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Altering the Cell Wall and Its Impact on Plant Disease: From Forage to Bioenergy

Altering the Cell Wall and Its Impact on Plant Disease: From Forage to Bioenergy | MycorWeb Plant-Microbe Interactions | Scoop.it

The individual sugars found within the major classes of plant cell wall polymers are dietary components of herbivores and are targeted for release in industrial processes for fermentation to liquid biofuels. With a growing understanding of the biosynthesis of the complex cell wall polymers, genetic modification strategies are being developed to target the cell wall to improve the digestibility of forage crops and to render lignocellulose less recalcitrant for bioprocessing. This raises concerns as to whether altering cell wall properties to improve biomass processing traits may inadvertently make plants more susceptible to diseases and pests. Here, we review the impacts of cell wall modification on plant defense, as assessed from studies in model plants utilizing mutants or transgenic modification and in crop plants specifically engineered for improved biomass or bioenergy traits. Such studies reveal that cell wall modifications can indeed have unintended impacts on plant defense, but these are not always negative.


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Where Should I Send It? Optimizing the Submission Decision Process

Where Should I Send It? Optimizing the Submission Decision Process | MycorWeb Plant-Microbe Interactions | Scoop.it
How do scientists decide where to submit manuscripts? Many factors influence this decision, including prestige, acceptance probability, turnaround time, target audience, fit, and impact factor. Here, we present a framework for evaluating where to submit a manuscript based on the theory of Markov decision processes. We derive two models, one in which an author is trying to optimally maximize citations and another in which that goal is balanced by either minimizing the number of resubmissions or the total time in review. We parameterize the models with data on acceptance probability, submission-to-decision times, and impact factors for 61 ecology journals. We find that submission sequences beginning with Ecology Letters, Ecological Monographs, or PLOS ONE could be optimal depending on the importance given to time to acceptance or number of resubmissions. This analysis provides some guidance on where to submit a manuscript given the individual-specific values assigned to these disparate objectives.
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Where Next for Microbiome Research?

The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of “van Leeuwenhoek”–like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what’s next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.
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Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism

Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism | MycorWeb Plant-Microbe Interactions | Scoop.it

Research on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)-driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host–pathogen–microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens.

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Tyranny of trees in grassy biomes

Tyranny of trees in grassy biomes | MycorWeb Plant-Microbe Interactions | Scoop.it
Tree planting, fire suppression, and exclusion of megafaunal herbivores (native or domestic) are ecologically reasonable restoration strategies in deforested landscapes, but similar interventions can be catastrophic when applied to grassy biomes such as grasslands, savannas, and open-canopy woodlands (1). As hopes grow that carbon payment schemes will finance forest restoration (2), we must clearly distinguish between “reforestation”—planting trees on deforested land—and “afforestation”—converting historically nonforest lands to forests or tree plantations (3). Afforestation of grassy biomes can severely compromise ecosystem services, including hydrology (4) and soil nutrient cycles (5), and markedly reduce biodiversity (6).

Despite these high environmental costs, grassy biomes, particularly those with seasonally dry tropical climates, are prime targets for carbon sequestration programs that emphasize tree planting (1, 7). Threats of afforestation and agricultural conversion are exacerbated because the grassy biomes are not formally recognized by the United Nations (UN) Framework Convention on Climate Change, the program for Reducing Emissions from Deforestation and Forest Degradation (REDD+), or the UN Food and Agriculture Organization. This lack of recognition reflects fundamental misperceptions about the ecology, conservation values, locations, and antiquity of the grassy biomes.
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Cetaceans evolution: insights from the genome sequences of common minke whales

Cetaceans evolution: insights from the genome sequences of common minke whales | MycorWeb Plant-Microbe Interactions | Scoop.it
Background
Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water.

Results
We present four common minke whale (Balaenoptera acutorostrata) genomes with depth of ×13 ~ ×17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 – 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales.

Conclusions
This whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth.
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Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products

In recent years, the genus Pestalotiopsis is receiving increasing attention, not only because of its economic impact as a plant pathogen but also as a commonly isolated endophyte which is an important source of bioactive natural products. Pestalotiopsis fici Steyaert W106-1/CGMCC3.15140 as an endophyte of tea produces numerous novel secondary metabolites, including chloropupukeananin, a derivative of chlorinated pupukeanane that is first discovered in fungi. Some of them might be important as the drug leads for future pharmaceutics.
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Rescooped by Francis Martin from Plant-Microbe Symbioses
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From mycoheterotrophy to mutualism: mycorrhizal specificity and functioning in Ophioglossum vulgatum sporophytes

Mycorrhizal functioning in the fern Ophioglossum is complex and poorly understood. It is unknown whether mature O. vulgatum sporophytes form mutualistic associations with fungi of the Glomeromycota and with what specificity. Are green sporophytes able to ‘repay’ fungal carbon (C) invested in them by mycorrhizal partners during the initially heterotrophic gametophyte and early sporophyte stages of the lifecycle?
We identified fungal partners of O. vulgatum sporophytes using molecular techniques and supplied them with 33P-orthophosphate and O. vulgatum sporophytes with 14CO2. We traced the movement of fungal-acquired nutrients and plant-fixed C between symbionts and analysed natural abundance 13C and 15N isotope signatures to assess nutritional interactions.
We found fungal specificity of O. vulgatum sporophytes towards a mycorrhizal fungus closely related to Glomus macrocarpum. Our radioisotope tracers revealed reciprocal C-for-phosphorus exchange between fern sporophytes and fungal partners, despite competition from surrounding vegetation. Monocultures of O. vulgatum were enriched in 13C and 15N, providing inconclusive evidence of mycoheterotrophy when experiencing competition from the surrounding plant community.
We show mutualistic and specific symbiosis between a eusporangiate fern and fungi of the Glomeromycota. Our findings suggest a ‘take now, pay later’ strategy of mycorrhizal functioning through the lifecycle O. vulgatum, from mycoheterotrophic gametophyte to mutualistic aboveground sporophyte.

Via Pierre-Marc Delaux, Jean-Michel Ané
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Jean-Michel Ané's curator insight, January 24, 12:31 PM

One more very nice study on AM associations in ferns

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Population genetic structure of the ectomycorrhizal fungus Laccaria sp. A resembles that of its host tree Nothofagus cunninghamii

Population genetic structure of the ectomycorrhizal fungus Laccaria sp. A resembles that of its host tree Nothofagus cunninghamii | MycorWeb Plant-Microbe Interactions | Scoop.it
The ectomycorrhizal fungus Laccaria sp. A is restricted to temperate rainforest of southeast Australia, associated with its host tree Nothofagus cunninghamii. Eight mitochondrial microsatellite markers were used to investigate the population genetic structure of L. sp. A across its distribution in Tasmania and Victoria. The highest allelic diversity was found in Tasmania, which appeared to contain a panmictic population, whereas the more fragmented Victorian populations were characterized by low allelic diversity and differentiation between east and west. There is evidence of glacial refugia in the west and the northeast of Tasmania, and in Victoria in the Otway Ranges and Central Highlands, with postglacial migration into the Strzelecki Ranges. Narrow host-specificity may have contributed to the presence of population structure in this fungus. Allelic diversity patterns in L. sp. A are largely congruent with diversity patterns already established in populations of its host, N. cunninghamii.
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Monitoring ectomycorrhizal fungi at large scales for science, forest management, fungal conservation and environmental policy

Monitoring ectomycorrhizal fungi at large scales for science, forest management, fungal conservation and environmental policy | MycorWeb Plant-Microbe Interactions | Scoop.it
The ICP Forests network can be a platform for large-scale mycorrhizal studies. Mapping and monitoring of mycorrhizas have untapped potential to inform science, management, conservation and policy regarding distributions, diversity hotspots, dominance and rarity, and indicators of forest changes.
Context
A dearth of information about fungi at large scales has severely constrained scientific, forest management, fungal conservation and environmental policy efforts worldwide. Nonetheless, fungi fulfil critical functional roles in our changing environments and represent a considerable proportion of terrestrial biodiversity. Mycorrhizal fungi are increasingly viewed as a major functional guild across forest ecosystems, and our ability to study them is expanding rapidly.
Aims
This study aimed to discuss the potential for starting a mycorrhizal monitoring programme built upon the existing forest monitoring network, raise questions, propose hypotheses and stimulate further discussion.
Results
An overview of the state-of-the-art regarding forest ectomycorrhizal ecology raises questions and recommendations for scaling up mycorrhizal assessments aimed at informing a variety of stakeholders, with a new focus on conservation and policy.
Conclusion
Fungal research and conservation are areas that can be informed by ICP Forests and may lead to useful spin-offs; research linked to long-term forest monitoring plots will enhance the relevance of science and conservation.
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Tissue-based map of the human proteome

Tissue-based map of the human proteome | MycorWeb Plant-Microbe Interactions | Scoop.it
Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray–based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.
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Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homo...

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ISME J: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

ISME J: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics | MycorWeb Plant-Microbe Interactions | Scoop.it

Symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. Recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. We have explored the metabolic potentials of the microbiome using the lung lichen Lobaria pulmonaria as the model. Metagenomic and proteomic data were comparatively assessed and visualized by Voronoi treemaps. The study was complemented with molecular, microscopic and physiological assays. We have found that more than 800 bacterial species have the ability to contribute multiple aspects to the symbiotic system, including essential functions such as (i) nutrient supply, especially nitrogen, phosphorous and sulfur, (ii) resistance against biotic stress factors (that is, pathogen defense), (iii) resistance against abiotic factors, (iv) support of photosynthesis by provision of vitamin B12, (v) fungal and algal growth support by provision of hormones, (vi) detoxification of metabolites, and (vii) degradation of older parts of the lichen thallus. Our findings showed the potential of lichen-associated bacteria to interact with the fungal as well as algal partner to support health, growth and fitness of their hosts. We developed a model of the symbiosis depicting the functional multi-player network of the participants, and argue that the strategy of functional diversification in lichens supports the longevity and persistence of lichens under extreme and changing ecological conditions.


Via Stéphane Hacquard
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Rescooped by Francis Martin from Plant immunity and legume symbiosis
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A fluorescent hormone biosensor reveals the dynamics of jasmonate signalling in plants : Nature Communications : Nature Publishing Group

A fluorescent hormone biosensor reveals the dynamics of jasmonate signalling in plants : Nature Communications : Nature Publishing Group | MycorWeb Plant-Microbe Interactions | Scoop.it
Activated forms of jasmonic acid (JA) are central signals coordinating plant responses to stresses, yet tools to analyse their spatial and temporal distribution are lacking. Here we describe a JA perception biosensor termed Jas9-VENUS that allows the quantification of dynamic changes in JA distribution in response to stress with high spatiotemporal sensitivity. We show that Jas9-VENUS abundance is dependent on bioactive JA isoforms, the COI1 co-receptor, a functional Jas motif and proteasome activity. We demonstrate the utility of Jas9-VENUS to analyse responses to JA in planta at a cellular scale, both quantitatively and dynamically. This included using Jas9-VENUS to determine the cotyledon-to-root JA signal velocities on wounding, revealing two distinct phases of JA activity in the root. Our results demonstrate the value of developing quantitative sensors such as Jas9-VENUS to provide high-resolution spatiotemporal data about hormone distribution in response to plant abiotic and biotic stresses.

Via Christophe Jacquet
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Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts

Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts | MycorWeb Plant-Microbe Interactions | Scoop.it

To survive in resource-limited and dynamic environments, microbial populations implement a diverse repertoire of regulatory strategies. These strategies often rely on anticipating impending environmental shifts, enabling the population to be prepared for a future change in conditions. It has long been known that cells optimize nutritional value from mixtures of carbon sources, for example glucose and galactose, by sequential activation of regulatory programs that allow for metabolizing the preferred carbon source first before metabolizing the secondary carbon source. Using automated flow-cytometry, we mapped the dynamical behavior of populations simultaneously presented with a large panel of different glucose and galactose concentrations. We show that, counter to expectations, in populations presented with glucose and galactose simultaneously, the galactose regulatory pathway is activated in a fraction of the cell population hours before glucose is fully consumed. We demonstrate that the size of this fraction of cells is tuned by the concentration of the two sugars. This population diversification may constitute a tradeoff between the benefit of rapid galactose consumption once glucose is depleted and the cost of expressing the galactose pathway.

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Building the interaction interfaces: host responses upon infection with microorganisms

Building the interaction interfaces: host responses upon infection with microorganisms | MycorWeb Plant-Microbe Interactions | Scoop.it
Research fields of plant symbiosis and plant immunity were relatively ignorant with each other until a little while ago. Recently, however, increasing intercommunications between those two fields have begun to provide novel aspects and knowledge for understanding relationships between plants and microorganisms. Here, we review recent reports on plant–microbe interactions, focusing on the infection processes, in order to elucidate plant cellular responses that are triggered by both symbionts and pathogens. Highlighting the core elements of host responses over biotic interactions will provide insights into general mechanisms of plant–microbe interactions.
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Do pathogen effectors play peek-a-boo?

Epigenetics is a burgeoning field of research and many organisms are found to regulate genes in a transient (“above genetics”) way due to (temporarily) decorating DNA or proteins that associate with DNA. This can change transcription of affected genes and since such DNA modifications are reversible, the expression potential over time and generations can therefore be extremely variable. This allows many organisms to readily adapt and experiment with changes to the environment they are living in or challenges they are facing, such as pathogens (Iwasaki and Paszkowski, 2014). This research topic deals mainly with epigenetic mechanisms of plant responses but in the field of plant pathology, recent experimental data illustrate the involvement of epigenetic changes in both plant host and their pathogens (e.g., Luna et al., 2012; Qutob et al., 2013; Yu et al., 2013; Soyer et al., 2014). Indeed, pathogen pressure is very much an environmental cue that will induce epigenetic changes in plant hosts, but, in response, pathogens seem equipped to respond in kind.
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Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots

Members of the fungal genus Trichoderma directly antagonize soil-borne fungal pathogens, and an increasing number of species are studied for their potential in biocontrol of plant pathogens in agriculture. Some species also colonize plant roots, promoting systemic resistance. The Trichoderma-root interaction is hosted by a wide range of plant species, including monocots and dicots.
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High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here, multiyear and multienvironment evaluation of cell wall phenotypes was conducted in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree and two partially overlapping populations of unrelated P. trichocarpa genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. QTL mapping was conducted using a high-density genetic map with 3,568 SNP markers. As a fine-mapping approach, chromosome-wide association mapping targeting a QTL hot-spot on linkage group XIV was performed in the two P. trichocarpa populations. Both populations were genotyped using the 34 K Populus Infinium SNP array and whole-genome resequencing of one of the populations facilitated marker-saturation of candidate intervals for gene identification.
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New world-class scientific collaboration to use genomics to combat devastating crop rusts

New world-class scientific collaboration to use genomics to combat devastating crop rusts | MycorWeb Plant-Microbe Interactions | Scoop.it

The newly formed Norwich Rust Group aims to develop durable resistance in crops. Exploiting advances in genomics, scientists will investigate how parasitic rust fungi invade and feed off plants. They will also use these new techniques to locate genes in some varieties of crops which are able to resist invasion. There are more than 7,000 species of rust fungi, some of which are among agriculture’s most devastating pathogens, causing diseases such as Wheat Stem Rust, Wheat Yellow (Stripe) Rust, Asian Soybean Rust and Coffee Rust.

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Pourquoi tweeter quand on est chercheur?

Pourquoi tweeter quand on est chercheur? | MycorWeb Plant-Microbe Interactions | Scoop.it

Dans un article du journal Le Monde paru en 2014 intitulé «Twitter et les chercheurs, l’exception française?», Sylvain Deville s’étonnait de la faible place qu’occupe l’oiseau bleu chez les chercheurs français par rapport à nos collègues anglo-saxons. Notre rapport à la communication en général serait lacunaire, pour des raisons tant culturelles qu’institutionnelles.

Aujourd’hui, grâce à En Direct Du Labo, nous vous proposons de participer à changer cet état de fait en constituant la première communauté de chercheurs francophones ouverts à la communication scientifique sur Twitter!

Pourquoi utiliser Twitter lorsqu’on est un(e) chercheur(se)? Si vous pensez que vous n’avez rien à y gagner, voici quelques raisons qui pourraient vous faire changer d’avis: ....


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Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi

Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
One hundred and eleven strains of Basidiomycota, 39 strains of Ascomycota and 2 strains of Mucoromycotina belonging to wood decomposers that cause white-rot (WR) or brown-rot (BR), other wood associated saprotrophs (WA), litter decomposing cord-forming Basidiomycota (LDF), and saprotrophic microfungi (SA), were screened for the production of hydrolytic enzymes and laccase. The presence of enzyme-encoding genes was also analysed in the published genomes of saprotrophic fungi. Several genes, including those for acidic phosphatase, β-glucosidase and N-acetylglucosaminidase, were common in the genomes with enzyme activity widely displayed by fungi, while other enzymes, such as certain hemicellulases or laccase, were produced less frequently. Enzyme production by saprotrophic fungi was shaped by the combination of their ecophysiology and taxonomy. Basidiomycota exhibited higher activities of all enzymes, except alkaline phosphatase, α-glucosidase, N-acetylglucosaminidase, α-mannosidase and α-fucosidase, than Ascomycota. The SA and BR fungi showed distinct enzyme production patterns, while the enzyme production by WR, LDF and WA was similar. Differences among species were typically reflected in the level of enzyme activity rather than in the absence of enzymes. Enzyme screening results showed that in several cases, fungi exhibited enzyme activity without the presence of the corresponding gene and vice versa. This indicates that the use of genome-derived information for the prediction of potential enzyme production has substantial limitations and cannot replace functional screening of fungal cultures.
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Rescooped by Francis Martin from The science toolbox
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PLOS Computational Biology: A Quick Guide to Organizing Computational Biology Projects

PLOS Computational Biology: A Quick Guide to Organizing Computational Biology Projects | MycorWeb Plant-Microbe Interactions | Scoop.it

Most bioinformatics coursework focuses on algorithms, with perhaps some components devoted to learning programming skills and learning how to use existing bioinformatics software. Unfortunately, for students who are preparing for a research career, this type of curriculum fails to address many of the day-to-day organizational challenges associated with performing computational experiments. In practice, the principles behind organizing and documenting computational experiments are often learned on the fly, and this learning is strongly influenced by personal predilections as well as by chance interactions with collaborators or colleagues.

The purpose of this article is to describe one good strategy for carrying out computational experiments. I will not describe profound issues such as how to formulate hypotheses, design experiments, or draw conclusions. Rather, I will focus on relatively mundane issues such as organizing files and directories and documenting progress. These issues are important because poor organizational choices can lead to significantly slower research progress. I do not claim that the strategies I outline here are optimal. These are simply the principles and practices that I have developed over 12 years of bioinformatics research, augmented with various suggestions from other researchers with whom I have discussed these issues.

 


Via Niklaus Grunwald
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Hanna Schempf's curator insight, January 27, 12:29 PM

Possibly useful in my SI modelling; read later.

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Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant

Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant | MycorWeb Plant-Microbe Interactions | Scoop.it

The Euphorbiaceae family includes some of the most efficient biomass accumulators. The whole genome sequencing and development of genetic map of these species are important components in molecular breeding and genetic improvement. Here we report the draft genome of physic nut (Jatropha curcas L.), a biodiesel plant. The assembled genome has a total length of 320.5 Mbp and contains 27,172 putative protein-coding genes. We established a linkage map contains 1,208 markers, and anchored the genome assembly (81.7%) to this map to produce eleven pseudochromosomes. After a gene family clustering, 15,268 families were identified, of which 13,887 existed in the castor bean genome. Analysis of the genome highlighted specific expansion and contraction of a number of gene families during the evolution of this species, including the ribosome inactivating proteins and oil biosynthesis pathway enzymes. The genomic sequence and linkage map provide a valuable resource not only for the fundamental and applied research on physic nut but also for evolutionary and comparative genomics analysis, particularly in the Euphorbiaceae.

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PNAS: Structure, variation, and assembly of the root-associated microbiomes of rice

PNAS: Structure, variation, and assembly of the root-associated microbiomes of rice | MycorWeb Plant-Microbe Interactions | Scoop.it

Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.


Via Stéphane Hacquard
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MPMI: 14-3-3 proteins in plant-pathogen interactions

MPMI: 14-3-3 proteins in plant-pathogen interactions | MycorWeb Plant-Microbe Interactions | Scoop.it
14-3-3 proteins define a eukaryotic-specific protein family with a general role in signal transduction. Primarily, 14-3-3 proteins act as phospho-sensors, binding phosphorylated client proteins and modulating their functions. Since phosphorylation regulates a plethora of different physiological responses in plants, 14-3-3 proteins play roles in multiple signalling pathways, including those controlling metabolism, hormone signalling, cell division, and responses to abiotic and biotic stimuli. Increasing evidence supports a prominent role of 14-3-3 proteins in regulating plant immunity against pathogens at various levels. In this review, potential links between 14-3-3 function and the regulation of plant-pathogen interactions are discussed, with a special focus on the regulation of 14-3-3s in response to pathogen perception, interactions between 14-3-3s and defence-related proteins, and 14-3-3s as targets of pathogen effectors.

Via Christophe Jacquet, Jim Alfano
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