the same resistance. “At least in the tomato plants we have, there was no detectable difference between the mutant and the wild type,” Kamoun says. “Obviously we’d need to do more detailed field trials, but there was certainly nothing obvious.”


But for now, that’s where Kamoun’s work stops. European regulations make the tomato essentially illegal—he and others can do the science, but probably can’t get it to field trials, and certainly can’t get it to market. “There’s more clarity in the US. One could probably get approval. But in Europe, it’s a big question mark,” he says. “I’m very frustrated by this, I have to be honest. Scientifically this plant is no different from any mutant we’d get from traditional breeding or traditional mutagenesis. I really don’t understand what the problem is.”


If you’re wondering how agriculture is going to feed 10 billion people on a climatically chaotic, hotter, more disaster-prone planet, you might not understand the problem, either.

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Marcus Jansen's curator insight, May 3, 10:24 AM
Great work, this plant has potential to avoid pesticide applications. It is good for the Environment, let's hope that European regulation authorities understand this.
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Video: European Research Council@10: the impact on science and scientists (2017)

Scientists at the John Innes Centre and The Sainsbury Laboratory reflect on the success of the ERC over the last ten years and the impact that ERC grant

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Scientific Reports: Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion (2017)

Scientific Reports: Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion (2017) | Publications | Scoop.it

Genome editing has emerged as a technology with a potential to revolutionize plant breeding. In this study, we report on generating, in less than ten months, Tomelo, a non-transgenic tomato variety resistant to the powdery mildew fungal pathogen using the CRISPR/Cas9 technology. We used whole-genome sequencing to show that Tomelo does not carry any foreign DNA sequences but only carries a deletion that is indistinguishable from naturally occurring mutations. We also present evidence for CRISPR/Cas9 being a highly precise tool, as we did not detect off-target mutations in Tomelo. Using our pipeline, mutations can be readily introduced into elite or locally adapted tomato varieties in less than a year with relatively minimal effort and investment.

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bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017)

bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017) | Publications | Scoop.it

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012, Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013, Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

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Phil. Trans. R. Soc. B: Emerging oomycete threats to plants and animals (2016)

Phil. Trans. R. Soc. B: Emerging oomycete threats to plants and animals (2016) | Publications | Scoop.it

Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans , Phytophthora palmivora , Phytophthora ramorum , Plasmopara obducens , and the animal pathogens Aphanomyces invadans , Saprolegnia parasitica and Halioticida noduliformans . For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities.

This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.

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BBC News: Four good things that happened in 2016

BBC News: Four good things that happened in 2016 | Publications | Scoop.it

A lot has gone wrong this year. We don't mean Brexit or the election of Donald Trump, both of which split opinion in Britain and the US.

 

We mean the thousands of migrants who died in the Med, the war in Syria, Zika virus, terror attacks all over the world, the hottest temperatures ever recorded. And, as if all that wasn't bad enough, David Bowie died.

 

So from the BBC World Service Inquiry programme here are four things that went right in 2016 from the perspective of four people who helped make them happen.

 

Four stories united by just one thing: the ambition to achieve the seemingly impossible.

 

Gene editing

 

Professor Sophien Kamoun is a plant biologist from Tunisia. He has always been interested in plant diseases, particularly after seeing the devastating effects of pesticides in developing countries.

 

Every year, thousands die after using pesticides on diseased crops. What if you could create a type of plant that doesn't get diseases?

 

That's what Sophien Kamoun has been experimenting with in his lab at Norwich University, using a new technique invented in the US that came of age this year - gene editing. It allows scientists to modify the genes of living things like plants.

 

Professor Kamoun experimented with editing the genes of a tomato plant so that it would no longer be susceptible to a particular disease.

 

First they isolated the gene that makes the tomato vulnerable to that disease. Then they removed the gene from the genome of the tomato. "And it became resilient to the fungal disease," he says.

 

Gene editing is an incredibly powerful tool. There are real concerns about how such a technology could be used, but regulate it properly, and you could change the way we feed the world.

 

"Every year we lose enough food to feed hundreds of millions of people to pathogens and parasites," he says. "If we could make some of our crops more resilient, then that would be an unique achievement."

 

It is not only plant biologists who are experimenting with gene editing: doctors are using it to reverse the mutations that cause blindness, to stop cancer cells from multiplying and to make cells resistant to the virus that causes AIDS.

 

It is why some have called gene editing the invention of the century.

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BBC World Service - The Inquiry: What Went Right in 2016?

BBC World Service - The Inquiry: What Went Right in 2016? | Publications | Scoop.it

What Went Right in 2016?

 

A lot has gone wrong this year. We’re not talking about Brexit or the election of Donald Trump – both of which split opinion in Britain and the US – we’re talking about terror attacks, the brutal conflict in Syria, and the thousands of migrants who died trying to reach Europe.

 

Good things did happen. But the good news was mostly buried under the bad. So for this edition of The Inquiry – our final show of the year – we wanted to find about four things that went right in 2016. And we wanted to talk to the people who made those things happen. That’s it.

 

Four amazing stories united by one thing: the ambition of a small number of extraordinary people to achieve the seemingly impossible.

 

Presenter: Helena Merriman

 

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BMC Biology: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016)

BMC Biology: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016) | Publications | Scoop.it

Background. In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields.

Results. Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae.

Conclusion. Our findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.

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