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The genome sequence and effector complement of the flax rust pathogen Melampsora lini

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

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Microsporidia: Eukaryotic Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfers - Annual Review of Microbiology

Microsporidia are eukaryotic parasites of many animals that appear to have adapted to an obligate intracellular lifestyle by modifying the morphology and content of their cells. Living inside other cells, they have lost many, or all, metabolic functions, resulting in genomes that are always gene poor and often very small. The minute content of microsporidian genomes led many to assume that these parasites are biochemically static and uninteresting. However, recent studies have demonstrated that these organisms can be surprisingly complex and dynamic. In this review I detail the most significant recent advances in microsporidian genomics and discuss how these have affected our understanding of many biological aspects of these peculiar eukaryotic intracellular pathogens.
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How Trees Calm Us Down - The New Yorker

How Trees Calm Us Down - The New Yorker | MycorWeb Plant-Microbe Interactions | Scoop.it
How a leafy sidewalk or a forest scene can make us feel richer, younger, and more focussed.
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Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417

Background
Plant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). In the past 30 years, the Pseudomonas spp. PGPR strains WCS358, WCS374 and WCS417 of the Willie Commelin Scholten (WCS) collection have been studied in detail in pioneering papers on the molecular basis of PGPR-mediated ISR and mechanisms of biological control of soil-borne pathogens via siderophore-mediated competition for iron.

Results
The genomes of the model WCS PGPR strains were sequenced and analyzed to unearth genetic cues related to biological questions that surfaced during the past 30 years of functional studies on these plant-beneficial microbes. Whole genome comparisons revealed important novel insights into iron acquisition strategies with consequences for both bacterial ecology and plant protection, specifics of bacterial determinants involved in plant-PGPR recognition, and diversity of protein secretion systems involved in microbe-microbe and microbe-plant communication. Furthermore, multi-locus sequence alignment and whole genome comparison revealed the taxonomic position of the WCS model strains within the Pseudomonas genus. Despite the enormous diversity of Pseudomonas spp. in soils, several plant-associated Pseudomonas spp. strains that have been isolated from different hosts at different geographic regions appear to be nearly isogenic to WCS358, WCS374, or WCS417. Interestingly, all these WCS look-a-likes have been selected because of their plant protective or plant growth-promoting properties.

Conclusions
The genome sequences of the model WCS strains revealed that they can be considered representatives of universally-present plant-beneficial Pseudomonas spp. With their well-characterized functions in the promotion of plant growth and health, the fully sequenced genomes of the WCS strains provide a genetic framework that allows for detailed analysis of the biological mechanisms of the plant-beneficial traits of these PGPR. Considering the increasing focus on the role of the root microbiome in plant health, functional genomics of the WCS strains will enhance our understanding of the diversity of functions of the root microbiome.

Via Jean-Michel Ané
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Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals | MycorWeb Plant-Microbe Interactions | Scoop.it

Trees and their associated rhizosphere organisms play a major role in mineral weathering driving calcium fluxes from the continents to the oceans that ultimately control long-term atmospheric CO2 and climate through the geochemical carbon cycle. Photosynthate allocation to tree roots and their mycorrhizal fungi is hypothesized to fuel the active secretion of protons and organic chelators that enhance calcium dissolution at fungal-mineral interfaces. This was tested using 14CO2 supplied to shoots of Pinus sylvestris ectomycorrhizal with the widespread fungus Paxillus involutus in monoxenic microcosms, revealing preferential allocation by the fungus of plant photoassimilate to weather grains of limestone and silicates each with a combined calcium and magnesium content of over 10 wt.%. Hyphae had acidic surfaces and linear accumulation of weathered calcium with secreted oxalate, increasing significantly in sequence: quartz, granite < basalt, olivine, limestone < gabbro. These findings confirmed the role of mineral-specific oxalate exudation in ectomycorrhizal weathering to dissolve calcium bearing minerals, thus contributing to the geochemical carbon cycle.

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Les mycorhizes

Les mycorhizes | MycorWeb Plant-Microbe Interactions | Scoop.it
Depuis la première édition de ce livre, en 2008, plus de 10000 nouvelles contributions à la connaissance des mycorhizes ont été publiées. Voilà pourquoi cette nouvelle édition augmentée et mise à jour a paru nécessaire.
Les mycorhizes sont formées par des champignons microscopiques qui font merveille en horticulture en travaillant en symbiose avec les racines des plantes. Les champignons aident les plantes à puiser des éléments nutritifs dans le sol et à s'adapter au milieu. En échange, les plantes fournissent aux champignons l'énergie qu'ils sont incapables de tirer eux-mêmes du soleil.
Au cours des dernières années, une multitude de travaux ont clairement démontré l'intérêt scientifique et pratique de ces symbioses pour l'ensemble des végétaux du monde entier, que ce soit dans les écosystèmes naturels ou ceux aménagés par l'homme. Pourtant, en dépit de ces preuves répétées et irréfutables, un grand nombre de praticiens en horticulture, en agriculture, en foresterie et en environnement comprennent encore mal l'importance concrète de ce phénomène. Les pratiques durables dans ces domaines d'application ont pourtant tout à gagner d'une utilisation judicieuse des symbioses mycorhiziennes.
C'est dans cet esprit que les auteurs – des sommités en matière de mycorhizes – ont préparé cette nouvelle édition d'un volume qui vise à la fois à faire comprendre la biologie des mycorhizes dans ce qu'elle a de plus fascinant et à montrer comment en tirer profit dans de très nombreux aspects de la culture des plantes et de leur protection, tout en assurant le maintien des équilibres naturels.

Via Jean-Michel Ané
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Marie Aizpuru's curator insight, Today, 4:31 AM

Via les murs d'actualités thématiques de Jean-Michel Ané si bien documentés. Merci.

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Rice researchers redress retraction

Rice researchers redress retraction | MycorWeb Plant-Microbe Interactions | Scoop.it
As for how the retraction saga has altered working practices in her lab, Ronald now requires that three independent researchers validate new experimental approaches before publication. And all lab members now use electronic notebooks to make it easier to find data once members have left the lab.
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Evidence for archaic adaptive introgression in humans : Nature Reviews Genetics

Evidence for archaic adaptive introgression in humans : Nature Reviews Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it
As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments — a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions.
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New mystery for Native American origins

New mystery for Native American origins | MycorWeb Plant-Microbe Interactions | Scoop.it

The Americas were the last great frontier to be settled by humans, and their peopling remains one of the great mysteries for researchers. This week, two major studies of the DNA of living and ancient people try to settle the big questions about the early settlers: who they were, when they came, and how many waves arrived. But instead of converging on a single consensus picture, the studies, published online in Science and Nature, throw up a new mystery: Both detect in modern Native Americans a trace of DNA related to that of native people from Australia and Melanesia. The competing teams, neither of which knew what the other was up to until the last minute, are still trying to reconcile and make sense of each other's data.

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Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life | MycorWeb Plant-Microbe Interactions | Scoop.it

Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.

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Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale | MycorWeb Plant-Microbe Interactions | Scoop.it

Background. With rapid advancements in technology, the sequences of thousands of species’ genomes are becoming available. Within the sequences are repeats that comprise significant portions of genomes. Successful annotations thus require accurate discovery of repeats. As species-specific elements, repeats in newly sequenced genomes are likely to be unknown. Therefore, annotating newly sequenced genomes requires tools to discover repeats de-novo. However, the currently available de-novo tools have limitations concerning the size of the input sequence, ease of use, sensitivities to major types of repeats, consistency of performance, speed, and false positive rate.

 

Results. To address these limitations, I designed and developed Red, applying Machine Learning. Red is the first repeat-detection tool capable of labeling its training data and training itself automatically on an entire genome. Red is easy to install and use. It is sensitive to both transposons and simple repeats; in contrast, available tools such as RepeatScout and ReCon are sensitive to transposons, and WindowMasker to simple repeats. Red performed consistently well on seven genomes; the other tools performed well only on some genomes. Red is much faster than RepeatScout and ReCon and has a much lower false positive rate than WindowMasker. On human genes with five or more copies, Red was more specific than RepeatScout by a wide margin. When tested on genomes of unusual nucleotide compositions, Red located repeats with high sensitivities and maintained moderate false positive rates. Red outperformed the related tools on a bacterial genome. Red identified 46,405 novel repetitive segments in the human genome. Finally, Red is capable of processing assembled and unassembled genomes.
Conclusions

Red’s innovative methodology and its excellent performance on seven different genomes represent a valuable advancement in the field of repeats discovery.

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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing | MycorWeb Plant-Microbe Interactions | Scoop.it
Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.
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Genetic evidence for two founding populations of the Americas : Nature

Genetic evidence for two founding populations of the Americas : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America1, 2, 3, 4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia)5, 6, 7, 8. Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
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‘Ghost population’ hints at long-lost migration to the Americas

‘Ghost population’ hints at long-lost migration to the Americas | MycorWeb Plant-Microbe Interactions | Scoop.it
Present-day Amazonians share an unexpected genetic link with Asian islanders, hinting at an ancient trek.
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Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function

Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function | MycorWeb Plant-Microbe Interactions | Scoop.it

Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20–24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.

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New Phytologist: Standards for plant synthetic biology: a common syntax for exchange of DNA parts (2015)

New Phytologist: Standards for plant synthetic biology: a common syntax for exchange of DNA parts (2015) | MycorWeb Plant-Microbe Interactions | Scoop.it

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.


Via Kamoun Lab @ TSL
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Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.

Via Jean-Michel Ané
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Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering

Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering | MycorWeb Plant-Microbe Interactions | Scoop.it
The goal of microbiome engineering is to manipulate the microbiome toward a certain type of community that will optimize plant functions of interest. For instance, in crop production the goal is to reduce disease susceptibility, increase nutrient availability increase abiotic stress tolerance and increase crop yields. Various approaches can be devised to engineer the plant–microbiome, but one particularly promising approach is to take advantage of naturally evolved plant–microbiome communication channels. This is, however, very challenging as the understanding of the plant–microbiome communication is still mostly rudimentary and plant–microbiome interactions varies between crops species (and even cultivars), between individual members of the microbiome and with environmental conditions. In each individual case, many aspects of the plant–microorganisms relationship should be thoroughly scrutinized. In this article we summarize some of the existing plant–microbiome engineering studies and point out potential avenues for further research.

Via Jean-Michel Ané
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We Want the Funk: The Ups and Downs of Wild Microbes in Beer - EveryONE

We Want the Funk: The Ups and Downs of Wild Microbes in Beer - EveryONE | MycorWeb Plant-Microbe Interactions | Scoop.it
Funky, floral, complex. No, this is not a description of a piece of vintage wallpaper. These are some of the words that are used to describe the enormous variety that exists within the world of beer. Whether you are enjoying … Continue reading »
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Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor

Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor | MycorWeb Plant-Microbe Interactions | Scoop.it
Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~104 cells cm−3. Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.
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Revolution in human evolution

Revolution in human evolution | MycorWeb Plant-Microbe Interactions | Scoop.it
ust 5 years ago, extracting and deciphering a single fossil's genome—and making sure the result was not muddied by contamination with modern DNA—was a titanic effort. Now, thanks to technological breakthroughs that have vastly accelerated sequencing and made the results more trustworthy, DNA researchers the world over are awash in data (see p. 359). The result is a series of revelations about humanity's past. Ancient DNA has led to the discovery of new types of ancient humans and revealed interbreeding between our ancestors and our archaic cousins, which left a genetic legacy that shapes our health and appearance today. And because investigators can now sequence entire ancient populations, as Reich's lab is doing, ancient DNA is adding layers of complexity to the story of how ancient populations migrated and mixed across the globe. “The whole field is exploding in terms of its impact,” says Christina Warinner of the University of Oklahoma, Norman. “The data that's coming out is completely rewriting what we know about human prehistory.”
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Lost worlds found

Lost worlds found | MycorWeb Plant-Microbe Interactions | Scoop.it
If time travel were possible, big game hunters would be clamoring to visit the Yukon during the last ice age. About 30,000 years ago, mammoths with 3-meter tusks and shaggy coats nosed about with bison, woolly rhinos, muskoxen, and small horses, while lions, short-faced bears, and scimitar-toothed cats lurked in the background. But the vast Pleistocene game park had vanished by 10,000 years ago. The great beasts were long gone, replaced by familiar elk and moose, with lynx and grizzlies as predators.

For decades, scientists have debated why these megafauna disappeared from the Arctic and much of the rest of the world. Did a fluctuating climate drive species to extinction? Or did humans, in their relentless expansion across the globe, kill off the big game in an ancient hunting spree?

Now, ancient DNA data have entered the fray, most recently in the form of molecules scooped directly from samples of soil or ice. By sequencing whatever DNA emerges from even a thimbleful of ancient soil, researchers are reconstructing ancient ecosystems as far back as 700,000 years ago with astonishing clarity. A single sample of so-called environmental DNA (eDNA), combining sequences from plant and animal detritus as well as microbes, can provide an inventory of ancient species, filling gaps in conventional fossil and pollen records. The method “could revolutionize our understanding of [ancient] ecosystems by giving us … a full picture of the food web from the ground up,” says geologist Fred Longstaffe of Western University in London, Canada.
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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 | MycorWeb Plant-Microbe Interactions | 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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Haere mai to the kiwi genome - On Biology

Haere mai to the kiwi genome - On Biology | MycorWeb Plant-Microbe Interactions | Scoop.it
The genome of the kiwi has just been published in Genome Biology, providing insights into this peculiar bird's physiology.
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Clonal reproduction in fungi

Clonal reproduction in fungi | MycorWeb Plant-Microbe Interactions | Scoop.it

Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest.


Via Steve Marek, Niklaus Grunwald
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Steve Marek's curator insight, July 21, 4:43 PM

Great review!

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Genomic evidence for the Pleistocene and recent population history of Native Americans

Genomic evidence for the Pleistocene and recent population history of Native Americans | MycorWeb Plant-Microbe Interactions | Scoop.it
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
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