Plant Pathogenomics
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PLoS Genetics: Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions (2012)

PLoS Genetics: Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions (2012) | Plant Pathogenomics | Scoop.it

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescensgroup was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

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PLOS Genetics: Interspecific Sex in Grass Smuts and the Genetic Diversity of Their Pheromone-Receptor System (2011)

PLOS Genetics: Interspecific Sex in Grass Smuts and the Genetic Diversity of Their Pheromone-Receptor System (2011) | Plant Pathogenomics | Scoop.it

The grass smuts comprise a speciose group of biotrophic plant parasites, so-called Ustilaginaceae, which are specifically adapted to hosts of sweet grasses, the Poaceae family. Mating takes a central role in their life cycle, as it initiates parasitism by a morphological and physiological transition from saprobic yeast cells to pathogenic filaments. As in other fungi, sexual identity is determined by specific genomic regions encoding allelic variants of a pheromone-receptor (PR) system and heterodimerising transcription factors. Both operate in a biphasic mating process that starts with PR–triggered recognition, directed growth of conjugation hyphae, and plasmogamy of compatible mating partners. So far, studies on the PR system of grass smuts revealed diverse interspecific compatibility and mating type determination. However, many questions concerning the specificity and evolutionary origin of the PR system remain unanswered. Combining comparative genetics and biological approaches, we report on the specificity of the PR system and its genetic diversity in 10 species spanning about 100 million years of mating type evolution. We show that three highly syntenic PR alleles are prevalent among members of the Ustilaginaceae, favouring a triallelic determination as the plesiomorphic characteristic of this group. Furthermore, the analysis of PR loci revealed increased genetic diversity of single PR locus genes compared to genes of flanking regions. Performing interspecies sex tests, we detected a high potential for hybridisation that is directly linked to pheromone signalling as known from intraspecies sex. Although the PR system seems to be optimised for intraspecific compatibility, the observed functional plasticity of the PR system increases the potential for interspecific sex, which might allow the hybrid-based genesis of newly combined host specificities.

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Frontiers Plant Science: The genome sequence and effector complement of the flax rust pathogen Melampsora lini (2014)

Frontiers Plant Science: The genome sequence and effector complement of the flax rust pathogen Melampsora lini (2014) | Plant Pathogenomics | Scoop.it

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimise parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analysed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.


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Francis Martin's curator insight, March 4, 11:30 AM

A long awaited genome! More rust genomes needed.

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Molecular Biology and Evolution: Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans (2014)

Molecular Biology and Evolution: Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans (2014) | Plant Pathogenomics | Scoop.it

The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in recent decades. Recently, complete P. infestans mitogenome sequences from 19th-century herbarium specimens were shown to belong to a unique lineage (HERB-1) predicted to be rare or extinct in modern times. We report 44 additional P. infestans mitogenomes: four from 19th-century Europe, three from 1950s U.K. and 34 from modern populations across the New World. We use phylogenetic analyses to identify the HERB-1 lineage in modern populations from both Mexico and South America, and to demonstrate distinct mitochondrial haplotypes were present in 19th-century Europe, with this lineage initially diversifying 75 years before the first reports of potato late blight.

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Steve Marek's curator insight, March 5, 5:59 AM

Herb-1 is still lurking about...

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BioEssays: Sex or no sex: Evolutionary adaptation occurs regardless (2014)

BioEssays: Sex or no sex: Evolutionary adaptation occurs regardless (2014) | Plant Pathogenomics | Scoop.it

All species continuously evolve to adapt to changing environments. The genetic variation that fosters such adaptation is caused by a plethora of mechanisms, including meiotic recombination that generates novel allelic combinations in the progeny of two parental lineages. However, a considerable number of eukaryotic species, including many fungi, do not have an apparent sexual cycle and are consequently thought to be limited in their evolutionary potential. As such organisms are expected to have reduced capability to eliminate deleterious mutations, they are often considered as evolutionary dead ends. However, inspired by recent reports we argue that such organisms can be as persistent as organisms with conventional sexual cycles through the use of other mechanisms, such as genomic rearrangements, to foster adaptation.

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Knapco's curator insight, February 19, 2:08 AM

Verticillium dahliae is among 20% of fungal species lacking sexual cycle of reproduction. However, the authors suggest that its genome contains a high amount of transposable elements (TE) which may drive genome evolution in this pathogen. TEs are DNA sequences that can change their position within genome and can impact the genome by inducing gene knockouts, modulating gene regulation or causing double-stranded DNA breaks. These sources of variability enable evolution: selection and adaptaion to plant hosts and evolution of fungal aggressiveness.

Similar asexual mechanisms facilitate genome evolution in other eukaryotes, known to be plant pathogens: Phytophthora infestans causing potato blight, Leptosphaeria maculans causing stem canker on Brassica, Blumeria graminis causing powdery mildew, Alternaria spp., Fusarium spp., Mycosphaerella graminicola...

Steve Marek's curator insight, March 5, 6:01 AM

Textbook stuff!

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PLOS Pathogens: Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici (2014)

PLOS Pathogens: Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici (2014) | Plant Pathogenomics | Scoop.it

Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen.

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Nature Communications: The locust genome provides insight into swarm formation and long-distance flight (2014)

Nature Communications: The locust genome provides insight into swarm formation and long-distance flight (2014) | Plant Pathogenomics | Scoop.it

Locusts are one of the world’s most destructive agricultural pests and represent a useful model system in entomology. Here we present a draft 6.5 Gb genome sequence of Locusta migratoria, which is the largest animal genome sequenced so far. Our findings indicate that the large genome size of L. migratoria is likely to be because of transposable element proliferation combined with slow rates of loss for these elements. Methylome and transcriptome analyses reveal complex regulatory mechanisms involved in microtubule dynamic-mediated synapse plasticity during phase change. We find significant expansion of gene families associated with energy consumption and detoxification, consistent with long-distance flight capacity and phytophagy. We report hundreds of potential insecticide target genes, including cys-loop ligand-gated ion channels, G-protein-coupled receptors and lethal genes. The L. migratoria genome sequence offers new insights into the biology and sustainable management of this pest species, and will promote its wide use as a model system.

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PLOS Pathogens: Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringe Phylogeny (2013)

PLOS Pathogens: Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringe Phylogeny (2013) | Plant Pathogenomics | Scoop.it

Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system (T3SS) and the type three secreted effector proteins (T3E) that are collectively essential for virulence. HrpL also regulates expression of an under-explored suite of non-type III effector genes (non-T3E), including toxin production systems and operons not previously associated with virulence. We implemented and refined genome-wide transcriptional analysis methods using cDNA-derived high-throughput sequencing (RNA-seq) data to characterize the HrpL regulon from six isolates of P. syringae spanning the diversity of the species. Our transcriptomes, mapped onto both complete and draft genomes, significantly extend earlier studies. We confirmed HrpL-regulation for a majority of previously defined T3E genes in these six strains. We identified two new T3E families from P. syringae pv. oryzae 1_6, a strain within the relatively underexplored phylogenetic Multi-Locus Sequence Typing (MLST) group IV. The HrpL regulons varied among strains in gene number and content across both their T3E and non-T3E gene suites. Strains within MLST group II consistently express the lowest number of HrpL-regulated genes. We identified events leading to recruitment into, and loss from, the HrpL regulon. These included gene gain and loss, and loss of HrpL regulation caused by group-specific cis element mutations in otherwise conserved genes. Novel non-T3E HrpL-regulated genes include an operon that we show is required for full virulence of P. syringae pv.phaseolicola 1448A on French bean. We highlight the power of integrating genomic, transcriptomic, and phylogenetic information to drive concise functional experimentation and to derive better insight into the evolution of virulence across an evolutionarily diverse pathogen species.

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MPMI: The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing (2013)

MPMI: The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing (2013) | Plant Pathogenomics | Scoop.it

Liberibacters form a Rhizobiaceae clade of phloem-limited pathogens of limited host range. Two obligately parasitic species have been sequenced: Candidatus Liberibacter asiaticus (Las), which causes citrus Huanglongbing (HLB) world-wide, and Ca. L. solanacearum (Lso), which causes potato “zebra chip” disease. A third species, Liberibacter crescens (Lcr), was isolated from mountain papaya, grown in axenic culture and sequenced. In an effort to identify common host determinants, the complete genomic DNA sequence of a second HLB species, Ca. L. americanus (Lam) strain “São Paulo” was determined. The circular genome of 1,195,201 bp had an average 31.12% GC content and 983 predicted protein encoding genes, 800 (81.4%) of which had a predicted function. There were 658 genes common to all sequenced liberibacters and only 8 genes common to Lam and Las but not found in Lso. Surprisingly, most of the lipopolysaccharide biosynthetic genes were missing from the Lam genome, as well OmpA and a key regulator of flagellin, all indicating a Lam strategy of avoiding production of major pathogen-associated molecular patterns (PAMPs) present in Las and Lso. As with Las, one of two Lam prophages replicated as an excision plasmid and carried potential lysogenic conversion genes that appeared fragmentary or degenerated in Lso.

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PNAS: Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013)

PNAS: Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013) | Plant Pathogenomics | Scoop.it

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularisgenes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

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Resource: Wheat Yellow Rust Genomics data now available (2013)

Resource: Wheat Yellow Rust Genomics data now available (2013) | Plant Pathogenomics | Scoop.it

We have been working with colleagues in India, Kenya, Ethiopia, Denmark and the UK to develop wheat yellow rust genomics through the re-sequencing of isolates from different continents. Our project also includes traditional field trials of a common set of germplasm which has been evaluated in these countries. One of our goals is to make the genomic data of wheat yellow rust isolates and phenotypic data (Yr, Sr, Lr) from the wheat Watkins landraces rapidly and broadly available to the scientific community, as stated at the BGRI workshop 2013.


We hope that this data will be of use to others in the community and we have made this information available (open access) through our project website (www.yellowrust.com). It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analyses. We strongly believe that as a global research community we can have a greater impact in our common goals if data is shared openly and used responsibly.


Diane Saunders and Cristobal Uauy on behalf of SCPRID project partners

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PLOS Pathogens: Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining (2013)

PLOS Pathogens: Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining (2013) | Plant Pathogenomics | Scoop.it

Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means.

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Arjen ten Have's curator insight, November 20, 2013 1:13 PM

My guess this is a rather stringent protocol. There will be many cool targets at intermediate levels of the filtration flow! But obviously a great piece of work. Love its simplicity! (likely much of the work actually performed is not shown).

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PLOS ONE: Evolution of RXLR-Class Effectors in the Oomycete Plant Pathogen Phytophthora ramorum (2013)

PLOS ONE: Evolution of RXLR-Class Effectors in the Oomycete Plant Pathogen Phytophthora ramorum (2013) | Plant Pathogenomics | Scoop.it

Phytophthora plant pathogens contain many hundreds of effectors potentially involved in infection of host plants. Comparative genomic analyses have shown that these effectors evolve rapidly and have been subject to recent expansions. We examined the recent sequence evolution of RXLR-class effector gene families in the sudden oak death pathogen, P. ramorum. We found that P. ramorum RXLR effectors have taken multiple evolutionary paths, including loss or gain of repeated domains, recombination or gene conversion among paralogs, and selection on point mutations. Sequencing of homologs from two subfamilies in P. ramorum’s closest known relatives revealed repeated gene duplication and divergence since speciation with P. lateralis. One family showed strong signatures of recombination while the other family has evolved primarily by point mutation. Comparison of a small number of the hundreds of RXLR-class effectors across three clonal lineages of P. ramorum shows striking divergence in alleles among lineages, suggesting the potential for functional differences between lineages. Our results suggest future avenues for examination of rapidly evolving effectors in P. ramorum, including investigation of the functional and coevolutionary significance of the patterns of sequence evolution that we observed.


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Niklaus Grunwald's curator insight, November 8, 2013 1:07 PM

Our paper on evoution of RXLR effectors in the sudden oak death pathogen Phytophthora ramorum describing loss or gain of repeated domains, recombination or gene conversion among paralogs, and selection on point mutations and more.

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PLOS ONE: Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs (2013)

PLOS ONE: Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs (2013) | Plant Pathogenomics | Scoop.it

In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.

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Methods in Molecular Biology: Two-Dimensional Data Binning for the Analysis of Genome Architecture in Filamentous Plant Pathogens and Other Eukaryotes (2014)

Methods in Molecular Biology: Two-Dimensional Data Binning for the Analysis of Genome Architecture in Filamentous Plant Pathogens and Other Eukaryotes (2014) | Plant Pathogenomics | Scoop.it

Genome architecture often reflects an organism’s lifestyle and can therefore provide insights into gene function, regulation, and adaptation. In several lineages of plant pathogenic fungi and oomycetes, characteristic repeat-rich and gene-sparse regions harbor pathogenicity-related genes such as effectors. In these pathogens, analysis of genome architecture has assisted the mining for novel candidate effector genes and investigations into patterns of gene regulation and evolution at the whole genome level. Here we describe a two-dimensional data binning method in R with a heatmap-style graphical output to facilitate analysis and visualization of whole genome architecture. The method is flexible, combining whole genome architecture heatmaps with scatter plots of the genomic environment of selected gene sets. This enables analysis of specific values associated with genes such as gene expression and sequence polymorphisms, according to genome architecture. This method enables the investigation of whole genome architecture and reveals local properties of genomic neighborhoods in a clear and concise manner.

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rougeforfire's curator insight, April 7, 1:42 AM

This seems pretty interesting.. That's a nice gift idea

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PLOS Genetics: Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans (2014)

PLOS Genetics: Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans (2014) | Plant Pathogenomics | Scoop.it

Plant pathogens secrete an arsenal of small secreted proteins (SSPs) acting as effectors that modulate host immunity to facilitate infection. SSP-encoding genes are often located in particular genomic environments and show waves of concerted expression at diverse stages of plant infection. To date, little is known about the regulation of their expression. The genome of the Ascomycete Leptosphaeria maculans comprises alternating gene-rich GC-isochores and gene-poor AT-isochores. The AT-isochores harbor mosaics of transposable elements, encompassing one-third of the genome, and are enriched in putative effector genes that present similar expression patterns, namely no expression or low-level expression during axenic cultures compared to strong induction of expression during primary infection of oilseed rape (Brassica napus). Here, we investigated the involvement of one specific histone modification, histone H3 lysine 9 methylation (H3K9me3), in epigenetic regulation of concerted effector gene expression in L. maculans. For this purpose, we silenced the expression of two key players in heterochromatin assembly and maintenance, HP1 and DIM-5 by RNAi. By using HP1-GFP as a heterochromatin marker, we observed that almost no chromatin condensation is visible in strains in which LmDIM5 was silenced by RNAi. By whole genome oligoarrays we observed overexpression of 369 or 390 genes, respectively, in the silenced-LmHP1 and -LmDIM5 transformants during growth in axenic culture, clearly favouring expression of SSP-encoding genes within AT-isochores. The ectopic integration of four effector genes in GC-isochores led to their overexpression during growth in axenic culture. These data strongly suggest that epigenetic control, mediated by HP1 and DIM-5, represses the expression of at least part of the effector genes located in AT-isochores during growth in axenic culture. Our hypothesis is that changes of lifestyle and a switch toward pathogenesis lift chromatin-mediated repression, allowing a rapid response to new environmental conditions.

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Scientific Reports: A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus (2104)

Scientific Reports: A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus (2104) | Plant Pathogenomics | Scoop.it

The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain ~750 years of age. Phylogenetic analysis of BSMV that includes this genome indicates the divergence of BSMV and its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa, and spread to North America and East Asia with their hosts along historical trade routes.

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PLOS Genetics: The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants (2014)

PLOS Genetics: The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants (2014) | Plant Pathogenomics | Scoop.it

Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While somePhytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, bothPhytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosomapossess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease.

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BMC Genomics: Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota)(2014)

BMC Genomics: Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota)(2014) | Plant Pathogenomics | Scoop.it

Background - Lichen is a classic mutualistic organism and the lichenization is one of the fungal symbioses. The lichen-forming fungus Endocarpon pusillum is living in symbiosis with the green alga Diplosphaera chodatii Bialsuknia as a lichen in the arid regions.

 

Results - 454 and Illumina technologies were used to sequence the genome of E. pusillum. A total of 9,285 genes were annotated in the 37.5 Mb genome of E. pusillum. Analyses of the genes provided direct molecular evidence for certain natural characteristics, such as homothallic reproduction and drought-tolerance. Comparative genomics analysis indicated that the expansion and contraction of some protein families in the E. pusillum genome reflect the specific relationship with its photosynthetic partner (D. chodatii). Co-culture experiments using the lichen-forming fungus E. pusillum and its algal partner allowed the functional identification of genes involved in the nitrogen and carbon transfer between both symbionts, and three lectins without signal peptide domains were found to be essential for the symbiotic recognition in the lichen; interestingly, the ratio of the biomass of both lichen-forming fungus and its photosynthetic partner and their contact time were found to be important for the interaction between these two symbionts.

 

Conclusions - The present study lays a genomic analysis of the lichen-forming fungus E. pusillum for demonstrating its general biological features and the traits of the interaction between this fungus and its photosynthetic partner D. chodatii, and will provide research basis for investigating the nature of its drought resistance and symbiosis.

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PLOS Genetics: Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus (2014)

PLOS Genetics: Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus (2014) | Plant Pathogenomics | Scoop.it

Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregulariswith other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

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Jean-Michel Ané's curator insight, January 10, 5:59 AM

Beautiful work

Steve Marek's curator insight, January 12, 9:36 AM

Hypervariable rDNA explains high internuclear diversity

Comparative genomics returns prodigal glomeraleans to the zygomycetes 

Jennifer Mach's curator insight, January 12, 1:20 PM

Single nucleus sequencing!

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BMC Genomics: Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex (2013)

BMC Genomics: Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex (2013) | Plant Pathogenomics | Scoop.it

Background. Ralstonia solanacearum is a soil-borne beta-proteobacterium that causes bacterial wilt disease in many food crops and is a major problem for agriculture in intertropical regions. R. solanacearum is a heterogeneous species, both phenotypically and genetically, and is considered as a species complex. Pathogenicity of R. solanacearum relies on the Type III secretion system that injects Type III effector (T3E) proteins into plant cells. T3E collectively perturb host cell processes and modulate plant immunity to enable bacterial infection.

 

Results. We provide the catalogue of T3E in the R. solanacearum species complex, as well as candidates in newly sequenced strains. 94 T3E orthologous groups were defined on phylogenetic bases and ordered using a uniform nomenclature. This curated T3E catalog is available on a public website and a bioinformatic pipeline has been designed to rapidly predict T3E genes in newly sequenced strains. Systematical analyses were performed to detect lateral T3E gene transfer events and identify T3E genes under positive selection. Our analyses also pinpoint the RipF translocon proteins as major discriminating determinants among the phylogenetic lineages.

 

Conclusions. Establishment of T3E repertoires in strains representatives of the R. solanacearum biodiversity allowed determining a set of 22 T3E present in all the strains but provided no clues on host specificity determinants. The definition of a standardized nomenclature and the optimization of predictive tools will pave the way to understanding how variation of these repertoires is correlated to the diversification of this species complex and how they contribute to the different strain pathotypes.

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Mol Plant Pathol: Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past (2013)

Mol Plant Pathol: Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past (2013) | Plant Pathogenomics | Scoop.it

Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non- or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum,Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment-based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi-gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).

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Arjen ten Have's curator insight, December 3, 2013 7:51 AM

Pseudogenes are among the poorly understood. Pseudogenes are not necessarily without function. Gene duplication results in functional redundancy. This can result in the complete los of selection or in functional diversification. Here pseudogenes are defined as genes with disruptive mutations, which is likely to results in loss of function. But still.... Pseudogenes are junk dna, junk is what we keep around, just in case you might have a function for it in the future. Plasticity!

 

I find the defintion of pseudogene a bit odd, but it makes sense.

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Plant J: Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations (...

Plant J: Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations (... | Plant Pathogenomics | Scoop.it

RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum ‘Heinz 1706’ extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.

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bioRxiv: Interactions Between Genome Architecture and Virulence Genes in Pseudomonas syringae, strain CC1557 as a model (2013)

bioRxiv: Interactions Between Genome Architecture and Virulence Genes in Pseudomonas syringae, strain CC1557 as a model (2013) | Plant Pathogenomics | Scoop.it

Both type III effector proteins and non-ribosomal peptide toxins play important roles for Pseudomonas syringae pathogenicity in host plants, but if and how these virulence pathways interact to promote infection remains unclear. Genomic evidence from one clade of P. syringae suggests a tradeoff between the total number of type III effector proteins and presence of syringomycin, syringopeptin, and syringolin A toxins. Here we report the complete genome sequence from P. syringae CC1557, which contains the lowest number of known type III effectors to date and has also acquired a highly similar toxin to syringomycin through horizontal transfer. We demonstrate that this strain is pathogenic on Nicotiana benthamiana and that both the type III secretion system and a new type III effector family, hopBJ1, contribute to virulence. Taken together, our results provide independent evolutionary confirmation of a negative correlation between type III effector repertoires and some non-ribosomal peptide toxins while also highlighting how genomic synteny can be used to identify novel virulence proteins.

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PLOS ONE: Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots (2013)

PLOS ONE: Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots (2013) | Plant Pathogenomics | Scoop.it

Comparative genomics of closely related pathogens that differ in host range can provide insights into mechanisms of host-pathogen interactions and host adaptation. Furthermore, sequencing of multiple strains with the same host range reveals information concerning pathogen diversity and the molecular basis of virulence. Here we present a comparative analysis of draft genome sequences for four strains of Pseudomonas cannabina pathovaralisalensis (Pcal), which is pathogenic on a range of monocotyledonous and dicotyledonous plants. These draft genome sequences provide a foundation for understanding host range evolution across the monocot-dicot divide. Like other phytopathogenic pseudomonads, Pcalstrains harboured a hrp/hrc gene cluster that codes for a type III secretion system. Phylogenetic analysis based on the hrp/hrc cluster genes/proteins, suggests localized recombination and functional divergence within the hrp/hrc cluster. Despite significant conservation of overall genetic content across Pcal genomes, comparison of type III effector repertoires reinforced previous molecular data suggesting the existence of two distinct lineages within this pathovar. Furthermore, all Pcal strains analyzed harbored two distinct genomic islands predicted to code for type VI secretion systems (T6SSs). While one of these systems was orthologous to known P. syringae T6SSs, the other more closely resembled a T6SS found within P. aeruginosa. In summary, our study provides a foundation to unravel Pcal adaptation to both monocot and dicot hosts and provides genetic insights into the mechanisms underlying pathogenicity.

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Nature Communications: High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus (2013)

Nature Communications: High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus (2013) | Plant Pathogenomics | Scoop.it

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a ‘fosmid-to-fosmid’ strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the ‘fosmid-to-fosmid’ strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens.

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