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BMC Genomics (2016): Comparative genomics of Beauveria bassiana : uncovering signatures of virulence against mosquitoes

BMC Genomics (2016): Comparative genomics of Beauveria bassiana : uncovering signatures of virulence against mosquitoes | WU_Phyto-Publications | Scoop.it

Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence.

A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85–16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1–1–1 or the MAT1–2–1 gene. Moreover, a putative new MAT gene (MAT1-2–8) was detected in the MAT1–2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented.

Our results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.

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PLoS Pathogens (2016): Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens

PLoS Pathogens (2016): Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens | WU_Phyto-Publications | Scoop.it
An organism’s adaptation to changing environments is fueled by its genetic variability, which is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale structural variations, all of which affect chromosomal shape, organization, and gene content [1]. These processes are particularly relevant for pathogens that must respond to continual selection pressure arising from host immune systems that evolved to detect the presence or activity of potential microbial pathogens through a variety of invasion patterns [2]. In their adaptive response, pathogens evolve strategies, often involving secreted effector molecules, to overcome host immunity and support host colonization [3]. Thus, it can be anticipated that this coevolutionary arms race leads to highly specific interactions between adapted pathogens and their specific hosts. Paradoxically, particular pathogens successfully colonize a broad range of hosts, yet how such pathogens cope in arms races with such a diversity of hosts remains unknown.
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Cellular and Molecular Life Sciences: Filamentous actin accumulates during plant cell penetration and cell wall plug formation in Phytophthora infestans

Cellular and Molecular Life Sciences: Filamentous actin accumulates during plant cell penetration and cell wall plug formation in Phytophthora infestans | WU_Phyto-Publications | Scoop.it
The oomycete Phytophthora infestans is the cause of late blight in potato and tomato. It is a devastating pathogen and there is an urgent need to design alternative strategies to control the disease. To find novel potential drug targets, we used Lifeact-eGFP expressing P. infestans for high resolution live cell imaging of the actin cytoskeleton in various developmental stages. Previously, we identified actin plaques as structures that are unique for oomycetes. Here we describe two additional novel actin configurations; one associated with plug deposition in germ tubes and the other with appressoria, infection structures formed prior to host cell penetration. Plugs are composed of cell wall material that is deposited in hyphae emerging from cysts to seal off the cytoplasm-depleted base after cytoplasm retraction towards the growing tip. Preceding plug formation there was a typical local actin accumulation and during plug deposition actin remained associated with the leading edge. In appressoria, formed either on an artificial surface or upon contact with plant cells, we observed a novel aster-like actin configuration that was localized at the contact point with the surface. Our findings strongly suggest a role for the actin cytoskeleton in plug formation and plant cell penetration.
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New Phytologist (2016): Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity

New Phytologist (2016): Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity | WU_Phyto-Publications | Scoop.it
All filamentous microbes produce and release a wide range of glycans, which are essential determinants of microbe–microbe and microbe–host interactions. Major cell wall constituents, such as chitin and β-glucans, are elicitors of host immune responses. The widespread capacity for glycan perception in plants has driven the evolution of various strategies that help filamentous microbes to evade detection. Common strategies include structural and chemical modifications of cell wall components as well as the secretion of effector proteins that suppress chitin- and β-glucan-triggered immune responses. Thus, the necessity to avoid glycan-triggered immunity represents a driving force in the convergent evolution of filamentous microbes towards its suppression.
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PLoS Genetics (2016): Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis ) Genomes Reveal Clues for Disease C...

PLoS Genetics (2016): Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen  Pseudocercospora fijiensis  (Synonym  Mycosphaerella fijiensis ) Genomes Reveal Clues for Disease C... | WU_Phyto-Publications | Scoop.it

Black Sigatoka or black leaf streak disease, caused by the ascomycete fungus Pseudocercospora fijiensis , inflicts huge costs on banana producers, due to crop losses and expenses for disease control. The global banana export trade relies on Cavendish clones that are highly susceptible to P . fijiensis . Sustainable production of the world’s number one fruit requires a better understanding of host resistance and sophisticated management of fungicide resistance in the pathogen. In the P . fijiensis genome sequence we identified an effector that induced an HR-like necrosis on a resistant banana accession but not on a susceptible cultivar. If validated, this assay may be useful for identifying resistance in banana breeding programs. We also used the genomic sequence to develop highly polymorphic molecular markers for analyzing P . fijiensis field populations and identified a strong enrichment (nearly 100%) for fungicide resistance markers in fungicide-treated banana plantations compared to untreated wild-type populations. This rapid evolution of fungicide resistance poses an immediate threat to sustainable banana production.

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Genome Research (2016): Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

Genome Research (2016): Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen | WU_Phyto-Publications | Scoop.it

Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in 'arms races' with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.

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Molecular Plant Pathology (2016): A gapless genome sequence of the fungus Botrytis cinerea 

Molecular Plant Pathology (2016): A gapless genome sequence of the fungus Botrytis cinerea  | WU_Phyto-Publications | Scoop.it
Following earlier incomplete and fragmented versions of a genome sequence for the grey mould Botrytis cinerea, we here report a gapless, near-finished genome sequence for B. cinerea strain B05.10. The assembly comprises 18 chromosomes and was confirmed by an optical map and a genetic map based on ∼75 000 SNP markers. All chromosomes contain fully assembled centromeric regions, and 10 chromosomes have telomeres on both ends. The genetic map consisted of 4153 cM and comparison of genetic distances with the physical distances identified 40 recombination hotspots. The linkage map also identified two mutations, located in the previously described genes Bos1 and BcsdhB, that confer resistance to the fungicides boscalid and iprodione.

The genome was predicted to encode 11 701 proteins. RNAseq data from >20 different samples were used to validate and improve gene models. Manual curation of chromosome 1 revealed interesting features, such as the occurrence of a dicistronic transcript and fully overlapping genes in opposite orientations, as well as many spliced antisense transcripts. Manual curation also revealed that UTRs of genes can be complex and long, with many UTRs exceeding lengths of 1 kb and possessing multiple introns. Community annotation is in progress. This article is protected by copyright. All rights reserved.
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Annual Review of Phytopathology (2016): Cladosporium fulvum Effectors: Weapons in the Arms Race with Tomato

Annual Review of Phytopathology (2016): Cladosporium fulvum Effectors: Weapons in the Arms Race with Tomato | WU_Phyto-Publications | Scoop.it
In this review, I recount my personal history. My drive to study host-pathogen interactions was to find alternatives for agrochemicals, which was triggered after reading the book “Silent Spring” by Rachel Carson. I reflect on my research at the Laboratory of Phytopathology at Wageningen University, where I have worked for my entire career on the interaction between Cladosporium fulvum and tomato, and related gene-for-gene pathosystems. I describe different methods used to identify and sequence avirulence (Avr) genes from the pathogen and resistance (R) genes from the host. The major genes involved in classical gene-for-gene interactions have now been identified, and breeders can produce plants with multiple R genes providing durable and environmentally safe protection against pathogens. In some cases, this might require the use of genetically modified plants when R genes cannot be introduced by classical breeding.
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Frontiers in Plant Sciences (2016): Analysis of Cryptic, Systemic Botrytis Infections in Symptomless Hosts

Frontiers in Plant Sciences (2016): Analysis of Cryptic, Systemic Botrytis Infections in Symptomless Hosts | WU_Phyto-Publications | Scoop.it
Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. B. cinerea and B. pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents) when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles.
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Frontiers in Microbiology (2016): Bcmimp1, a Botrytis cinerea Gene Transiently Expressed in planta, Encodes a Mitochondrial Protein

Frontiers in Microbiology (2016): Bcmimp1, a Botrytis cinerea Gene Transiently Expressed in planta, Encodes a Mitochondrial Protein | WU_Phyto-Publications | Scoop.it
Botrytis cinerea is a widespread necrotrophic fungus which infects more than 200 plant species. In an attempt to characterize the physiological status of the fungus in planta and to identify genetic factors contributing to its ability to infect the host cells, a differential gene expression analysis during the interaction B. cinerea-tomato was carried out. Gene Bcmimp1 codes for a mRNA detected by differential display in the course of this analysis. During the interaction with the host, it shows a transient expression pattern with maximal expression levels during the colonization and maceration of the infected tissues. Bioinformatic analysis suggested that BCMIMP1 is an integral membrane protein located in the mitochondrial inner membrane. Co-localization experiments with a BCMIMP1-GFP fusion protein confirmed that the protein is targeted to the mitochondria. ΔBcmimp1 mutants do not show obvious phenotypic differences during saprophytic growth and their infection ability was unaltered as compared to the wild-type. Interestingly, the mutants produced increased levels of reactive oxygen species, likely as a consequence of disturbed mitochondrial function. Although Bcmimp1 expression is enhanced in planta it cannot be considered a pathogenicity factor.
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Phytopathology (2016): The age of effectors: genome-based discovery and applications

Phytopathology (2016): The age of effectors: genome-based discovery and applications | WU_Phyto-Publications | Scoop.it
Microbial pathogens cause devastating diseases on economically and ecologically important plant species, threatening global food security, and causing billions of dollars of losses annually. During the infection process, pathogens secrete so-called effectors that support host colonization, often by deregulating host immune responses. Over the last decades, much of the research on molecular plant-microbe interactions has focused on the identification and functional characterization of such effectors. The increasing availability of sequenced plant pathogen genomes has enabled genomics-based discovery of effector candidates. Nevertheless, identification of full plant pathogen effector repertoires is often hampered by erroneous gene annotation and the localization effector genes in genomic regions that are notoriously difficult to assemble. Here, we argue that recent advances in genome sequencing technologies, genome assembly, gene annotation, as well as effector identification methods hold promise to disclose complete and correct effector repertoires. This allows to exploit complete effector repertoires, and knowledge of their diversity within pathogen populations, to develop durable and sustainable resistance breeding strategies, disease control and management of plant pathogens.
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Plant Pathology (2016): Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi

Plant Pathology (2016): Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi | WU_Phyto-Publications | Scoop.it
Soybean is a major source of oil and proteins worldwide. The demand for soybean has increased in Africa, driven by the growing feed industry for poultry, aquaculture and home consumption in the form of processed milk, baked beans and for blending with maize and wheat flour. Soybean, in addition to being a major source of cooking oil, is also used in other industrial processes such as in the production of paints and candle wax. The demand for soybean in Africa so far outweighs the supply, hence the deficit is mainly covered through imports of soybean products such as soybean meal. The area under soybean production has increased in response to the growing demand, a trend that is expected to continue in the coming years. As the production area increases, diseases and insect pests, declining soil fertility and other abiotic factors pose a major challenge. Soybean rust disease, caused by the fungus Phakopsora pachyrhizi, presents one of the major threats to soybean production in Africa due to its rapid spread as a result of the ease by which its spores are dispersed by the wind. Disease control by introducing resistant soybean varieties has been difficult due to the presence of different populations of the fungus that vary in pathogenicity, virulence and genetic composition. Improved understanding of the dynamics of rust ecology, epidemiology and population genetics will enhance the effectiveness of targeted interventions that, in turn, will safeguard soybean productivity.
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Journal of Microscopy (2016): Interaction between the moss Physcomitrella patens and Phytophthora: a novel pathosystem for live-cell imaging of subcellular defence  

Journal of Microscopy (2016): Interaction between the moss Physcomitrella patens and Phytophthora: a novel pathosystem for live-cell imaging of subcellular defence   | WU_Phyto-Publications | Scoop.it
Live-cell imaging of plant–pathogen interactions is often hampered by the tissue complexity and multicell layered nature of the host. Here, we established a novel pathosystem with the moss Physcomitrella patens as host for Phytophthora. The tip-growing protonema cells of this moss are ideal for visualizing interactions with the pathogen over time using high-resolution microscopy. We tested four Phytophthora species for their ability to infect P. patens and showed that P. sojae and P. palmivora were only rarely capable to infect P. patens. In contrast, P. infestans and P. capsici frequently and successfully penetrated moss protonemal cells, showed intracellular hyphal growth and formed sporangia. Next to these successful invasions, many penetration attempts failed. Here the pathogen was blocked by a barrier of cell wall material deposited in papilla-like structures, a defence response that is common in higher plants. Another common response is the upregulation of defence-related genes upon infection and also in moss we observed this upregulation in tissues infected with Phytophthora. For more advanced analyses of the novel pathosystem we developed a special set-up that allowed live-cell imaging of subcellular defence processes by high-resolution microscopy. With this set-up, we revealed that Phytophthora infection of moss induces repositioning of the nucleus, accumulation of cytoplasm and rearrangement of the actin cytoskeleton, but not of microtubules.
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Molecular Plant Pathology (2016): Host-induced gene silencing compromises Verticillium wilt in tomato and Arabidopsis

Molecular Plant Pathology (2016): Host-induced gene silencing compromises Verticillium wilt in tomato and Arabidopsis | WU_Phyto-Publications | Scoop.it
Verticillium wilt, caused by soil-borne fungi of the genus Verticillium, is an economically important disease that affects a wide range of host plants. Unfortunately, host resistance against Verticillium wilts is not available for many plant species, and the disease is notoriously difficult to combat. Host-induced gene silencing (HIGS) is an RNA interference (RNAi) based process in which small RNAs are produced by the host plant to target parasite transcripts. HIGS has emerged as a promising strategy for improving plant resistance against pathogens by silencing genes that are essential for these pathogens. Here, we assessed whether HIGS can be utilized to suppress Verticillium wilt disease by silencing three previously identified virulence genes of V. dahliae (encoding Ave1, Sge1 and NLP1) through the host plants tomato and Arabidopsis. In transient assays, tomato plants were agroinfiltrated with Tobacco rattle virus (TRV) constructs to target V. dahliae transcripts. Subsequent V. dahliae inoculation revealed suppression of Verticillium wilt disease upon treatment only with one of the three TRV constructs. Next, expression of RNAi constructs targeting transcripts of the same three V. dahliae virulence genes was pursued in stable transgenic Arabidopsis thaliana plants. In this host, V. dahliae inoculation revealed reduced Verticillium wilt disease in for two out of three targets. Thus, our study suggests that, depending on the target gene chosen, HIGS against V. dahliae is operational in tomato and A. thaliana plants and may be exploited to engineer resistance in Verticillium wilt-susceptible crops. This article is protected by copyright. All rights reserved.
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Frontiers in Plant Sciences (2016): Role of the GacS Sensor Kinase in the Regulation of Volatile Production by Plant Growth-Promoting Pseudomonas fluorescens SBW25

Frontiers in Plant Sciences (2016): Role of the GacS Sensor Kinase in the Regulation of Volatile Production by Plant Growth-Promoting Pseudomonas fluorescens SBW25 | WU_Phyto-Publications | Scoop.it
In plant-associated Pseudomonas species, the production of several secondary metabolites and exoenzymes is regulated by the GacS/GacA two-component regulatory system (the Gac-system). Here, we investigated if a mutation in the GacS sensor kinase affects the production of volatile organic compounds (VOCs) in P. fluorescens SBW25 (Pf.SBW25) and how this impacts on VOCs-mediated growth promotion and induced systemic resistance of Arabidopsis and tobacco. A total of 205 VOCs were detected by Gas Chromatography Mass Spectrometry for Pf. SBW25 and the gacS-mutant grown on two different media for 3 and 6 days. Discriminant function analysis followed by hierarchical clustering revealed 24 VOCs that were significantly different in their abundance between Pf.SBW25 and the gacS-mutant, which included three acyclic alkenes (3-nonene, 4-undecyne, 1-undecene). These alkenes were significantly reduced by the gacS mutation independently of the growth media and of the incubation time. For Arabidopsis, both Pf.SBW25 and the gacS-mutant enhanced, via VOCs, root and shoot biomass, induced systemic resistance against leaf infections by P. syringae and rhizosphere acidification to the same extent. For tobacco, however, VOCs-mediated effects on shoot and root growth were significantly different between Pf.SBW25 and the gacS-mutant. While Pf.SBW25 inhibited tobacco root growth, the gacS-mutant enhanced root biomass and lateral root formation relative to the non-treated control plants. Collectively these results indicate that the sensor kinase GacS is involved in the regulation of VOCs production in Pf.SBW25, affecting plant growth in a plant species-dependent manner.
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PhD thesis Xu Cheng (2016): Plant growth promotion by Pseudomonas fluorescens : mechanisms, genes and regulation

PhD thesis Xu Cheng (2016): Plant growth promotion by Pseudomonas fluorescens : mechanisms, genes and regulation | WU_Phyto-Publications | Scoop.it
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New Phytologist (2016): Apoplastic fungal effectors in historic perspective

New Phytologist (2016): Apoplastic fungal effectors in historic perspective | WU_Phyto-Publications | Scoop.it
Soon after the gene-for-gene hypothesis was formulated in the 1940s, the search for the postulated gene products started. The hypothesis proposed that products of fungal avirulence (Avr) genes induce defense responses in plants, after recognition by matching resistance (R) gene-encoded proteins, often associated with a hypersensitive response (HR) effective against (obligate) biotrophic fungal pathogens. Here, I present a short overview of this research over the last 40 yr, which has led to new paradigms and terms, including nonspecific and race-specific elicitors, microbe-associated molecular patterns (MAMPs), MAMP-triggered immunity, effectors, effector-triggered susceptibility (ETS), effector-triggered immunity (ETI), biotrophic and necrotrophic effectors and the inverse gene-for-gene or matching allele hypothesis. The molecular arms race between plants and pathogenic fungi is now well understood, and biotrophic and necrotrophic effectors are exploited in plant disease resistance breeding, which presently occurs on science-based strategies, making agriculture more sustainable and less dependent on agrochemicals. Next-generation sequencing has accelerated the discovery of new types of effector, including secondary metabolite effectors and small RNAs derived from noncoding fungal genome sequences, which suppress basal plant defense responses. The identification of the biological functions of effectors remains a challenge that requires new technologies, including gene silencing and gene editing using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats)-CRISPR-associated protein 9) technology.
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Molecular Plant Pathology (2016): The Arabidopsis thaliana lectin receptor kinase LecRK-I.9 is required for full resistance to Pseudomonas syringae and affects jasmonate signalling

Molecular Plant Pathology (2016): The Arabidopsis thaliana lectin receptor kinase LecRK-I.9 is required for full resistance to Pseudomonas syringae and affects jasmonate signalling | WU_Phyto-Publications | Scoop.it
Upon microbial attack, plants can detect the invaders and activate the plant innate immunity system. For detecting pathogen molecules or cell wall damage, plants employ receptors that trigger the activation of defence responses. Cell surface proteins that belong to large families of lectin receptor kinases are candidates to function as immune receptors. Here the function of LecRK-I.9 (At5g60300), a legume-type lectin receptor kinase involved in cell wall – plasma membrane contacts and in eATP perception, was studied through biochemical, gene expression and reverse genetics approaches. In Arabidopsis thaliana, LecRK-I.9 expression is rapidly, highly and locally induced upon inoculation with avirulent strains of Pseudomonas syringae pv. tomato (Pst). Two allelic lecrk-I.9 knock-out mutants showed decreased resistance to Pst. Conversely, over-expression of LecRK-I.9 led to increased resistance to Pst. Analysis of defence gene expression suggests an alteration of both the salicylic acid (SA) and the jasmonic acid (JA) signalling pathways. In particular, LecRK-I.9 expression during the plant-pathogen interaction was dependent on COI-1 and JAR-1 components and JA-responsive transcription factors (TFs) showed altered levels of expression in plants over-expressing LecRK-I.9. A similar misregulation of these TFs was obtained by JA treatment. This study identified LecRK-I.9 as necessary for full resistance to Pst and pointed out its involvement in the control of defence towards pathogens through a regulation of JA signalling components. The role of LecRK-I.9 is discussed with regard to the potential molecular mechanisms linking JA signalling to cell wall damages and/or eATP perception
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PhD thesis Yiying Liu (2016): The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia

PhD thesis Yiying Liu (2016): The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia | WU_Phyto-Publications | Scoop.it
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Fungal Genetics and Biology (2016): RNA-sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction

Fungal Genetics and Biology (2016): RNA-sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction | WU_Phyto-Publications | Scoop.it
Cercospora beticola causes Cercospora leaf spot of sugar beet. Cercospora leaf spot management measures often include application of the sterol demethylation inhibitor (DMI) class of fungicides. The reliance on DMIs and the consequent selection pressures imposed by their widespread use has led to the emergence of resistance in C. beticola populations. Insight into the molecular basis of tetraconazole resistance may lead to molecular tools to identify DMI-resistant strains for fungicide resistance management programs. Previous work has shown that expression of the gene encoding the DMI target enzyme (CYP51) is generally higher and inducible in DMI-resistant C. beticola field strains. In this study, we extended the molecular basis of DMI resistance in this pathosystem by profiling the transcriptional response of two C. beticola strains contrasting for resistance to tetraconazole. A majority of the genes in the ergosterol biosynthesis pathway were induced to similar levels in both strains with the exception of CbCyp51, which was induced several-fold higher in the DMI-resistant strain. In contrast, a secondary metabolite gene cluster was induced in the resistance strain, but repressed in the sensitive strain. Genes encoding proteins with various cell membrane fortification processes were induced in the resistance strain. Site-directed and ectopic mutants of candidate DMI-resistance genes all resulted in significantly higher EC50 values than the wild-type strain, suggesting that the cell wall and/or membrane modified as a result of the transformation process increased resistance to tetraconazole. Taken together, this study identifies important cell membrane components and provides insight into the molecular events underlying DMI resistance in C. beticola.
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Molecular Plant Pathology (2016): Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae

Molecular Plant Pathology (2016): Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae | WU_Phyto-Publications | Scoop.it
The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so-called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules such as glycans, has been less appreciated. Here we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae that causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide-sugar precursor formation as it encodes a putative nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in biosysnthesis of the nucleotide sugar dTDP-rhamnose, a precursor of L-rhamnose that was shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known as a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal-host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and N. benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of UDP-rhamnose, and further analysis revealed that VdNRS/ER deletion strains are impaired in colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only being a minor cell wall component, is essential for pathogenicity of V. dahliae. This article is protected by copyright. All rights reserved.
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Journal of Experimental Botany (2016): Transcriptional regulation of receptor-like protein genes by environmental stresses and hormones and their overexpression activities in Arabidopsis thaliana

Journal of Experimental Botany (2016): Transcriptional regulation of receptor-like protein genes by environmental stresses and hormones and their overexpression activities in Arabidopsis thaliana | WU_Phyto-Publications | Scoop.it
Receptor-like proteins (RLPs) have been implicated in multiple biological processes, including plant development and immunity to microbial infection. Fifty-seven AtRLP genes have been identified in Arabidopsis, whereas only a few have been functionally characterized. This is due to the lack of suitable physiological screening conditions and the high degree of functional redundancy among AtRLP genes. To overcome the functional redundancy and further understand the role of AtRLP genes, we studied the evolution of AtRLP genes and compiled a comprehensive profile of the transcriptional regulation of AtRLP genes upon exposure to a range of environmental stresses and different hormones. These results indicate that the majority of AtRLP genes are differentially expressed under various conditions that were tested, an observation that will help to select certain AtRLP genes involved in a specific biological process for further experimental studies to eventually dissect their function. A large number of AtRLP genes were found to respond to more than one treatment, suggesting that one single AtRLP gene may be involved in multiple physiological processes. In addition, we performed a genome-wide cloning of the AtRLP genes, and generated and characterized transgenic Arabidopsis plants overexpressing the individual AtRLP genes, presenting new insight into the roles of AtRLP genes, as exemplified by AtRLP3, AtRLP11 and AtRLP28. Our study provides an overview of biological processes in which AtRLP genes may be involved, and presents valuable resources for future investigations into the function of these genes.
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Molecular Microbiology (2016): A novel Zn2Cys6 transcription factor BcGaaR regulates D-galacturonic acid utilization in Botrytis cinerea

Molecular Microbiology (2016): A novel Zn2Cys6 transcription factor BcGaaR regulates D-galacturonic acid utilization in Botrytis cinerea | WU_Phyto-Publications | Scoop.it
D-galacturonic acid (GalA) is the most abundant monosaccharide component of pectin. Previous transcriptome analysis in the plant pathogenic fungus Botrytis cinerea identified eight GalA-inducible genes involved in pectin decomposition, GalA transport and utilization. Co-expression of these genes indicates that a specific regulatory mechanism occurs in B. cinerea. In this study, promoter regions of these genes were analysed and eight conserved sequence motifs identified. The Bclga1 promoter, containing all these motifs, was functionally analysed and the motif designated GalA Responsive Element (GARE) was identified as the crucial cis-regulatory element in regulation of GalA utilization in B. cinerea. Yeast one-hybrid screening with the GARE motif led to identification of a novel Zn2Cys6 transcription factor (TF), designated BcGaaR. Targeted knockout analysis revealed that BcGaaR is required for induction of GalA-inducible genes and growth of B. cinerea on GalA. A BcGaaR-GFP fusion protein was predominantly localized in nuclei in mycelium grown in GalA. Fluorescence in nuclei was much stronger in mycelium grown in GalA, as compared to fructose and glucose. This study provides the first report of a GalA-specific TF in filamentous fungi. Orthologs of BcGaaR are present in other ascomycete fungi that are able to utilize GalA, including Aspergillus spp., Trichoderma reesei and Neurospora crassa.
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Plant Disease (2016): First report of Neonectria candida causing postharvest decay on ‘Conference’ pears in the Netherlands 

Plant Disease (2016): First report of Neonectria candida causing postharvest decay on ‘Conference’ pears in the Netherlands  | WU_Phyto-Publications | Scoop.it
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Fungal Genetics and Biology (2016): Mind the gap; seven reasons to close fragmented genome assemblies

Fungal Genetics and Biology (2016): Mind the gap; seven reasons to close fragmented genome assemblies | WU_Phyto-Publications | Scoop.it
Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.
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