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Plant J: Deployment of Burkholderia glumae type III secretion system as an efficient tool for translocating pathogen effectors to monocot cells (2013)

Plant J: Deployment of Burkholderia glumae type III secretion system as an efficient tool for translocating pathogen effectors to monocot cells (2013) | Publications | Scoop.it

Genome sequences of plant fungal pathogens have enabled the identification of effectors that cooperatively modulate the cellular environment for successful fungal growth and suppress host defense. Identification and characterization of novel effector proteins are crucial to understand pathogen virulence and host plant defense mechanisms. Previous reports indicate that the Pseudomonas syringae pv. tomato DC3000 type III secretion system (T3SS) can be used to study how non-bacterial effectors manipulate dicot plant cell function using the Effector Detector Vector (pEDV) system. Here we report a pEDV-based effector delivery system in which the T3SS of Burkholderia glumae, an emerging rice pathogen, is used to translocate the AVR-Pik and AVR-Pii effectors of fungal pathogen Magnaporthe oryzae to rice cytoplasm. The translocated AVR-Pik and AVR-Pii showed avirulence activity when tested in rice cultivars containing the cognate R genes. AVR-Pik reduced and delayed the hypersensitive response triggered by B. glumae in the non-host plant Nicotiana benthamiana indicative of an immunosuppressive virulence activity. AVR proteins fused with fluorescent protein and nuclear localization signal were delivered by B. glumae T3SS and observed in the nuclei of infected cells in rice, wheat, barley and N. benthamiana. Our bacterial T3SS-enabled eukaryotic effector delivery and subcellular localization assays provide a useful method to identify and study effector functions in monocot plants.


Via Nicolas Denancé, Freddy Monteiro, Kamoun Lab @ TSL
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Freddy Monteiro's comment, March 10, 2013 12:50 PM
Nico, this paper comes in time to feature in the general discussion of my dissertation, in a section where I explore if a temporal effector translocation hirarchy would exist in R. solanacearum. I wanted to cite a couple papers characterizing effector translocation in planta and this one is a perfect fit. It is amazing how the principle behind the use of NLS, so common nowadays for the characterization of oomycete effectors, could be successfully applied to bacteria pathogens. I hope this method could be useful in the future to the validation (re-validation) of pathogen effector proteins. Thank you for sharing.
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Nature Ecology & Evolution: The ash dieback invasion of Europe was founded by two genetically divergent individuals (2018)

Nature Ecology & Evolution: The ash dieback invasion of Europe was founded by two genetically divergent individuals (2018) | Publications | Scoop.it

Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H.fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H.fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H.fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.


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BMC Bioinformatics: nQuire: a statistical framework for ploidy estimation using next generation sequencing (2018)

BMC Bioinformatics: nQuire: a statistical framework for ploidy estimation using next generation sequencing (2018) | Publications | 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 https://github.com/clwgg/nQuire under the MIT license.


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MPMI: The ELR-SOBIR1 complex functions as a two-component RLK to mount defense against Phytophthora infestans (2018)

MPMI: The ELR-SOBIR1 complex functions as a two-component RLK to mount defense against Phytophthora infestans (2018) | Publications | Scoop.it
The ELICITIN RESPONSE (ELR) protein from Solanum microdontum can recognize INF1 elicitin of Phytophthora infestans and trigger defense responses. ELR is a receptor-like protein (RLP) that lacks a cytoplasmic signaling domain and is anticipated to require interaction with a signaling-competent receptor-like kinase (RLK). SUPPRESSOR OF BIR1-1 (SOBIR1) has been proposed as a general interactor for RLPs involved in immunity and as such, is a potential interactor for ELR. Here we investigate whether SOBIR1 is required for response to INF1 and resistance to P. infestans and whether it associates with ELR. Our results show that virus-induced gene silencing (VIGS) of SOBIR1 in Nicotiana benthamiana leads to loss of INF1-triggered cell death and increased susceptibility to P. infestans. Using genetic complementation, we found that the kinase activity of SOBIR1 is required for INF1-triggered cell death. Co-immunoprecipitation experiments showed that ELR constitutively associates with potato SOBIR1 in planta, forming a bi-partite receptor complex. Upon INF1 elicitation, this ELR-SOBIR1 complex recruits SOMATIC EMPBRYOGENESIS RECEPTOR KINASE 3 (SERK3) leading to downstream signaling activation. Overall, our study shows that SOBIR1 is required for basal resistance to P. infestans and for INF1-triggered cell death, and functions as an adaptor kinase for ELR.

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Slides: Pathogenomics of emerging plant pathogens: too little, too late (2018)

Presented at the conference “Building resilience against crop diseases: A global surveillance system”, February 14, 2018, Rockefeller Foundation Bellagio Center in Lake Como, Italy.

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Figshare: Golden-Gate compatible Magnaporthe oryzae Agrobacterium transformation vectors (2018)

Figshare: Golden-Gate compatible Magnaporthe oryzae Agrobacterium transformation vectors (2018) | Publications | Scoop.it

The Golden Gate cloning system uses standardised parts to facilitate the assembly of multiple transcriptional units, to ensure that future work with these genes can be carried out with ease (Patron et al., 2015 New Phytologist, v. 208, p. 13-19).

 
We have developed the Golden Gate compatible vector pBHt2G-RFP (Addgene #107162) from the pCAMBIA-derived (Mullins et al., 2001) pBHt2G vector (Khang et al, 2010). The vector was domesticated through removal of BsaI cloning sites. An RFP-marker was inserted, which is expressed in E. coli, allowing for red-white selection of transformants. The marker is lost during the Golden Gate reaction, as it is replaced by the inserted transcriptional units.
 
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bioRxiv: An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity (2017)

bioRxiv: An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity (2017) | Publications | Scoop.it

A subset of plant nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins carry extraneous integrated domains that have been proposed to mediate pathogen effector recognition. The current view is that these unconventional domains function by directly binding or serving as substrates for pathogen effectors, yet only a few domains have been functionally characterized to date. Here we report that the integrated NOI domain of the rice NLR protein Pii-2, together with its partner Pii-1, mediates immunity to the rice blast fungus Magnaporthe oryzae by indirect recognition of the AVR-Pii effector. We discovered that the Pii-2 NOI domain does not physically interact with the effector itself but instead binds the host protein OsExo70-F3, which is a target of AVR-Pii. We further identified mutations within the NOI core motif (PxFGxW) of Pii-2 that abolish both OsExo70-F3 binding and Pii-mediated resistance to M. oryzae expressing AVR-Pii. This led us to propose a novel conceptual model in which an NLR-integrated domain functions to detect host proteins targeted by pathogen effectors, in a framework that extends classical indirect recognition models.

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Genome Biology: Stranger in a strange land: the experiences of immigrant researchers (2017)

Genome Biology: Stranger in a strange land: the experiences of immigrant researchers (2017) | Publications | Scoop.it

Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three researchers on their experiences as immigrants.

 

International collaborations are key to advancing scientific research globally and often require mobility on the part of researchers. Migration of scientists enables the spread of ideas and skills around the world, giving researchers the opportunity to follow the best resources. Of course, migration adds a new set of challenges to the already monumental task of starting and running a lab. Genome Biology spoke to Sophien Kamoun, Rosa Lozano-Durán, and Luay Nakhleh about their personal experiences.

 

What influenced your choice to move to your current country?

 

SK: There is this old German expression “wo die Musik spielt”—you go where it’s happening, where the “music is played”. I think that sums it up. When I was a student in the 1980s, almost everyone wanted to do a Ph.D. in the USA. I felt that to have the best training and to be among the best, I had no choice but to study in the USA. I think that was a pretty correct assessment of the state of affairs in the 1980s. Indeed, I had a fantastic experience at the University of California, Davis. Also, at that time, Europe wasn’t really open to non-Western scientists, and international mobility wasn’t recognized like it is today [1]. Later, I moved to the Netherlands and then back to the USA before landing in my current position at The Sainsbury Laboratory (TSL) in Norwich, UK. I moved to Norwich exactly 10 years ago, primarily because of the reputation of the laboratory as a center of excellence for plant pathology research and the generous support provided by David Sainsbury through the Gatsby Foundation. I have had a phenomenal time at TSL these past 10 years, where I have had the opportunity to work with outstanding scientists from perhaps about 30–40 countries. An interesting point is that when TSL was founded in 1988, all the group leaders were British [2], but currently our principal investigators are from all over the world [3]. I think TSL truly reflects the emergence of the #ScienceisGlobal movement on social media [4], which is so evident in the UK and other corners of Europe.

 

RL-D: Three years ago, having worked as a postdoctoral researcher for almost four years, I was eager to establish my own laboratory. I had known what I wanted to devote my research to for a long time and could not wait to get started. Unfortunately, the economic climate in Europe, where I am originally from and where I was working at the time, was not particularly propitious for science in academia, with research budgets being slashed and increasing competition—not the most favorable situation for new group leaders, I heard over and over again. My partner was also a scientist at the same career stage, and so we needed to find two positions, not just one, complicating matters even more. One day, just by chance, we came across a job advertisement for group leader positions at the Shanghai Center for Plant Stress Biology in China. We had heard about the place—a new institute with the ambition to become a powerhouse for plant sciences. I was very excited at the prospects of leading my own research group, and that excitement overrode any qualms or self-imposed geographical restrictions. I am also fortunate enough to have an incredibly supportive family and friends who unconditionally encouraged me to pursue my scientific career, even if that involved moving far away; they may not always understand the nitty-gritty details of what I do, but they know how important it is for me.

It was my first job application, and I was offered the position following an interview at the center. They were willing to support me and give me the freedom to develop my own research program—it was an unbeatable opportunity to start my independent career. And the fact that I would be living in Asia, with the immense chance to broaden my experience that entailed, added some extra appeal (despite the slight vertigo I also felt). There was not much to think about, really—it was a deal I simply could not turn down.

 

LN: I was born to a Christian Arab family in Israel and did my undergraduate studies at the Technion (Israel Institute of Technology). Although I was an atheist by the time I started my studies at the Technion, I still considered myself to be “culturally” Christian, in that I celebrated Christmas and New Year with my family (eating and drinking, not going to church!). However, almost every year, my exams were scheduled on December 25th and January 1st (the Fall semester in Israel starts in October and ends in February). Being unable to take exams on different dates affected my performance in my studies and my interest in pursuing graduate studies at the same institution. Also, more generally, I was the only Christian Arab student in my class, and one of a handful of Arab students; I never felt comfortable at the time. So, I decided to pursue graduate studies in computer science outside Israel. The choice to come to the USA was an easy one because the USA had (and still has, in my opinion) the best graduate programs in computer science.

 

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MPMI: Lessons in Effector and NLR Biology of Plant-Microbe Systems (2017)

MPMI: 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 region (NLR)-containing 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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BMC Biology: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination (2017)

BMC Biology: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination (2017) | Publications | Scoop.it

Background. Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop.

 

Results. To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage.

 

Conclusions. Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.

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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

https://www.ismpmi.org/members/Interactions/Lists/Posts/Post.aspx?ID=152

 

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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Current Opinion Plant Biology: The coming of age of EvoMPMI: evolutionary molecular plant–microbe interactions across multiple timescales (2018)

Current Opinion Plant Biology: The coming of age of EvoMPMI: evolutionary molecular plant–microbe interactions across multiple timescales (2018) | Publications | Scoop.it
Plant–microbe interactions are great model systems to study co-evolutionary dynamics across multiple timescales. However, mechanistic research on plant–microbe interactions has often been conducted with little consideration of evolutionary concepts and methods. Conversely, evolutionary research has rarely integrated the range of mechanisms and models from the molecular plant–microbe interactions field. In recent years, the incipient field of evolutionary molecular plant–microbe interactions (EvoMPMI) has emerged to bridge this gap. Here, we report on some of the recent advances in EvoMPMI. In particular, we highlight new systems to study microbe interactions with early diverging land plants, and new findings from studies of adaptive evolution in pathogens and plants. By linking mechanistic and evolutionary research, EvoMPMI promises to expand our understanding of plant–microbe interactions.

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mBio: The Blast Fungus Decoded: Genomes in Flux (2018)

mBio: The Blast Fungus Decoded: Genomes in Flux (2018) | Publications | Scoop.it

Plant disease outbreaks caused by fungi are a chronic threat to global food security. A prime case is blast disease, which is caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), which is infamous as the most destructive disease of the staple crop rice. However, despite its Linnaean binomial name, M. oryzae is a multihost pathogen that infects more than 50 species of grasses. A timely study by P. Gladieux and colleagues (mBio 9:e01219-17, 2018, https://doi.org/10.1128/mBio.01219-17) reports the most extensive population genomic analysis of the blast fungus thus far. M. oryzae consists of an assemblage of differentiated lineages that tend to be associated with particular host genera. Nonetheless, there is clear evidence of gene flow between lineages consistent with maintaining M. oryzae as a single species. Here, we discuss these findings with an emphasis on the ecologic and genetic mechanisms underpinning gene flow. This work also bears practical implications for diagnostics, surveillance, and management of blast diseases.

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bioRxiv: The coming of age of EvoMPMI: evolutionary molecular plant-microbe interactions across multiple timescales (2018)

bioRxiv: The coming of age of EvoMPMI: evolutionary molecular plant-microbe interactions across multiple timescales (2018) | Publications | Scoop.it

Plant-microbe interactions are great model systems to study co-evolutionary dynamics across multiple timescales, ranging from multimillion year macroevolution to extremely rapid evolutionary adaptations. However, mechanistic research on plant-microbe interactions has often been conducted with little consideration of the insights that can be gained from evolutionary concepts and methods. Conversely, evolutionary research has rarely integrated the diverse range of molecular mechanisms and models that continue to emerge from the molecular plant-microbe interactions field. These trends are changing. In recent years, the incipient field of evolutionary molecular plant-microbe interactions (EvoMPMI) has emerged to bridge the gap between mechanistic molecular research and evolutionary approaches. Here, we report on recent advances in EvoMPMI. In particular, we highlight new systems to study microbe interactions with early diverging land plants, and new findings from studies of adaptive evolution in pathogens and plants. By linking mechanistic and evolutionary research, EvoMPMI promises to add a new dimension to our understanding of plant-microbe interactions.

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Figshare: Golden-Gate compatible Magnaporthe oryzae protoplast transformation vectors (2017)

Figshare: Golden-Gate compatible Magnaporthe oryzae protoplast transformation vectors (2017) | Publications | Scoop.it
The Golden Gate cloning system uses standardised parts to facilitate the assembly of multiple transcriptional units, to ensure that future work with these genes can be carried out with ease (Patron et al., 2015 New Phytologist, v. 208, p. 13-19).
 
Three fungal transformation vectors have been adapted from the pCB1532 vector series (Sweigard et al., 1997. Fungal Genetics Newsletter 44: 52-53). Vector pCB1532B-RFP Addgene #101854 encodes bialaphos/basta/L-phosphinothricin resistance, pCB1532H-RFP #101855 hygromycin resistance and pCB1532S-RFP #101856 sulfonylurea/chlorimuron ethyl resistance.
 
Vectors were domesticated through removal of BsaI cloning sites. An RFP-marker was inserted. The RFP is expressed in E. coli, allowing for red-white selection of transformants. The marker is lost during the Golden Gate reaction, as it is replaced by the inserted transcriptional units.
 
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Horizon: Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018

Horizon: Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018 | Publications | Scoop.it

We asked a selection of European scientists which scientific breakthroughs they'd like to see in 2018.

 

Gene-editing to improve crop immunity

 

For Professor Sophien Kamoun at Sainsbury Laboratory in the UK, a breakthrough would be to adapt plant immune systems to defend them against a wider range of diseases. ‘One approach would be to design improved immune receptors that can then be edited into crop genomes. This approach requires a better biochemical and biophysical understanding of how plant receptors detect pathogens and activate immunity. It also necessitates a better knowledge of pathogen diversity and (their ability to evolve). Ultimately, we require a framework to rapidly generate new disease resistance traits and introduce them into crop genomes. Only then we can keep up with rapidly evolving pathogens.’

 

Read: Can CRISPR feed the world?

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BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017)

BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017) | Publications | Scoop.it

Background. Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches’ broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S. graminicola.

 

Results. Sequence reads were generated from S. graminicola using an Illumina sequencing platform and assembled de novo into a draft genome sequence comprising approximately 360 Mbp. Of this sequence, 73% comprised repetitive elements, and a total of 16,736 genes were predicted from the RNA-seq data. The predicted genes included those encoding effector-like proteins with high sequence similarity to those previously identified in other oomycete pathogens. Genes encoding jacalin-like lectin-domain-containing secreted proteins were enriched in S. graminicola compared to other oomycetes. Of a total of 1220 genes encoding putative secreted proteins, 91 significantly changed their expression levels during the infection of plant tissues compared to the sporangia and zoospore stages of the S. graminicola lifecycle.

 

Conclusions. We established the draft genome sequence of a downy mildew pathogen that infects Gramineae plants. Based on this sequence and our transcriptome analysis, we generated a catalog of in planta-induced candidate effector genes, providing a solid foundation from which to identify the effectors causing phyllody.

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bioRxiv: Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions (2017)

bioRxiv: Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions (2017) | Publications | Scoop.it

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

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IS-MPMI Interactions: Fat Cats Can Jump Over The Wall: Plant Biotic Interactions Workshop in Hohhot, Inner Mongolia, China (2017)

IS-MPMI Interactions: Fat Cats Can Jump Over The Wall: Plant Biotic Interactions Workshop in Hohhot, Inner Mongolia, China (2017) | Publications | Scoop.it
 
On a cloudy Norwich day in 2011, post-docs Sebastian Schornack, Sylvain Raffaele, and Tolga Bozkurt were having a typical British lunch of fish and chips with mushy peas with their supervisor Sophien Kamoun. Somehow, the discussion turned to the importance of sustained productivity. Kamoun, in his usual hyperbolic style, pointed out that now that each one of them had just published notable papers (Schornack et al., 2010; Raffaele et al., 2010; Bozkurt et al., 2011), they should beware of not behaving like “lazy fat cats” and think hard about their next papers. Not everyone left the lunch in the happiest mood. One day later, after discussion with another post-doc, Mireille van Damme, Schornack and colleagues decided to found the Lazy Fat Cat Club (#LFCats). Schornack drafted a chart and was appointed as Chairman Féi māo (fat cat in Mandarin). The #LFCats ethos is that productive research requires a significant amount of communication and knowledge exchange, and informally discussing research is a perfect way of solving roadblocks and laying paths for the future. Casual meetings took place on a regular basis at The Sainsbury Laboratory, mainly on afternoon coffee breaks. The club continued to loosely grow and several other researchers joined the #LFCats. As the members moved on to start their own labs, the #LFCats “brand” helped nurture a lasting bond. Suomeng Dong, now a professor in the Department of Plant Pathology at Nanjing Agricultural University, coined the Chinese proverb “Fat cats cannot jump over the wall” to challenge the #LFCats to work collaboratively to solve problems and “jump over the wall.”
 
It should be noted that the #LFCats are neither lazy (well, maybe a bit sometimes…) nor overweight (no comments...). Instead the club’s name relates to the initial discussion and stands for the importance of moving out your comfort zone and looking forward to the next goal in science or in life. It also grew to reflect the importance of informal interactions as a means to enhance efficiency and creativity. To promote such interactions, Schornack organized the first #LFCats research meeting at the Sainsbury Laboratory Cambridge University in 2013. Dong (Nanjing Agricultural University, China) and Ruofang Zhang (Inner Mongolia University, China) led a second meeting in August 2017 in Hohhot, Inner Mongolia. The local host, Zhang, is the director of the Potato Research Center at Inner Mongolian University and the Plant Protection section in the Chinese Modern Agricultural Industry Technology System. Indeed, the autonomous region of Inner Mongolia is the largest potato production area in China and has contributed to making this country the leading potato producer in the world.
 
In this report, we summarize the key findings presented at the workshop.
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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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