MycorWeb Plant-Microbe Interactions
60.8K views | +12 today
Follow
 
Scooped by Francis Martin
onto MycorWeb Plant-Microbe Interactions
Scoop.it!

Horizontal Gene Transfer in Eukaryotic Plant Pathogens - Annu Rev Phytopath

Horizontal Gene Transfer in Eukaryotic Plant Pathogens - Annu Rev Phytopath | MycorWeb Plant-Microbe Interactions | Scoop.it

Gene transfer has been identified as a prevalent and pervasive phenomenon and an important source of genomic innovation in bacteria. The role of gene transfer in microbial eukaryotes seems to be of a reduced magnitude but in some cases can drive important evolutionary innovations, such as new functions that underpin the colonization of different niches. The aim of this review is to summarize published cases that support the hypothesis that horizontal gene transfer (HGT) has played a role in the evolution of phytopathogenic traits in fungi and oomycetes. Our survey of the literature identifies 46 proposed cases of transfer of genes that have a putative or experimentally demonstrable phytopathogenic function. When considering the life-cycle steps through which a pathogen must progress, the majority of the HGTs identified are associated with invading, degrading, and manipulating the host. Taken together, these data suggest HGT has played a role in shaping how fungi and oomycetes colonize plant hosts.

more...
No comment yet.
MycorWeb Plant-Microbe Interactions
Your new post is loading...
Your new post is loading...
Rescooped by Francis Martin from How microbes emerge
Scoop.it!

Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete - PLoS Genetics

Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete - PLoS Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it

Author Summary Some fungi are capable of sexual reproduction without the need for a sexually compatible partner, a behavior called homothallism. For some of these fungi, it was observed that they carried in a single individual all the genes normally determining sexual identity in two distinct sexually compatible individuals, but in most cases the role of these genes is still unclear. Here we examined in detail the homothallic sexual cycle of the yeast Phaffia rhodozyma that belongs to the Basidiomycota, which is the fungal lineage that also includes the mushrooms. Phaffia rhodozyma produces astaxanthin, a pigment with antioxidant properties used in the food and cosmetic industries and is accessible to genetic modifications, so far aimed mainly at improving astaxanthin production. Here we harnessed these genetic tools to dissect the self-fertile life cycle of this yeast and found that all genes normally involved in two-partner sexual reproduction are also required for self-fertile sex in P. rhodozyma and propose a model describing molecular interactions required to trigger sexual development. We also generated preferably outcrossing strains, which are potentially useful for further improvement of P. rhodozyma as an industrial organism.


Via Ronny Kellner, Niklaus Grunwald
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists | MycorWeb Plant-Microbe Interactions | Scoop.it
Comparably little is known about soil protists, which represent the often forgotten remaining microbial group (Caron et al., 2008). The majority of the few studies investigating the community structure of soil protists applied time-consuming microscopic determinations that require profound taxonomic expertise [e.g. (Finlay and Fenchel, 2001; Scherber et al., 2010; Domonell et al., 2013; Geisen et al., 2014)]. Molecular approaches, nowadays more and more based on HTS, start replacing those classical approaches (Baldwin et al., 2013; Bates et al., 2013; Lentendu et al., 2014; Geisen et al., 2015b; Fiore-Donno et al., 2016). Still, HTS targeting protists are extremely underrepresented in comparison to other microbes (Mitchell, 2015). The major reason for the profound gap stems from the immense, paraphyletic diversity of protists that span over the entire eukaryotic tree of life with plants, fungi and metazoans representing monophyletic branches at different places therein (Adl et al., 2012; Burki et al., 2016). Therefore, designing universal protist-specific primers is impossible. This is of little relevance when studying microbes in aquatic systems, where protists can be easily extracted and focused upon through subsequent size-filtering (de Vargas et al., 2015). Close attachment of many protists to soil particles eliminates straight-forward extraction, while directly applying universal eukaryotic primers to extracted DNA/RNA will ultimately result in sequencing mostly fungi due to their dominance in soils. To avoid this issue, more focused group specific primers targeting e.g. Cercozoa, Kinetoplastida, Chrysophyceae, acanthamoebae and Myxomycetes have been applied (Lentendu et al., 2014; Bass et al., 2016; Fiore-Donno et al., 2016).
more...
No comment yet.
Rescooped by Francis Martin from Plant pathogenic fungi
Scoop.it!

SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species

SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species | MycorWeb Plant-Microbe Interactions | Scoop.it
Defining syntenic relationships among orthologous gene clusters is a frequent undertaking of biologists studying organismal evolution through comparative genomic approaches. With the increasing availability of genome data made possible through next-generation sequencing technology, there is a growing need for user-friendly tools capable of assessing synteny. Here we present SimpleSynteny, a new web-based platform capable of directly interrogating collinearity of local genomic neighbors across multiple species in a targeted manner. SimpleSynteny provides a pipeline for evaluating the synteny of a preselected set of gene targets across multiple organismal genomes. An emphasis has been placed on ease-of-use, and users are only required to submit FASTA files for their genomes and genes of interest. SimpleSynteny then guides the user through an iterative process of exploring and customizing genomes individually before combining them into a final high-resolution figure. Because the process is iterative, it allows the user to customize the organization of multiple contigs and incorporate knowledge from additional sources, rather than forcing complete dependence on the computational predictions. Additional tools are provided to help the user identify which contigs in a genome assembly contain gene targets and to optimize analyses of circular genomes. SimpleSynteny is freely available at: http://www.SimpleSynteny.com.

Via Steve Marek
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Microbiome Evolution Along Divergent Branches of the Vertebrate Tree of Life: What's Known and Unknown

Microbiome Evolution Along Divergent Branches of the Vertebrate Tree of Life: What's Known and Unknown | MycorWeb Plant-Microbe Interactions | Scoop.it
Vertebrates harbor microbes both internally and externally, and collectively these microorganisms (the “microbiome”) contain genes that outnumber the host's genetic information ten-fold. The majority of the microorganisms associated with vertebrates are found within the gut; where they influence host physiology, immunity, and development. The development of next generation sequencing has led to a surge in effort to characterize the microbiomes of various vertebrate hosts, a necessary first step to determine the functional role these communities play in host evolution or ecology. This shift away from a culture-based microbiological approach, limited in taxonomic breadth, has resulted in the emergence of patterns suggesting a core vertebrate microbiome dominated by members of the bacterial phyla Bacteroidetes, Proteobacteria and Firmicutes. Still, there is substantial variation in the methodology used to characterize the microbiome, from differences in sample type to issues of sampling captive or wild hosts; and the majority (>90%) of studies have characterized the microbiome of mammals, which represent just 8% of described vertebrate species. Here, we review the state of microbiome studies of non-mammalian vertebrates and provide a synthesis of emerging patterns in the microbiome of those organisms. We highlight the importance of collection methods, and the need for greater taxonomic sampling of natural rather than captive hosts; a shift in approach that is needed to draw ecologically and evolutionarily relevant inferences. Finally, we recommend future directions for vertebrate microbiome research, so that attempts can be made to determine the role that microbial communities play in vertebrate biology and evolution.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Dimensions of biodiversity in the Earth mycobiome

Dimensions of biodiversity in the Earth mycobiome | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Plant microRNAs: key regulators of root architecture and biotic interactions

Plant microRNAs: key regulators of root architecture and biotic interactions | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants have evolved a remarkable faculty of adaptation to deal with various and changing environmental conditions. In this context, the roots have taken over nutritional aspects and the root system architecture can be modulated in response to nutrient availability or biotic interactions with soil microorganisms. This adaptability requires a fine tuning of gene expression. Indeed, root specification and development are highly complex processes requiring gene regulatory networks involved in hormonal regulations and cell identity. Among the different molecular partners governing root development, microRNAs (miRNAs) are key players for the fast regulation of gene expression. miRNAs are small RNAs involved in most developmental processes and are required for the normal growth of organisms, by the negative regulation of key genes, such as transcription factors and hormone receptors. Here, we review the known roles of miRNAs in root specification and development, from the embryonic roots to the establishment of root symbioses, highlighting the major roles of miRNAs in these processes.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Arbuscular mycorrhiza Symbiosis Induces a Major Transcriptional Reprogramming of the Potato SWEET Sugar Transporter Family

Arbuscular mycorrhiza Symbiosis Induces a Major Transcriptional Reprogramming of the Potato SWEET Sugar Transporter Family | MycorWeb Plant-Microbe Interactions | Scoop.it
Biotrophic microbes feeding on plants must obtain carbon from their hosts without killing the cells. The symbiotic Arbuscular mycorrhizal (AM) fungi colonizing plant roots do so by inducing major transcriptional changes in the host that ultimately also reprogram the whole carbon partitioning of the plant. AM fungi obtain carbohydrates from the root cortex apoplast, in particular from the periarbuscular space that surrounds arbuscules. However, the mechanisms by which cortical cells export sugars into the apoplast for fungal nutrition are unknown. Recently a novel type of sugar transporter, the SWEET, able to perform not only uptake but also efflux from cells was identified. Plant SWEETs have been shown to be involved in the feeding of pathogenic microbes and are, therefore, good candidates to play a similar role in symbiotic associations. Here we have carried out the first phylogenetic and expression analyses of the potato SWEET family and investigated its role during mycorrhiza symbiosis. The potato genome contains 35 SWEETs that cluster into the same four clades defined in Arabidopsis. Colonization of potato roots by the AM fungus Rhizophagus irregularis imposes major transcriptional rewiring of the SWEET family involving, only in roots, changes in 22 of the 35 members. None of the SWEETs showed mycorrhiza-exclusive induction and most of the 12 induced genes belong to the putative hexose transporters of clade I and II, while only two are putative sucrose transporters from clade III. In contrast, most of the repressed transcripts (10) corresponded to clade III SWEETs. Promoter-reporter assays for three of the induced genes, each from one cluster, showed re-localization of expression to arbuscule-containing cells, supporting a role for SWEETs in the supply of sugars at biotrophic interfaces. The complex transcriptional regulation of SWEETs in roots in response to AM fungal colonization supports a model in which symplastic sucrose in cortical cells could be cleaved in the cytoplasm by sucrose synthases or cytoplasmic invertases and effluxed as glucose, but also directly exported as sucrose and then converted into glucose and fructose by cell wall-bound invertases. Precise biochemical, physiological and molecular analyses are now required to profile the role of each potato SWEET in the arbuscular mycorrhizal symbiosis.
more...
No comment yet.
Rescooped by Francis Martin from Plant & Evolution
Scoop.it!

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana | MycorWeb Plant-Microbe Interactions | Scoop.it
Highlights •The genomes of 1,135 naturally inbred lines of Arabidopsis thaliana are presented •Relict populations that continue to inhabit ancestral habitats were discovered •The last glacial maximum was important in structuring the distribution of relicts •This collection will connect genotypes and phenotypes on a species-wide level Summary Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Via Pierre-Marc Delaux
more...
No comment yet.
Rescooped by Francis Martin from Plant & Evolution
Scoop.it!

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression

Evolution of High Cellulolytic Activity in Symbiotic  Streptomyces  through Selection of Expanded Gene Content and Coordinated Gene Expression | MycorWeb Plant-Microbe Interactions | Scoop.it

The evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in Streptomyces, a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the Streptomyces genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in Streptomyces, key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in Streptomyces, including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic Streptomyces for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology.


Via Pierre-Marc Delaux
more...
No comment yet.
Rescooped by Francis Martin from Plant pathogenic fungi
Scoop.it!

Tales and mysteries of fungal fruiting: How morphological and physiological traits affect a pileate lifestyle

Tales and mysteries of fungal fruiting: How morphological and physiological traits affect a pileate lifestyle | MycorWeb Plant-Microbe Interactions | Scoop.it

Highlights
• Functionality of the agaricoid fruit body design and its adaptive potential.
• Ecological functions of morphological and physiological fruit body traits.
• Trade-offs among protecting and attracting traits.
• Fruit body development and phenology.

Abstract
Mushroom-forming fungi exhibit a tremendous variety of morphological, physiological and behavioural traits. Though science had taken up the challenge to relate these traits to functions in the 20th century, such deliberations became much rarer in recent decades. In the review presented here we aim at reviving this research area, particularly in regard to ecological implications. We have therefore compiled fruit body traits with their evidenced or suggested functions. Some traits have no immediate functional meaning, but many are suggestive of some ecological importance. Many traits serve more than one function, and traits interact in the sense of trade-offs, patterns that reflect the economy of fungal design. In conclusion, the review comes up with well and little-known mushroom properties, and the numerous gaps in attributing traits to functions.


Via Steve Marek
more...
No comment yet.
Rescooped by Francis Martin from Plant pathogenic fungi
Scoop.it!

Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum

Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus  Colletotrichum higginsianum | MycorWeb Plant-Microbe Interactions | Scoop.it
Abstract

Even though the fungal kingdom contains more than 3 million species, little is known about the biological roles of RNA silencing in fungi. The Colletotrichum genus comprises fungal species that are pathogenic for a wide range of crop species worldwide. To investigate the role of RNA silencing in the ascomycete fungus Colletotrichum higginsianum, knock-out mutants affecting genes for three RNA-dependent RNA polymerase (RDR), two Dicer-like (DCL), and two Argonaute (AGO) proteins were generated by targeted gene replacement. No effects were observed on vegetative growth for any mutant strain when grown on complex or minimal media. However, Δdcl1, Δdcl1Δdcl2 double mutant, and Δago1 strains showed severe defects in conidiation and conidia morphology. Total RNA transcripts and small RNA populations were analyzed in parental and mutant strains. The greatest effects on both RNA populations was observed in the Δdcl1, Δdcl1Δdcl2, and Δago1 strains, in which a previously uncharacterized dsRNA mycovirus [termed Colletotrichum higginsianum non-segmented dsRNA virus 1 (ChNRV1)] was derepressed. Phylogenetic analyses clearly showed a close relationship between ChNRV1 and members of the segmented Partitiviridae family, despite the non-segmented nature of the genome. Immunoprecipitation of small RNAs associated with AGO1 showed abundant loading of 5’U-containing viral siRNA. C. higginsianum parental and Δdcl1 mutant strains cured of ChNRV1 revealed that the conidiation and spore morphology defects were primarily caused by ChNRV1. Based on these results, RNA silencing involving ChDCL1 and ChAGO1 in C. higginsianum is proposed to function as an antiviral mechanism.

Via Serenella A Sukno, Steve Marek
more...
No comment yet.
Rescooped by Francis Martin from Plants and Microbes
Scoop.it!

Annual Review of Plant Biology: The Haustorium, a Specialized Invasive Organ in Parasitic Plants (2016)

Annual Review of Plant Biology: The Haustorium, a Specialized Invasive Organ in Parasitic Plants (2016) | MycorWeb Plant-Microbe Interactions | Scoop.it

Parasitic plants thrive by infecting other plants. Flowering plants evolved parasitism independently at least 12 times, in all cases developing a unique multicellular organ called the haustorium that forms upon detection of haustorium-inducing factors derived from the host plant. This organ penetrates into the host stem or root and connects to its vasculature, allowing exchange of materials such as water, nutrients, proteins, nucleotides, pathogens, and retrotransposons between the host and the parasite. In this review, we focus on the formation and function of the haustorium in parasitic plants, with a specific emphasis on recent advances in molecular studies of root parasites in the Orobanchaceae and stem parasites in the Convolvulaceae.


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

Accounting for reciprocal host–microbiome interactions in experimental science

Accounting for reciprocal host–microbiome interactions in experimental science | MycorWeb Plant-Microbe Interactions | Scoop.it
Mammals are defined by their metagenome, a combination of host and microbiome genes. This knowledge presents opportunities to further basic biology with translation to human diseases. However, the now-documented influence of the metagenome on experimental results and the reproducibility of in vivo mammalian models present new challenges. Here we provide the scientific basis for calling on all investigators, editors and funding agencies to embrace changes that will enhance reproducible and interpretable experiments by accounting for metagenomic effects. Implementation of new reporting and experimental design principles will improve experimental work, speed discovery and translation, and properly use substantial investments in biomedical research.
more...
No comment yet.
Rescooped by Francis Martin from Plant-Microbe Symbiosis
Scoop.it!

Isolating a functionally relevant guild of fungi from the root microbiome of Populus

Isolating a functionally relevant guild of fungi from the root microbiome of Populus | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant roots interact with a bewilderingly complex community of microbes, including root-associated fungi that are essential for maintaining plant health. To improve understanding of the diversity of fungi in the rhizobiome of Populus deltoides, Populus trichocarpa and co-occurring plant hosts Quercus alba and Pinus taeda, we conducted field and greenhouse studies and sampled, isolated, and characterized the diversity of culturable root-associated fungi on these hosts. Using both general and selective isolation media we obtained more than 1800 fungal isolates from individual surface sterilized root tips. Sequences from the ITS and/or D1– D2 regions of the LSU rDNA were obtained from 1042 of the >1800 pure culture isolates and were compared to accessions in the NCBI nucleotide database and analyzed through phylogenetics for preliminary taxonomic identification. Sequences from these isolates were also compared to 454 sequence datasets obtained directly from the Populus rhizosphere and endosphere. Although most of the ectomycorrhizal taxa known to associate with Populus evaded isolation, many of the abundant sequence types from rhizosphere and endosphere 454 datasets were isolated, including novel species belonging to the Atractiellales. Isolation and identification of key endorrhizal fungi will enable more targeted study of plant-fungal interactions. Genome sequencing is currently underway for a subset of our culture library with the aim of understanding the mechanisms involved in host-endophyte establishment and function. This diverse culture library of fungal root associates will be a valuable resource for metagenomic research, experimentation and further studies on plant-fungal interactions.


Via Jean-Michel Ané
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Location, location, location: priority effects in wood decay communities may vary between sites

Location, location, location: priority effects in wood decay communities may vary between sites | MycorWeb Plant-Microbe Interactions | Scoop.it
Priority effects are known to have a major influence on fungal community development in decomposing wood, but it has not yet been established whether these effects are consistent between different geographical locations. Here, beech (Fagus sylvatica) wood disks that had been pre-colonized with three wood decay basidiomycetes were placed in seven woodland sites with similar characteristics for 12–24 months, and the successor communities profiled using culture-based techniques coupled with amplicon sequencing. On the majority of sites, assembly history differed as a result of primary versus secondary resource capture only (i.e. different communities developed in uncolonized control disks compared with those that had been pre-colonized), but on certain sites distinct successor communities followed each pre-colonizer species. This study provides preliminary evidence that differences in abiotic factors and species pools between sites can cause spatial variation in how priority effects influence wood decay communities.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Ectomycorrhizal and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment

Ectomycorrhizal and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment | MycorWeb Plant-Microbe Interactions | Scoop.it
Exploring the link between above- and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well-recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field-based tree experiment in Minnesota, USA to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length, and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). While the phylum effect was driven by differences in ectomycorrhizal fungal community composition, the origin effect was driven by differences in community heterogeneity. Taken together, this study emphasizes the guild-specific nature of plant-associated effects on soil fungal communities and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness.
more...
Brian P. Looney's curator insight, June 22, 1:37 PM

When ECM plant hosts abound, do ECM fungi go wild and outcompete SAP fungi? Race for the nitrogen...

Scooped by Francis Martin
Scoop.it!

Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus

Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungi interact with their environment by secreting proteins to obtain nutrients, elicit responses and modify their surroundings. Because the set of proteins secreted by a fungus is related to its lifestyle, it should be possible to use it as a tool to predict fungal lifestyle. To test this hypothesis, we bioinformatically identified 538 and 554 secretable proteins in the monokaryotic strains PC9 and PC15 of the white rot basidiomycete Pleurotus ostreatus. Functional annotation revealed unknown functions (37.2%), glycosyl hydrolases (26.5%) and redox enzymes (11.5%) as the main groups in the two strains. When these results were combined with RNA-seq analyses, we found that the relative importance of each group was different in different strains and culture conditions and the relevance of the unknown function proteins was enhanced. Only a few genes were actively expressed in a given culture condition in expanded multigene families, suggesting that family expansi on could increase adaptive opportunities rather than activity under a specific culture condition. Finally, we used the set of P. ostreatus secreted proteins as a query to search their counterparts in other fungal genomes and found that the secretome profiles cluster the tested basidiomycetes into lifestyle rather than phylogenetic groups.
more...
No comment yet.
Scooped by Francis Martin
Scoop.it!

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

Transposable Elements  versus  the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles | MycorWeb Plant-Microbe Interactions | Scoop.it

Transposable elements (TEs) are enigmatic genetic units that have played important roles in the evolution of eukaryotic genomes. Since their discovery in the 1950s, they have gained increasing attention and are known today as active genome modelers in multiple species. Although these elements have been widely studied in plants, much less is known about their occurrence and impact on the fungal kingdom. Using a diverse set of basidiomycete and ascomycete fungi, we quantified and characterized a huge diversity of DNA and RNA transposable elements, and we identified species that had 0.02 to 29.8% of their genomes occupied by transposable elements. In addition, using our basidiomycete model Pleurotus ostreatus , we demonstrated how TE insertions produced detrimental effects on the expression of upstream and downstream genes, which were downregulated compared with the control groups. This silencing mechanism was present in the basidiomycetes tested but exhibited a patchy distribution in ascomycetes, and might be related to specific genome defense mechanisms that control transposon proliferation. This finding reveals the broader impact of transposable elements in fungi. In addition to their importance as long-term evolutionary forces, they play major roles in the more dynamic transcriptome regulation of certain species.

more...
No comment yet.
Rescooped by Francis Martin from Ecology, evolution, pathogens, genomics, fungi, biotic interactions, human history ...
Scoop.it!

Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella - JW Taylor et al.

Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella - JW Taylor et al. | MycorWeb Plant-Microbe Interactions | Scoop.it
With the termination of dual nomenclature, each fungus may have only one name. Now mycologists must choose between genus names formerly applied to taxa with either asexual or sexual reproductive modes, a choice that often influences the breadth of genotypic and phenotypic diversity in a genus, and even its monophyly. We use the asexual genus Aspergillus to examine the problems involved in such choices because (a) 11 sexual generic names are associated with it and (b) phenotypic variation and genetic divergence within sexual genera are low but between sexual genera are high. As a result, in the case of Aspergillus, applying the asexual name to the many sexual genera masks information now conveyed by the genus names and would lead to taxonomic inconsistency in the Eurotiales because this large Aspergillus would then embrace more genetic divergence than neighboring clades comprised of two or more genera. Two proposals have been published concerning this problem as it relates to Aspergillus: one advocates a broad concept, referred to here as "Wide Aspergillus";, which embraces as many Aspergillus species as possible while maintaining Penicillium as a separate genus; the other, referred to here as "Narrow Aspergillus";, preserves this genus for a much smaller group of closely related species and retains many of the sexual genera. Phylogenetic analyses detailed here show that, to be monophyletic, Wide Aspergillus must embrace several genera morphologically discordant with Aspergillus, including Penicillium, Phialosimplex and Polypaecilum. Likelihood ratio tests reject a Wide Aspergillus that excludes Phialosimplex and Polypaecilum. Phylogenetic Rank Boundary Optimization, which employs the genetic divergence measure, maximum subtree height, to assess inconsistency in the ranking of genera and species, shows that Narrow Aspergillus provides a more consistent taxonomy than Wide Aspergillus. Adopting Narrow Aspergillus and retaining sexual names instead of adopting Wide Aspergillus will result in genera that convey precise morphological and physiological information, that are monophyletic, and that are taxonomically consistent.

Via Pierre Gladieux
more...
No comment yet.
Rescooped by Francis Martin from Plant & Evolution
Scoop.it!

Carlactone-type strigolactones and their synthetic analogues as inducers of hyphal branching in arbuscular mycorrhizal fungi

Carlactone-type strigolactones and their synthetic analogues as inducers of hyphal branching in arbuscular mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Abstract Hyphal branching in the vicinity of host roots is a host recognition response of arbuscular mycorrhizal fungi. This morphological event is elicited by strigolactones. Strigolactones are carotenoid-derived terpenoids that are synthesized from carlactone and its oxidized derivatives. To test the possibility that carlactone and its oxidized derivatives might act as host-derived precolonization signals in arbuscular mycorrhizal symbiosis, carlactone, carlactonoic acid, and methyl carlactonoate as well as monohydroxycarlactones, 4-, 18-, and 19-hydroxycarlactones, were synthesized chemically and evaluated for hyphal branching-inducing activity in germinating spores of the arbuscular mycorrhizal fungus Gigaspora margarita. Hyphal branching activity was found to correlate with the degree of oxidation at C-19 methyl. Carlactone was only weakly active (100 ng/disc), whereas carlactonoic acid showed comparable activity to the natural canonical strigolactones such as strigol and sorgomol (100 pg/disc). Hydroxylation at either C-4 or C-18 did not significantly affect the activity. A series of carlactone analogues, named AD ester and AA’D diester, was synthesized by reacting formyl Meldrum’s acid with benzyl, cyclohexylmethyl, and cyclogeranyl alcohols (the A-ring part), followed by coupling of the potassium enolates of the resulting formylacetic esters with the D-ring butenolide. AD ester analogues exhibited moderate activity (1 ng–100 pg/disc), while AA’D diester analogues having cyclohexylmethyl and cyclogeranyl groups were highly active on the AM fungus (10 pg/disc). These results indicate that the oxidation of methyl to carboxyl at C-19 in carlactone is a prerequisite but BC-ring formation is not essential to show hyphal branching activity comparable to that of canonical strigolactones.

Via Pierre-Marc Delaux
more...
No comment yet.
Rescooped by Francis Martin from Plant & Evolution
Scoop.it!

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs

Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5′ untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.

Via Pierre-Marc Delaux
more...
No comment yet.
Rescooped by Francis Martin from Fungal|Oomycete Biology
Scoop.it!

Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis

Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis | MycorWeb Plant-Microbe Interactions | 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.
See it on Scoop.it, via The Plant Microbiome
Via Jessie Uehling, Alejandro Rojas
more...
No comment yet.
Rescooped by Francis Martin from Plant pathogenic fungi
Scoop.it!

A Phytophthora sojae effector suppresses endoplasmic reticulum stress-mediated immunity by stabilizing plant Binding immunoglobulin Proteins

A Phytophthora sojae effector suppresses endoplasmic reticulum stress-mediated immunity by stabilizing plant Binding immunoglobulin Proteins | MycorWeb Plant-Microbe Interactions | Scoop.it
Phytophthora pathogens secrete an array of specific effector proteins to manipulate host innate immunity to promote pathogen colonization. However, little is known about the host targets of effectors and the specific mechanisms by which effectors increase susceptibility. Here we report that the soybean pathogen Phytophthora sojae uses an essential effector PsAvh262 to stabilize endoplasmic reticulum (ER)-luminal binding immunoglobulin proteins (BiPs), which act as negative regulators of plant resistance to Phytophthora. By stabilizing BiPs, PsAvh262 suppresses ER stress-triggered cell death and facilitates Phytophthora infection. The direct targeting of ER stress regulators may represent a common mechanism of host manipulation by microbes.

Via Steve Marek
more...
No comment yet.
Rescooped by Francis Martin from Plants and Microbes
Scoop.it!

New Phytologist: Seeing is believing: cell biology at the plant–microbe interface (2016)

New Phytologist: Seeing is believing: cell biology at the plant–microbe interface (2016) | MycorWeb Plant-Microbe Interactions | Scoop.it

36th New Phytologist Symposium ‘Cell biology at the plant–microbe interface’ Munich, Germany, November/December 2015

 

The advances made during the twentieth century in understanding the genetics of host–pathogen interactions transformed crop breeding; however the field of plant pathology was founded from the earliest cell biology of Hooke and his contemporaries. During the twenty-first century phytopathologists have refocused their attention to the microscopic world to identify the molecular mechanisms responsible for inherited disease resistance, mutualistic interactions and virulence. For the first time a symposium was organized to specifically discuss the latest insights into plant– microbe interactions gained by merging rediscovered techniques, such as electron-microscopy, with new tools that allow in vivo highresolution tracking of cellular dynamics. These methods, together with the implementation of state-of-the-art proteomic and chemical biology approaches, are helping to elucidate the intricate mechanism of the interaction between two organisms. In this report we highlight emergent themes from the meeting and some of the cognate fundamental biological questions driving the contemporary study of phytopathology and mutualism.


Via Kamoun Lab @ TSL
more...
Jessie Uehling's curator insight, June 8, 11:10 AM
Seeing is believing isnt it?
Scooped by Francis Martin
Scoop.it!

Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)

Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood) | MycorWeb Plant-Microbe Interactions | Scoop.it
Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species Populus balsamifera and identified candidate genes for local adaptation. Here, we explored the patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or subfunctionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.
more...
No comment yet.