Fungal|Oomycete Biology
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Host-jump drives rapid and recent ecological speciation of the emergent fungal pathogen Colletotrichum kahawae

Host-jump drives rapid and recent ecological speciation of the emergent fungal pathogen Colletotrichum kahawae | Fungal|Oomycete Biology | Scoop.it

Ecological speciation through host-shift has been proposed as a major route for the appearance of novel fungal pathogens. The growing awareness of their negative impact on global economies and public health created an enormous interest in identifying the factors that are most likely to promote their emergence in nature. In this work, a combination of pathological, molecular and geographical data was used to investigate the recent emergence of the fungus Colletotrichum kahawae. C. kahawae emerged as a specialist pathogen causing coffee berry disease in Coffea arabica, owing to its unparalleled adaptation of infecting green coffee berries. Contrary to current hypotheses, our results suggest that a recent host-jump underlay the speciation of C. kahawae from a generalist group of fungi seemingly harmless to coffee berries. We posit that immigrant inviability and a predominantly asexual behaviour could have been instrumental in driving speciation by creating pleiotropic interactions between local adaptation and reproductive patterns. Moreover, we estimate that C. kahawae began its diversification at <2200 bp leaving a very short time frame since the divergence from its sibling lineage (c. 5600 bp), during which a severe drop in C. kahawae’s effective population size occurred. This further supports a scenario of recent introduction and subsequent adaptation to C. arabica. Phylogeographical data revealed low levels of genetic polymorphism but provided the first geographically consistent population structure of C. kahawae, inferring the Angolan population as the most ancestral and the East African populations as the most recently derived. Altogether, these results highlight the significant role of host specialization and asexuality in the emergence of fungal pathogens through ecological speciation.

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Fungal|Oomycete Biology
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Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage

Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage | Fungal|Oomycete Biology | Scoop.it
The study of biological diversification of oomycetes has been a difficult task for more than a century. Pioneer researchers used morphological characters to describe this heterogeneous group, and physiological and genetic tools expanded knowledge of these microorganisms. However, research on oomycete diversification is limited by conflicting phylogenies. Using whole genomic data from 17 oomycete taxa, we obtained a dataset of 277 core orthologous genes shared among these genomes. Analyses of this dataset resulted in highly congruent and strongly supported estimates of oomycete phylogeny when we used concatenated maximum likelihood and coalescent-based methods; the one important exception was the position of Albugo. Our results supported the position of Phytopythium vexans (formerly in Pythium clade K) as a sister clade to the Phytophthora-Hyaloperonospora clade. The remaining clades comprising Pythium sensu lato formed two monophyletic groups. One group was composed of three taxa that correspond to Pythium clades A, B and C, and the other group contained taxa representing clades F, G and I, in agreement with previous Pythium phylogenies. However, the group containing Pythium clades F, G and I was placed as sister to the Phytophthora-Hyaloperonospora-Phytopythium clade, thus confirming the lack of monophyly of Pythium sensu lato. Multispecies coalescent methods revealed that the white blister rust, Albugo laibachii, could not be placed with a high degree of confidence. Our analyses show that genomic data can resolve the oomycete phylogeny and provide a phylogenetic framework to study the evolution of oomycete lifestyles.
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Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici

Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici | Fungal|Oomycete Biology | Scoop.it

The oomycete, Phytophthora capsici, infects cucumber (Cucumis sativus L.) fruit. An age-related resistance (ARR) to this pathogen was previously observed in fruit of cultivar ‘Vlaspik’ and shown to be associated with the peel. Young fruits are highly susceptible, but develop resistance at ~10–12 days post pollination (dpp). Peels from resistant (16 dpp) versus susceptible (8 dpp) age fruit are enriched with genes associated with defense, and methanolic extracts from resistant age peels inhibit pathogen growth. Here we compared developing fruits from ‘Vlaspik’ with those of ‘Gy14’, a line that does not exhibit ARR. Transcriptomic analysis of peels of the two lines at 8 and 16 dpp identified 80 genes that were developmentally upregulated in resistant ‘Vlaspik’ 16 dpp versus 8 dpp, but not in susceptible ‘Gy14’ at 16 dpp. A large number of these genes are annotated to be associated with defense and/or specialized metabolism, including four putative resistance (R) genes, and numerous genes involved in flavonoid and terpenoid synthesis and decoration. Untargeted metabolomic analysis was performed on extracts from 8 and 16 dpp ‘Vlaspik’ and ‘Gy14’ fruit peels using Ultra-Performance Liquid Chromatography and Quadrupole Time-of-Flight Mass Spectrometry. Multivariate analysis of the metabolomes identified 113 ions uniquely abundant in resistant ‘Vlaspik’ 16 dpp peel extracts. The most abundant compounds in this group had relative mass defects consistent with terpenoid glycosides. Two of the three most abundant ions were annotated as glycosylated nor-terpenoid esters. Together, these analyses reveal potential mechanisms by which ARR to P. capsici may be conferred.

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Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria | Fungal|Oomycete Biology | Scoop.it
BACKGROUND
Among the extensive cortège of plant-associated microorganisms (the so-called plant microbiota), mutualistic fungal and bacterial symbionts are striking examples of soil microorganisms that have successfully coevolved with their hosts since plants adapted to terrestrial ecosystems. They promote plant growth by facilitating the acquisition of scarce nutrients. In these associations, plant root colonization requires complex molecular cross-talk between symbiotic partners to activate a variety of host developmental pathways and specialized symbiotic tissues and organs. Despite the evolutionary distances that separate mycorrhizal and nitrogen-fixing symbioses, recent research has identified certain highly conserved features associated with early stages of root colonization. We focus on recent and emerging areas of investigation concerning these major mutualistic symbioses and discuss some of the molecular pathways and cellular mechanisms involved in their evolution and development.
ADVANCES
Phylogenomic analyses and divergence time estimates based on symbiotic plant fossils are shedding light on the evolution of mutualistic symbioses. The earliest land plants [~407 million years ago (Ma)] were associated with fungi producing mycorrhiza-like intracellular structures similar to extant symbioses involving Glomeromycotina and Mucoromycotina. Arbuscular mycorrhizal endosymbioses then diversified by the Late Carboniferous. Pinaceae species from the Late Jurassic and Early Cretaceous (~180 Ma) formed the first ectomycorrhizal associations involving Dikarya. More recently, certain angiosperms evolved a “predisposition” for the evolution of nitrogen-fixing root nodule symbioses (~100 Ma) with bacteria.

A conserved core module of the “common symbiotic signaling pathway” (CSSP) is shared by all host plants that establish endosymbioses, including arbuscular mycorrhizal, rhizobial, and actinorhizal associations. This striking conservation among widely divergent host species underlines the shared evolutionary origin for this ancient symbiotic signaling pathway. Furthermore, chitin-based signaling molecules secreted by both arbuscular mycorrhizal fungi and rhizobia activate the host CSSP after perception by related receptor-like kinases. Downstream signal transduction pathways then lead to the apoplastic intracellular infection modes that characterize the majority of these associations and, finally, to the coordinated development of sophisticated bidirectional symbiotic interfaces found in both arbuscules and nitrogen-fixing nodules. A common feature of all these mutualistic associations is phytohormone-associated modifications of root development, which lead to an increase in potential colonization sites as well as major structural and functional changes to the root during the establishment of symbiotic tissues.
OUTLOOK
Although we are at last beginning to understand how mutualistic microorganisms communicate with plants, how associated root developmental pathways are modulated, and how plant immune responses are successfully circumvented, many important questions remain. For example, little is currently known about more primitive modes of intercellular apoplastic colonization, whether for ectomycorrhizal fungi or for certain nitrogen-fixing symbioses. Neither do we know whether the CSSP has a key role in ectomycorrhizal associations, nor how host plants distinguish between structurally similar chitin-based “symbiotic” and “pathogenic” microbial signals. Answering these questions should contribute to our understanding of the underlying mechanisms that govern the relationships between plants and their entire microbiota. On a broader level, improved understanding of how environmental and genetic cues, together with plant metabolism, modulate microbial colonization will be crucial for the future exploitation of the microbiota for the benefit of sustainable plant growth.

Via Steve Marek
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Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations | Fungal|Oomycete Biology | Scoop.it
Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.
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Rescooped by Alejandro Rojas from MycorWeb Plant-Microbe Interactions
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Ericaceous plant–fungus network in a harsh alpine–subalpine environment

Ericaceous plant–fungus network in a harsh alpine–subalpine environment | Fungal|Oomycete Biology | Scoop.it
In terrestrial ecosystems, plant species and diverse root-associated fungi form complex networks of host–symbiont associations. Recent studies have revealed that structures of those below-ground plant–fungus networks differ between arbuscular mycorrhizal and ectomycorrhizal symbioses. Nonetheless, we still remain ignorant of how ericaceous plant species, which dominate arctic and alpine tundra, constitute networks with their root-associated fungi. Based on a high-throughput DNA sequencing data set, we characterized the statistical properties of a network involving 16 ericaceous plant species and more than 500 fungal taxa in the alpine–subalpine region of Mt. Tateyama, central Japan. While all the 16 ericaceous species were associated mainly with fungi in the order Helotiales, they varied remarkably in association with fungi in other orders such as Sebacinales, Atheliales, Agaricales, Russulales and Thelephorales. The ericaceous plant–fungus network was characterized by high symbiont/host preferences. Moreover, the network had a characteristic structure called ‘anti-nestedness’, which has been previously reported in ectomycorrhizal plant–fungus networks. The results lead to the hypothesis that ericaceous plants in harsh environments can host unexpectedly diverse root-associated fungal taxa, constituting networks whose structures are similar to those of previously reported ectomycorrhizal networks but not to those of arbuscular mycorrhizal ones.

Via Francis Martin
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Developing educational resources for population genetics in R: an open and collaborative approach

Developing educational resources for population genetics in R: an open and collaborative approach | Fungal|Oomycete Biology | Scoop.it
The R computing and statistical language community has developed a myriad of resources for conducting populations genetic analyses. However, resources for learning how to carry out population genetic analyses in R are scattered and often incomplete, which can make acquiring this skill unnecessarily difficult and time-consuming. To address this gap, we developed an online community resource with guidance and working demonstrations for conducting population genetic analyses in R. The resource is freely available at http://popgen.nescent.org, and includes material for both novices and advanced users of R for population genetics. To facilitate continued maintenance and growth of this resource, we developed a toolchain, process, and conventions designed to (1) minimize financial and labor costs of upkeep; (2) to provide a low barrier to contribution; and (3) to ensure strong quality assurance. The toolchain includes automatic integration testing of every change and rebuilding of the website when new vignettes or edits are accepted. The process and conventions largely follow a common, distributed version control-based contribution workflow, which is used to provide and manage open peer review by designated website editors. The online resources include detailed documentation of this process, including video tutorials. We invite the community of population geneticists working in R to contribute to this resource, whether for a new use-case of their own, or as one of the vignettes from the “wish list” we maintain, or by improving existing vignettes.
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This is a great resource! Indirectly related to the focus on this scoop.it, but quite valuable for those digging into the population genetics of plant associated fungi and oomycetes!
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Rescooped by Alejandro Rojas from Plants and Microbes
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Storify: #OMGN16 Annual meeting Twitter dialogue (with images, tweets)


Via Kamoun Lab @ TSL
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Correspondence between symptom development of Colletotrichum graminicola and fungal biomass, quantified by a newly developed qPCR assay, depends on the maize variety

Correspondence between symptom development of Colletotrichum graminicola and fungal biomass, quantified by a newly developed qPCR assay, depends on the maize variety | Fungal|Oomycete Biology | Scoop.it
Abstract

Background
Penetration attempts of the hemibiotroph Colletotrichum graminicola may activate PAMP-triggered immunity (PTI) on different cultivars of Zea mays to different extent. However, in most events, this does not prevent the establishment of a compatible pathogenic interaction. In this study, we investigate the extent to which the host variety influences PTI. Furthermore, we assess whether visual disease symptoms occurring on different maize varieties reliably reflect fungal biomass development in planta as determined by qPCR and GFP tracing.

Results
Employing a set of four maize varieties, which were selected from a panel of 27 varieties, for in-depth assessment of pathogenesis of the wild type strain of C. graminicola, revealed considerable differences in susceptibility as evidenced by symptom severity that decreased from variety Golden Jubilee to Mikado to Farmtop to B73. However, a newly developed qPCR assay and microscopical observation of a GFP-labelled strain showed that disease symptoms are in some instances inconsistent when compared with other indicators of susceptibility. Of the four varieties assessed, either Golden Jubilee, Mikado and B73, or Golden Jubilee, Farmtop and B73 showed a direct correlation between symptom and fungal biomass development. In a pairwise comparison, however, Mikado and Farmtop showed an inverse correlation for these features.

Conclusions
The genotype of maize contributes to the severity of symptoms resulting from an infection with C. graminicola. Partially, this may be attributed to the extent of PTI activated in different varieties, as reflected by papilla formation. Furthermore, when evaluating the susceptibility of a variety, it should be considered that symptom severity must not have to reflect the extent of fungal growth in the infected tissue.

Via Serenella A Sukno, Steve Marek
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Rescooped by Alejandro Rojas from Adaptive Evolution and Speciation
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Forest area and connectivity influence root-associated fungal communities in a fragmented landscape - Ecology

Forest area and connectivity influence root-associated fungal communities in a fragmented landscape - Ecology | Fungal|Oomycete Biology | Scoop.it
Habitat fragmentation is well known to affect plant and animal diversity as a result of reduced habitat area and connectivity, but its effects on microorganisms are poorly understood. Using high-throughput sequencing of two regions of the rRNA gene, we studied the effects of forest area and connectivity on the diversity and composition of fungi associated with the roots of the dominant tree, Metrosideros polymorpha, in a lava-fragmented landscape on the Island of Hawaii. We found that local fungal diversity increased with forest area, whereas fungal species composition was correlated with fragment connectivity.

Via Ronny Kellner
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Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics 

Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics  | Fungal|Oomycete Biology | Scoop.it
On the basis of its downy mildew-like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLRs, 30 NLPs and 14 CRNs. The typical motifs, phylogenies and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preference of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew-like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens.
 
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Nuclear dynamics and genetic rearrangement in heterokaryotic colonies of Fusarium oxysporum

Nuclear dynamics and genetic rearrangement in heterokaryotic colonies of Fusarium oxysporum | Fungal|Oomycete Biology | Scoop.it
Recent studies have shown horizontal transfer of chromosomes to be a potential key contributor to genome plasticity in asexual fungal pathogens. However, the mechanisms behind horizontal chromosome transfer in eukaryotes are not well understood. Here we investigated the role of conidial anastomosis in heterokaryon formation between incompatible strains of Fusarium oxysporum and determined the importance of heterokaryons for horizontal chromosome transfer. Using live-cell imaging we demonstrate that conidial pairing of incompatible strains under carbon starvation can result in the formation of viable heterokaryotic hyphae in F. oxysporum. Nuclei of the parental lines presumably fuse at some stage as conidia with a single nucleus harboring both marker histones (GFP- and RFP-tagged) are produced. Upon colony formation, this hybrid offspring is subject to progressive and gradual genome rearrangement. The parental genomes appear to become spatially separated and RFP-tagged histones, deriving from one of the strains, Fol4287, are eventually lost. With a PCR-based method we showed that markers for most of the chromosomes of this strain are lost, indicating a lack of Fol4287 chromosomes. This leaves offspring with the genomic background of the other strain (Fo47), but in some cases together with one or two chromosomes from Fol4287, including the chromosome that confers pathogenicity towards tomato.
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Lotus Lofgren's curator insight, April 24, 2016 10:22 PM
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Plant root pathogens over 120,000 years of temperate rainforest ecosystem development

Plant root pathogens over 120,000 years of temperate rainforest ecosystem development | Fungal|Oomycete Biology | Scoop.it

The role of pathogens, including oomycetes, in long-term ecosystem development has remained largely unknown, despite hypotheses that pathogens drive primary succession, determine mature ecosystem plant diversity, or dominate in retrogressive, nutrient-limited ecosystems. Using DNA sequencing from roots, we investigated the frequency and host relationships of oomycete communities along a 120 000 year glacial chronosequence. Oomycetes were frequent in early successional sites (5 - 70 yrs), occurring in 38 - 65% of plant roots, but rare (average 3%) in all older ecosystems (280 yrs and older). Oomycetes were highly host specific, and more frequent on plant species that declined most strongly in abundance between ecosystem ages. In contrast, oomycetes were not correlated with plant abundance or plant root traits associated with retrogression. The results support the importance of root pathogens in early succession, but not thereafter, suggesting root pathogen-driven dynamics may be important in driving succession but not long-term diversity maintenance.

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Development and characterization of microsatellite markers for Fusarium virguliforme and their utility within clade 2 of the Fusarium solani species complex

Development and characterization of microsatellite markers for Fusarium virguliforme and their utility within clade 2 of the Fusarium solani species complex | Fungal|Oomycete Biology | Scoop.it
Clade 2 of the Fusarium solani species complex contains plant pathogens including Fusarium virguliforme and closely related species Fusarium brasiliense, Fusarium crassistipitatum, Fusarium tucumaniae, which are the primary causal agents of soybean sudden death syndrome (SDS), a significant threat to soybean production. In this study, we developed microsatellite markers from a F. virguliforme genome sequence and applied them to a F. virguliforme population collection of 38 isolates from Michigan and four reference strains from other locations. Of the 225 detected microsatellite loci, 108 loci were suitable for primer design, and 12 of the microsatellite markers were determined to be highly polymorphic, amplifying on average 5.7 alleles per locus. Using these markers, F. virguliforme isolates were partitioned into three distinct clusters, but isolates were not grouped based on relatedness of sampling sites. In addition, 11 out of 12 markers were demonstrated to be highly transferrable to other closely related species.
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Rescooped by Alejandro Rojas from The Plant Microbiome
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Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits | Fungal|Oomycete Biology | Scoop.it
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant–microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.

Via Stéphane Hacquard
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Best practices for population genetic analyses | Phytopathology

Best practices for population genetic analyses | Phytopathology | Fungal|Oomycete Biology | Scoop.it
Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.

Via Niklaus Grunwald, Steve Marek
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Elizabeth A Bowman's curator insight, May 27, 5:10 PM
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A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination | Fungal|Oomycete Biology | Scoop.it
Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS.

Via Ryohei Thomas Nakano
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Rescooped by Alejandro Rojas from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen | Fungal|Oomycete Biology | 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.


Via Pierre Gladieux
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Rescooped by Alejandro Rojas from Adaptive Evolution and Speciation
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Fungal identification biases in microbiome projects - Environmental Microbiology Reports

Fungal identification biases in microbiome projects - Environmental Microbiology Reports | Fungal|Oomycete Biology | Scoop.it
Fungi are the key players in ecosystems as well as in plant and human health. High-throughput molecular identification of fungi has greatly progressed our understanding about the diversity of mutualists, saprotrophs, and pathogens. We argue that the methods promoted by the microbiome consortia are suboptimal for detection of the most important fungal pathogens and ecologically important degraders. We recommend several sets of optimized primers for analysis of fungi or all eukaryote groups based on either short or long amplicons that cover the ITS region as well as part of 18S and 28S rDNA.

Via Ronny Kellner
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Soil immune responses

Soil immune responses | Fungal|Oomycete Biology | Scoop.it
Soil microorganisms are central to the provision of food, feed, fiber, and medicine. Engineering of soil microbiomes may promote plant growth and plant health, thus contributing to food security and agricultural sustainability ( 1 , 2 ). However, little is known about most soil microorganisms and their impact on plant health. Disease-suppressive soils offer microbiome-mediated protection of crop plants against infections by soil-borne pathogens. Understanding of the microbial consortia and mechanisms involved in disease suppression may help to better manage plants while reducing fertilizer and pesticide inputs.

Via Steve Marek
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The legacy effect of cover crops on soil fungal populations in a cereal rotation

The legacy effect of cover crops on soil fungal populations in a cereal rotation | Fungal|Oomycete Biology | Scoop.it

Highlights
• Significant effect of forages on fungal communities and diversity.
• Novel methodology to assess soil fungal biodiversity in a field experiment.
• The effect on fungal community diminished after rotation sowing with cereal crops.
• Diversity increased on direct drilled plots.
• Fungal diversity affected by soil nitrate-N levels.

Abstract
The use of rotations and minimum tillage in agriculture can permit more sustainable production through increasing soil organic matter and nutrients, and breaking of pathogen lifecycles. Soil fungal populations make an important physical and chemical contribution to soil. For example, mycorrhizal species are important in plant nutrition but are often overlooked when considering management practices for efficient soil function. We undertook DNA metabarcoding (Ion Torrent) using novel PCR primers and high-throughput sequencing of the D1 region of the large ribosomal subunit of the rRNA locus, to assess the effect of different forages and cereal tillage methods on the soil fungal community. The study comprised five forage treatments, perennial ryegrass (Lolium perenne) with either low or high N, chicory (Cichorium intybus), red clover (Trifolium pratense) or white clover (Trifolium repens) grown over 3 harvest years (2010–2012). Cultivation of chicory, red clover or white clover led to significantly divergent soil fungal communities, with a notably lower diversity of fungal populations under clover, suggesting a link to soil N dynamics. Consistent with this, was a negative correlation of soil nitrate-N levels with populations of arbuscular mycorrhizal fungi (AMF) and other root-associated fungal groupings (dark septate endophytes, ‘CHEG’, Sebacinales and Ceratobasidiaceae). In contrast, abundance of Fungi belonging to the genera Mortierella and Cryptococcus were positively correlated with soil nitrate-N, with Mortierella also being negatively correlated with soil P. Spring wheat was sown on the same plots (April 2013) followed by winter barley (October 2013). Half of each plot was sown either after ploughing or by direct drilling. A legacy effect of the preceding forage crop on the fungal community was detected after both cereal crops, with plots previously cultivated with ryegrass being most divergent. No overall effect of establishment method on fungal communities was detected but AMF and CHEG fungi were more abundant on direct-drilled plots and pathogenic fungi were more abundant on ploughed plots after the sowing of winter barley.


Via Steve Marek
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Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis

Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis | Fungal|Oomycete Biology | Scoop.it
Mutualistic interactions between plants and fungi often occur in the rhizosphere, although examples exist where shoot-endophytes support host growth and increase resistance to pathogens and herbivores. Fungal endophytes which colonize their hosts without any visible disease symptoms have been recognized to be fundamental components of various ecosystems. Initial efforts have been taken to decipher the genetic basis of beneficial plant–fungus interactions and of lifestyle transitions. This review gives a short overview on well established experimental systems amenable to genetic manipulation and of known genome sequence for dissecting plant–fungal endophyte interactions with a special focus on Arabidopsis thaliana associations.
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Via Jessie Uehling
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Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize

Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize | Fungal|Oomycete Biology | Scoop.it
During a study on the phylogenetic relationships between species in the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, 19 hybrid isolates with multiple polymorphisms in the nuclear sequences were observed. Molecular characterization of hybrids was achieved by sequencing three nuclear (internal transcribed spacers, ß-tubulin, heat shock protein 90) and two mitochondrial (cytochrome c oxidase subunit I, NADH dehydrogenase subunit I) gene regions and cloning of the single copy nuclear gene, ß-tubulin. Based on the molecular studies the hybrid isolates belonged to six distinct groups between P. cryptogea, P. erythroseptica, P. pseudocryptogea, P. sansomeana and P. sp. kelmania. In all cases, only a single cytochrome c oxidase subunit I and NADH dehydrogenase subunit I allele was detected and nuclear genes were biparentally inherited, suggesting that the hybrids arose from sexual recombination events. Colony morphology, growth rate, cardinal temperatures, breeding system, and morphology of sporangia, oogonia, oospores and antheridia were also determined. Some morphological differences between the hybrids and the parental species were noted; however, they were not sufficient to reliably distinguish the taxa and DNA markers from nuclear and mitochondrial genes will to be necessary for their identification. The parental species are all important pathogens of agricultural fields that have been transported globally. With the apparent ease of hybridization within this group there is ample opportunity for virulent hybrids to form, perhaps with extended host ranges.
Alejandro Rojas's insight:
It is really interesting since we also found P. sansomeana on corn and soybean, so what are the species of Phytophthora hybridizing in this host/environment? It could be P. cryptogea species complex since it is widely present (most often on tree species). 
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Hijacked cell division helped fuel rise of fungi: Research could point to new antifungals that stop cell growth in fungi but not in their plant or animal hosts

Hijacked cell division helped fuel rise of fungi: Research could point to new antifungals that stop cell growth in fungi but not in their plant or animal hosts | Fungal|Oomycete Biology | Scoop.it
The more than 90,000 known species of fungi may owe their abilities to spread and even cause disease to an ancient virus that hijacked their cell division machinery, researchers report. Over a billion years ago, a viral protein invaded the fungal genome, generating a family of proteins that now play key roles in fungal growth. The research could point to new antifungals that inhibit cell division in fungi but not in their plant or animal hosts.

Via Francis Martin
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Development and characterization of microsatellite markers for the oomyceta Aphanomyces euteiches

Development and characterization of microsatellite markers for the oomyceta Aphanomyces euteiches | Fungal|Oomycete Biology | Scoop.it
Aphanomyces euteiches Drechsler is a serious pathogen of leguminous crops that causes devastating root rot of pea worldwide. Given that A. euteiches is a diploid organism, robust, codominant markers are needed for population genetics studies. We have developed and screened a microsatellite-enriched small-insert genomic library for identification of A. euteiches SSR containing sequences. Fourteen out of the 48 primer pairs designed to amplify SSR, produced unambiguous polymorphic products in our test population of 94 isolates. The number of alleles at each locus ranged from one to four. The identification of new markers would enhance the ability to evaluate the genetic structure of A. euteiches populations, and pathogen evolution.
Aphanomyces euteiches Drechsler is a serious pathogen of leguminous crops that causes devastating root rot of pea worldwide. Given that A. euteiches is a diploid organism, robust, codominant markers are needed for population genetics studies. We have developed and screened a microsatellite-enriched small-insert genomic library for identification of A. euteiches SSR containing sequences. Fourteen out of the 48 primer pairs designed to amplify SSR, produced unambiguous polymorphic products in our test population of 94 isolates. The number of alleles at each locus ranged from one to four. The identification of new markers would enhance the ability to evaluate the genetic structure of A. euteiches populations, and pathogen evolution.
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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild | Fungal|Oomycete Biology | Scoop.it
Fungi typically live in highly diverse communities composed of multiple ecological guilds. Although high-throughput sequencing has greatly increased the ability to quantify the diversity of fungi in environmental samples, researchers currently lack a simple and consistent way to sort large sequence pools into ecologically meaningful categories. We address this issue by introducing FUNGuild, a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline. Using a database and an accompanying bioinformatics script, we demonstrate the application of FUNGuild to three high-throughput sequencing datasets from different habitats: forest soils, grassland soils, and decomposing wood. We found that guilds characteristic of each habitat (i.e., saprotrophic and ectomycorrhizal fungi in forest soils, saprotrophic and arbuscular mycorrhizal fungi in grassland soils, saprotrophic, wood decomposer, and plant pathogenic fungi in decomposing wood) were each well represented. The example datasets demonstrate that while we could quickly and efficiently assign a large portion of the data to guilds, another large portion could not be assigned, reflecting the need to expand and improve the database as well as to gain a better understanding of natural history for many described and undescribed fungal species. As a community resource, FUNGuild is dependent on third-party annotation, so we invite researchers to populate it with new categories and records as well as refine those already in existence.
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