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Rescooped by Sociedad Española de Fitopatologia from Plants and Microbes
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Nature: Pathogens and insect herbivores drive rainforest plant diversity and composition (2014)

Nature: Pathogens and insect herbivores drive rainforest plant diversity and composition (2014) | SEFitopatologia | Scoop.it

Tropical forests are important reservoirs of biodiversity1, but the processes that maintain this diversity remain poorly understood2. The Janzen–Connell hypothesis3, 4 suggests that specialized natural enemies such as insect herbivores and fungal pathogens maintain high diversity by elevating mortality when plant species occur at high density (negative density dependence; NDD). NDD has been detected widely in tropical forests5, 6, 7, 8, 9, but the prediction that NDD caused by insects and pathogens has a community-wide role in maintaining tropical plant diversity remains untested. We show experimentally that changes in plant diversity and species composition are caused by fungal pathogens and insect herbivores. Effective plant species richness increased across the seed-to-seedling transition, corresponding to large changes in species composition5. Treating seeds and young seedlings with fungicides significantly reduced the diversity of the seedling assemblage, consistent with the Janzen–Connell hypothesis. Although suppressing insect herbivores using insecticides did not alter species diversity, it greatly increased seedling recruitment and caused a marked shift in seedling species composition. Overall, seedling recruitment was significantly reduced at high conspecific seed densities and this NDD was greatest for the species that were most abundant as seeds. Suppressing fungi reduced the negative effects of density on recruitment, confirming that the diversity-enhancing effect of fungi is mediated by NDD. Our study provides an overall test of the Janzen–Connell hypothesis and demonstrates the crucial role that insects and pathogens have both in structuring tropical plant communities and in maintaining their remarkable diversity.


Via Kamoun Lab @ TSL
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Rescooped by Sociedad Española de Fitopatologia from Pest risk analysis
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EU official measures to prevent the spread of Xylella fastidiosa

EU official measures to prevent the spread of Xylella fastidiosa | SEFitopatologia | Scoop.it

The European Union has banned the movement of some plants out of the Lecce, in Italy’s Apulia region, to help prevent the spread of the devastating disease which has already infected hundreds of olive trees there.

In a regulation published on Saturday, the EU also requires all its member states to start annual checks for the presence of the plant pathogen responsible, Xylella fastidiosa (Xf), and to report on their first such survey by the end of October.

 

EU 2014. COMMISSION IMPLEMENTING DECISION of 13 February 2014
as regards measures to prevent the spread within the Union of Xylella fastidiosa (Well and Raju) http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2014:045:0029:0033:EN:PDF


Via Muriel Suffert
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Muriel Suffert's curator insight, February 24, 2014 7:05 AM

Xylella fastidiosa was detected recently for the first time in Europe. It causes several diseases of economic importance: grapevine Pierce's disease; citrus variegated chlorosis; peach phony disease; plum leaf scald; as well as leaf scorch diseases on oleander, almond, coffee, pecan, and amenity tree species. For background information, see http://www.eppo.int/QUARANTINE/special_topics/Xylella_fastidiosa/Xylella_fastidiosa.htm

See also http://sco.lt/9BrN9l

Rescooped by Sociedad Española de Fitopatologia from Plant Pathogenomics
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PLOS Genetics: Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade (2013)

PLOS Genetics: Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade (2013) | SEFitopatologia | Scoop.it

Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms.


Via Kamoun Lab @ TSL
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Rescooped by Sociedad Española de Fitopatologia from Plant Pathogenomics
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Nature Communications: The evolution and pathogenic mechanisms of the rice sheath blight pathogen (2013)

Nature Communications: The evolution and pathogenic mechanisms of the rice sheath blight pathogen (2013) | SEFitopatologia | Scoop.it

Rhizoctonia solani is a major fungal pathogen of rice (Oryza sativa L.) that causes great yield losses in all rice-growing regions of the world. Here we report the draft genome sequence of the rice sheath blight disease pathogen, R. solani AG1 IA, assembled using next-generation Illumina Genome Analyser sequencing technologies. The genome encodes a large and diverse set of secreted proteins, enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, which probably reflect an exclusive necrotrophic lifestyle. We find few repetitive elements, a closer relationship to Agaricomycotina among Basidiomycetes, and expand protein domains and families. Among the 25 candidate pathogen effectors identified according to their functionality and evolution, we validate 3 that trigger crop defence responses; hence we reveal the exclusive expression patterns of the pathogenic determinants during host infection.


Via Kamoun Lab @ TSL
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Rescooped by Sociedad Española de Fitopatologia from Plant Pathogenomics
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Eukaryotic Cell: Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution (2012)

Eukaryotic Cell: Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution (2012) | SEFitopatologia | Scoop.it

The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments, and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer, in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.


Via IPM Lab, Kamoun Lab @ TSL
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Rescooped by Sociedad Española de Fitopatologia from Plant Pathogenomics
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PLOS Pathogens: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi (2012)

PLOS Pathogens: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi (2012) | SEFitopatologia | Scoop.it

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.


Via Kamoun Lab @ TSL
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Revenge of the Weeds | The Scientist Magazine®

Revenge of the Weeds  | The Scientist Magazine® | SEFitopatologia | Scoop.it
Plant pests are evolving to outsmart common herbicides, costing farmers crops and money.
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Rescooped by Sociedad Española de Fitopatologia from Pest risk analysis
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EFSA Scientific Opinion: Xanthomonas citri pv. citri and Xanthomonas citri pv. aurantifolii pest risk assessment

EFSA Scientific Opinion: Xanthomonas citri pv. citri and Xanthomonas citri pv. aurantifolii pest risk assessment | SEFitopatologia | Scoop.it

The Panel conducted a pest risk assessment for Xanthomonas campestris (all strains pathogenic to Citrus) for the EU territory and an assessment of the effectiveness of present EU requirements against Xanthomonas strains pathogenic to citrus. 

The strains of X. campestris pathogenic to citrus have been reclassified as four distinct infraspecific taxa within two species: X. citri and X. alfalfae. Only two pathovars (X. citri pv. citri and X. citri pv. aurantifolii) are responsible for the citrus bacterial canker that presents a major risk for the citrus industry in the EU.

The combined EU regulations have been shown to be effective in preventing the introduction of X. citri pv. citri or X. citri pv. aurantifolii in the EU, as no outbreaks of citrus canker in the EU territory have been reported.

 

EFSA 2014. Scientific Opinion on the risk to plant health of Xanthomonas citri pv. citri and Xanthomonas citri pv. aurantifolii for the EU territory. http://www.efsa.europa.eu/en/efsajournal/doc/3556.pdf

 


Via Muriel Suffert
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Muriel Suffert's curator insight, February 21, 2014 11:04 AM

The PRA was open for public consultation in summer 2013. A report of the outcome of this consultation is also available http://www.efsa.europa.eu/en/supporting/pub/554e.htm

Rescooped by Sociedad Española de Fitopatologia from Plant Pathogenomics
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PLOS Pathogens: Indifferent, Affectionate, or Deceitful: Lifestyles and Secretomes of Fungi (2012)

PLOS Pathogens: Indifferent, Affectionate, or Deceitful: Lifestyles and Secretomes of Fungi (2012) | SEFitopatologia | Scoop.it

Fungi occupy a myriad of niches. They can be free-living (indifferent) as saprophytes recycling nutrients in the natural environment and/or have a range of relationships (affectionate and deceitful) with insect, animal, or plant hosts. Interactions with plants can be a continuum and range from obligate biotrophy where fungi cannot be cultured outside living hosts to necrotrophy where fungi kill and live on released nutrients. Biotrophic fungi need to avoid or suppress defence responses. They include symbionts, which confer a benefit to the host, and pathogens, which can cause devastating diseases such as stem rust, which threatens production of wheat worldwide [1]. Mycorrhizae colonise roots of >80% of land plants and are symbiotic, increasing nitrogen and phosphorus uptake from the soil, while feeding on sugars from the host photosynthate. Secreted proteins are on the front line of host–fungal interactions, and a particular class, effectors, is a hot topic. Here, we examine a range of fungi and consider their complement of secreted proteins (secretome) and roles of effectors in fungal lifestyles.


Via Kamoun Lab @ TSL
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Mary Williams's curator insight, March 29, 2013 10:15 AM

Love the title!

 

 

Rescooped by Sociedad Española de Fitopatologia from Plant Pathogenomics
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Nucleic Acids Research: CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes (2012)

Nucleic Acids Research: CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes (2012) | SEFitopatologia | Scoop.it

In 2007, Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr/) was publicly open with 65 genomes corresponding to 58 fungal and Oomycete species. The CFGP provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since 2007, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants and 105 animals. In addition, the number of tools in Favorite increased to 27. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, several systematic platforms designed to support studies on selected gene families have been developed. Most of them are connected through Favorite to allow of sharing data across the platforms.


Via Kamoun Lab @ TSL
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BMC Genomics: Structure and evolution of barley powdery mildew effector candidates (2013)

BMC Genomics: Structure and evolution of barley powdery mildew effector candidates (2013) | SEFitopatologia | Scoop.it

Background - Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to suppress or avoid host immunity if it is to survive and cause disease.

 

Results - Here we characterise a superfamily predicted to be the full complement of Candidates for Secreted Effector Proteins (CSEPs) in the fungal barley powdery mildew parasite B. graminis f.sp. hordei. The 491 genes encoding these proteins constitute over 7% of this pathogen’s annotated genes and most were grouped into 72 families of up to 59 members. They were predominantly expressed in the intracellular feeding structures called haustoria, and proteins specifically associated with the haustoria were identified by large-scale mass spectrometry-based proteomics. There are two major types of effector families: one comprises shorter proteins (100–150 amino acids), with a high relative expression level in the haustoria and evidence of extensive diversifying selection between paralogs; the second type consists of longer proteins (300–400 amino acids), with lower levels of differential expression and evidence of purifying selection between paralogs. An analysis of the predicted protein structures underscores their overall similarity to known fungal effectors, but also highlights unexpected structural affinities to ribonucleases throughout the entire effector super-family. Candidate effector genes belonging to the same family are loosely clustered in the genome and are associated with repetitive DNA derived from retro-transposons.

 

Conclusions - We employed the full complement of genomic, transcriptomic and proteomic analyses as well as structural prediction methods to identify and characterize the members of the CSEPs superfamily in B. graminis f.sp. hordei. Based on relative intron position and the distribution of CSEPs with a ribonuclease-like domain in the phylogenetic tree we hypothesize that the associated genes originated from an ancestral gene, encoding a secreted ribonuclease, duplicated successively by repetitive DNA-driven processes and diversified during the evolution of the grass and cereal powdery mildew lineage.


Via Kamoun Lab @ TSL
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PLOS Pathogens: Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen (2012)

PLOS Pathogens: Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen (2012) | SEFitopatologia | Scoop.it

Pest and pathogen losses jeopardise global food security and ever since the 19th century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.


Via Nicolas Denancé, Kamoun Lab @ TSL
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Rescooped by Sociedad Española de Fitopatologia from Plant Pathogenomics
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G3: Population Dynamics of Phytophthora infestans in the Netherlands Reveals Expansion and Spread of Dominant Clonal Lineages and Virulence in Sexual Offspring (2012)

G3: Population Dynamics of Phytophthora infestans in the Netherlands Reveals Expansion and Spread of Dominant Clonal Lineages and Virulence in Sexual Offspring (2012) | SEFitopatologia | Scoop.it

For a comprehensive survey of the structure and dynamics of the Dutch Phytophthora infestans population, 652 P. infestans isolates were collected from commercial potato fields in the Netherlands during the 10-year period 2000–2009. Genotyping was performed using 12 highly informative microsatellite markers and mitochondrial haplotypes. In addition, for each isolate, the mating type was determined. STRUCTURE analysis grouped the 322 identified genotypes in three clusters. Cluster 1 consists of a single clonal lineage NL-001, known as “Blue_13”; all isolates in this cluster have the A2 mating type and the Ia mitochondrial haplotype. Clusters 2 and 3 display a more elaborate substructure containing many unique genotypes. In Cluster 3, several distinct clonal lineages were also identified. This survey witnesses that the Dutch population underwent dramatic changes in the 10 years under study. The most notable change was the emergence and spread of A2 mating type strain NL-001 (or “Blue_13”). The results emphasize the importance of the sexual cycle in generating genetic diversity and the importance of the asexual cycle as the propagation and dispersal mechanism for successful genotypes. Isolates were also screened for absence of the Avrblb1/ipiO class I gene, which is indicative for virulence on Rpi-blb1. This is also the first report of Rpi-blb1 breakers in the Netherlands. Superimposing the virulence screening on the SSR genetic backbone indicates that lack the Avrblb1/ipiO class I gene only occurred in sexual progeny. So far, the asexual spread of the virulent isolates identified has been limited.


Via Kamoun Lab @ TSL
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Opinion: Academia Suppresses Creativity | The Scientist Magazine®

Opinion: Academia Suppresses Creativity | The Scientist Magazine® | SEFitopatologia | Scoop.it
By discouraging change, universities are stunting scientific innovation, leadership, and growth.
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