Publications
25.3K views | +2 today
Follow
Publications
Updates from the group of Sophien Kamoun at The Sainsbury Lab
Your new post is loading...
Your new post is loading...
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

#TwitterWisdom "I'm not a fan of the persistent PAMP-triggered (PTI) vs. effector-triggered immunity (ETI) nomenclature... #plantpath #plantsci" (2018)

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

Nature Plants: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen (2018)

Nature Plants: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen (2018) | Publications | Scoop.it

Accelerated adaptive evolution is a hallmark of plant–pathogen interactions. Plant intracellular immune receptors (NLRs) often occur as allelic series with differential pathogen specificities. The determinants of this specificity remain largely unknown. Here, we unravelled the biophysical and structural basis of expanded specificity in the allelic rice NLR Pik, which responds to the effector AVR-Pik from the rice blast pathogen Magnaporthe oryzae. Rice plants expressing the Pikm allele resist infection by blast strains expressing any of three AVR-Pik effector variants, whereas those expressing Pikp only respond to one. Unlike Pikp, the integrated heavy metal-associated (HMA) domain of Pikm binds with high affinity to each of the three recognized effector variants, and variation at binding interfaces between effectors and Pikp-HMA or Pikm-HMA domains encodes specificity. By understanding how co-evolution has shaped the response profile of an allelic NLR, we highlight how natural selection drove the emergence of new receptor specificities. This work has implications for the engineering of NLRs with improved utility in agriculture.


Via The Sainsbury Lab, Kamoun Lab @ TSL
more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plant Pathogenomics
Scoop.it!

BMC Evolutionary Biology: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2018)

BMC Evolutionary Biology: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2018) | Publications | Scoop.it

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 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 (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans.


Via The Sainsbury Lab, Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: The MoT3 assay does not distinguish between Magnaporthe oryzae wheat and rice blast isolates from Bangladesh (2018)

bioRxiv: The MoT3 assay does not distinguish between Magnaporthe oryzae wheat and rice blast isolates from Bangladesh (2018) | Publications | Scoop.it

The blast fungus Magnaporthe oryzae is comprised of lineages that exhibit varying degrees of specificity on about 50 grass hosts, including rice, wheat and barley. Reliable diagnostic tools are essential given that the pathogen has a propensity to jump to new hosts and spread to new geographic regions. Of particular concern is wheat blast, which has suddenly appeared in Bangladesh in 2016 before spreading to neighboring India. In these Asian countries, wheat blast strains are now co-occurring with the destructive rice blast pathogen raising the possibility of genetic exchange between these destructive pathogens. We assessed the recently described MoT3 diagnostic assay and found that it did not distinguish between wheat and rice blast isolates from Bangladesh. The assay is based on primers matching the WB12 sequence corresponding to a fragment of the M. oryzae MGG_02337 gene annotated as a short chain dehydrogenase. These primers could not reliably distinguish between wheat and rice blast isolates from Bangladesh based on DNA amplification experiments performed in separate laboratories in Bangladesh and in the UK. In addition, comparative genomics of the WB12 sequence revealed a complex underlying genetic structure with related sequences across M. oryzae strains and in both rice and wheat blast isolates. We, therefore, caution against the indiscriminate use of this assay to identify wheat blast.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

YouTube: Plants have an immune system… and it’s complicated (2018)

Just like humans, plants have an immune system that they use to fend off pathogens and pests. Research involving plant immunity was guided by Harold Flor’s influential “gene-for-gene” model but this model is now supplanted by a more complex view of pant immunity. Disease resistance genes appear to work together in intricate networks that enable plants to detect and resist parasites more effectively. An in-depth understanding of the immune system can help us breed disease resistant crops.

 

Chih-Hang Wu, Lida Derevnina, Sophien Kamoun. 2018. Receptor networks underpin plant immunity. Science, 360:1300-1301.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

Phytopathology: A new resistance gene in combination with Rmg8 confers strong resistance against Triticum isolates of Pyricularia oryzae in a common wheat landrace (2018)

Phytopathology: A new resistance gene in combination with Rmg8 confers strong resistance against Triticum isolates of Pyricularia oryzae in a common wheat landrace (2018) | Publications | Scoop.it

The wheat blast fungus (Triticum pathotype of Pyricularia oryzae) first arose in Brazil in 1985 and has recently spread to Asia. Resistance genes against this new pathogen are very rare in common wheat populations. We screened 520 local landraces of common wheat collected worldwide with Br48, a Triticum isolate collected in Brazil, and found a highly resistant, unique accession, GR119. When F2 seedlings derived from a cross between GR119 and Chinese Spring (CS, susceptible control) were inoculated with Br48, resistant and susceptible seedlings segregated in a 15:1 ratio, suggesting that GR119 carries two resistance genes. When the F2 seedlings were inoculated with Br48△A8 carrying a disrupted allele of AVR-Rmg8 (an avirulence gene corresponding to a previously reported resistance gene, Rmg8), however, the segregation fitted a 3:1 ratio. These results suggest that one of the two genes in GR119 was Rmg8. The other, new gene was tentatively designated as RmgGR119. GR119 was highly resistant to all Triticum isolates tested. Spikes of GR119 were highly resistant to Br48, moderately resistant to Br48△A8 and a hybrid culture carrying avr-Rmg8 (nonfunctional allele), and highly resistant to its transformant carrying AVR-Rmg8. The strong resistance of GR119 was attributed to the combined effects of Rmg8 and RmgGR119.


Via The Sainsbury Lab, Kamoun Lab @ TSL
more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Publications from The Sainsbury Laboratory
Scoop.it!

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.

Via The Sainsbury Lab
more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

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.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.
 
more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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?

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plant Pathogenomics
Scoop.it!

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.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

Talking Biotech: Winning the disease resistance 'arms race' against plant pathogens to ensure food security (2018)

Talking Biotech: Winning the disease resistance 'arms race' against plant pathogens to ensure food security (2018) | Publications | Scoop.it

Plant disease resistance is a complicated arms race between the plant and pathogens. Bacteria, viruses and fungi evolve in lock-step with plants, creating new ways to overcome new disease resistance strategies. Resistance to disease has a foundation in the gene-for-gene model, a model that hypothesizes that plants and pathogens have a molecular relationship with each other that mediates pathogenicity.

 

Today’s podcast features Drs. Lida Derevnina and Chih-Hang Wu, postdoctoral researchers with Sophien Kamoun (@KamounLab) at the Sainsbury Laboratory (@TheSainsburyLab) in Norwich, England. They describe the new thinking of disease resistance as a number of complex layers that integrates many gene-for-gene interactions with other mechanisms in mediating plant defense.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

Annual Reviews of Phytopathology: CRISPR Crops: Plant Genome Editing Toward Disease Resistance (2018)

Annual Reviews of Phytopathology: CRISPR Crops: Plant Genome Editing Toward Disease Resistance (2018) | Publications | Scoop.it

Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.


Via The Sainsbury Lab, Kamoun Lab @ TSL
more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plant Pathogenomics
Scoop.it!

BMC Series blog: Phenotypic plasticity in a pandemic lineage of the Irish potato famine pathogen (2018)

BMC Series blog: Phenotypic plasticity in a pandemic lineage of the Irish potato famine pathogen (2018) | Publications | Scoop.it

What did you find?

We studied two different races of the Irish potato famine pathogen, and we discovered that the difference invirulence between these races could not be ascribed to a genetic difference but rather to a difference in the expression of the underlying virulence gene. This adds to our knowledge of how this important scourge on world agriculture evolves to evade plant immunity.

 

Why is this work important?

As our colleague Mark Gijzen tweeted, “is this a rare and unusual curiosity or another example of a widespread biological phenomenon?” Indeed, there are few other examples in related plant pathogens, including the soybean root rot pathogen that Mark studies. This finding has far reaching implications. It indicates that these pathogens can evolve even more rapidly than anticipated thus counteracting the efforts of plant breeders to deploy disease resistant crops.

 

Are potato varieties resistant to the pathogen available?

Yes, there are. But there are several examples of potato cultivars that were initially resistant to late blight when farmers started to grow them, but succumbed to the disease a few years later. The ability to switch on and off virulence genes such as we found in this research may partly explain why the pathogen is so effective at overcoming the plants defense barriers.

 

What is currently done to control the disease?

Susceptible potato cultivars must be protected by repeated applications of fungicides. If left unchecked, the disease will destroy the leaves and stems in a matter of days as in the pictured trial plot of potato varieties in the highlands of Peru.

 

Is chemical protection the only way to control late blight?

In nature, there are wild relatives of the cultivated potato and many of them can withstand the disease (see image of potato variety field trial). Breeders identify the genes in these plants and introduce them to cultivated potato through crosses or genetic transformation.

 

How did you put this project together?

We studied an Andean lineage of the Irish potato famine pathogen known as EC-1 so the project had an international flavor from day one. Ours was a wide reaching multinational collaboration bringing together scientists based in the UK, Japan, Netherlands, USA, Philippines, and Peru. It’s how science often goes on these days. Experts from all over the world team up to solve problems, make new discoveries and advance our knowledge.

 

Anything you would have done differently?

DNA sequencing technology develops so fast that by the time the paper gets published you wish you could apply a different method. It also takes more time to analyze the data, write up the paper etc. than to generate the sequence data. This can be frustrating.

 

You posted the paper in bioRxiv before submission. Why?

Why not? Posting the article on bioRxiv enabled us to share our findings with our colleagues and hear about it from the community as soon as possible. The tweet by Mark Gijzen we referred to above is an example of such feedback. Posting a preprint relieves some of the delays associated with publishing. It’s a liberating feeling to finish writing up a paper and immediately share it with anyone who’s interested.

 

Authors

 

Dr. Vivianne Vleeshouwers is assistant professor in Wageningen University & Research, the Netherlands. Her research is dedicated to understand the molecular interaction between the potato late blight pathogen Phytophthora infestans and potato, and exploit this knowledge to achieve a better and more durable disease resistance.

 

Dr. Hannele Lindqvist-Kreuze works as a Molecular Breeder at the International Potato Center (CIP) in Lima, Peru. Her current work focuses on the discovery and application of molecular markers in the potato and sweet potato breeding programs of CIP. She describes her work as a Haiku: Searching for Hidden Patterns, Coded in the DNA, Unknowingly selected.

 

Dr. Sophien Kamoun is a Senior Scientist at The Sainsbury Laboratory and a Professor of Biology at the University of East Anglia in Norwich, UK. He studies the interactions between plants and filamentous pathogens, notably the Irish potato famine pathogen and the rice and wheat blast fungus. He’s known for saying “Don’t bet against the pathogen.”

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

eLife: Host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen (2018)

eLife: Host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen (2018) | Publications | Scoop.it

During plant cell invasion, the oomycete Phytophthora infestans remains enveloped by host-derived membranes whose functional properties are poorly understood. P. infestans secretes a myriad of effector proteins through these interfaces for plant colonization. Recently we showed that the effector protein PexRD54 reprograms host-selective autophagy by antagonising antimicrobial-autophagy receptor Joka2/NBR1 for ATG8CL binding (Dagdas, 2016). Here, we show that during infection, ATG8CL/Joka2 labelled defense-related autophagosomes are diverted toward the perimicrobial host membrane to restrict pathogen growth. PexRD54 also localizes to autophagosomes across the perimicrobial membrane, consistent with the view that the pathogen remodels host-microbe interface by co-opting the host autophagy machinery. Furthermore, we show that the host-pathogen interface is a hotspot for autophagosome biogenesis. Notably, overexpression of the early autophagosome biogenesis protein ATG9 enhances plant immunity. Our results implicate selective autophagy in polarized immune responses of plants and point to more complex functions for autophagy than the widely known degradative roles.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

Science: Receptor networks underpin plant immunity (2018)

Science: Receptor networks underpin plant immunity (2018) | Publications | Scoop.it

Plants are attacked by a multitude of pathogens and pests, some of which cause epidemics that threaten food security. Yet a fundamental concept in plant pathology is that most plants are actively resistant to most pathogens and pests. Plants fend off their innumerable biotic foes primarily through innate immune receptors that detect the invading pathogens and trigger a robust immune response. The conceptual basis of such interactions was elegantly articulated by Harold H. Flor, who, in 1942, proposed the hypothesis that single genes in plants and pathogens define the outcome of their interactions; that is, a plant harboring a specific gene displays resistance against a pathogen that carries an interacting virulence gene (1). This gene-for-gene model was hugely insightful and influential—it has helped to guide applied and basic research on disease resistance. However, recent findings are taking the field beyond this simplified binary view of plant-pathogen interactions. Plants carry extremely diverse and dynamic repertoires of immune receptors that are interconnected in complex ways. Conversely, plant pathogens secrete a diversity of virulence proteins and metabolites called effectors, and pathogen genomics has revealed hundreds of effector genes in many species. These effectors have evidently evolved to favor pathogen infection and spread, but a subset of them inadvertently activate plant immune receptors. The emerging paradigm is that dynamic webs of genetic and biochemical networks underpin the early stages of plant-pathogen interactions.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Publications from The Sainsbury Laboratory
Scoop.it!

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.


Via The Sainsbury Lab
more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Publications from The Sainsbury Laboratory
Scoop.it!

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.


Via The Sainsbury Lab
more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plants and Microbes
Scoop.it!

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.

Via The Sainsbury Lab, Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.
 
more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

 

more...
No comment yet.