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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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Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites | MycorWeb Plant-Microbe Interactions | Scoop.it
The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga.
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Genome sequence of Valsa canker pathogens uncovers a potential adaptation of colonization of woody bark

Genome sequence of Valsa canker pathogens uncovers a potential adaptation of colonization of woody bark | MycorWeb Plant-Microbe Interactions | Scoop.it
Canker caused by ascomycetous Valsa species are among the most destructive diseases of woody plants worldwide. These pathogens are distinct from other pathogens because they only effectively attack tree bark in the field. To unravel the potential adaptation mechanism of bark colonization, we examined the genomes of Valsa mali and Valsa pyri that preferentially infect apple and pear, respectively.We reported the 44.7 and 35.7 Mb genomes of V. mali and V. pyri, respectively. We also identified the potential genomic determinants of wood colonization by comparing them with related cereal pathogens.Both genomes encode a plethora of pathogenicity-related genes involved in plant cell wall degradation and secondary metabolite biosynthesis. In order to adapt to the nutrient limitation and low pH environment in bark, they seem to employ membrane transporters associated with nitrogen uptake and secrete proteases predominantly with acidic pH optima. Remarkably, both Valsa genomes are especially suited for pectin decomposition, but are limited in lignocellulose and cutin degradation. Besides many similarities, the two genomes show distinct variations in many secondary metabolism gene clusters.Our results show a potential adaptation of Valsa canker pathogens to colonize woody bark. Secondary metabolism gene clusters are probably responsible for this host specificity.
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Darcy's law predicts widespread forest mortality under climate warming : Nature Climate Change

Darcy's law predicts widespread forest mortality under climate warming : Nature Climate Change | MycorWeb Plant-Microbe Interactions | Scoop.it
Drought and heat-induced tree mortality is accelerating in many forest biomes as a consequence of a warming climate, resulting in a threat to global forests unlike any in recorded history1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. Forests store the majority of terrestrial carbon, thus their loss may have significant and sustained impacts on the global carbon cycle11, 12. We use a hydraulic corollary to Darcy’s law, a core principle of vascular plant physiology13, to predict characteristics of plants that will survive and die during drought under warmer future climates. Plants that are tall with isohydric stomatal regulation, low hydraulic conductance, and high leaf area are most likely to die from future drought stress. Thus, tall trees of old-growth forests are at the greatest risk of loss, which has ominous implications for terrestrial carbon storage. This application of Darcy’s law indicates today’s forests generally should be replaced by shorter and more xeric plants, owing to future warmer droughts and associated wildfires and pest attacks. The Darcy’s corollary also provides a simple, robust framework for informing forest management interventions needed to promote the survival of current forests. Given the robustness of Darcy’s law for predictions of vascular plant function, we conclude with high certainty that today’s forests are going to be subject to continued increases in mortality rates that will result in substantial reorganization of their structure and carbon storage.
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Rock black fungi: excellence in the extremes, from the Antarctic to space

Rock black fungi: excellence in the extremes, from the Antarctic to space | MycorWeb Plant-Microbe Interactions | Scoop.it
This work focuses on rock-inhabiting fungi (RIF) of Antarctic rocky deserts, considered the closest to a possible Martian habitat, as the best example of adaptation to the extremes. The study of RIF ecophysiology, resistance and adaptation provides tools that shed light on the evolution of extremophily. These studies also help define the actual limits for life and provide insight for investigating its existence beyond our planet. The scientific results obtained from over 20 years of research on the biodiversity, phylogeny and evolution toward extremotolerance reviewed here demonstrate how these fascinating organisms can withstand conditions well beyond those in their natural environment. A final focus is given on results and perspectives arising from a recent proteomic approach, and from astrobiological experiments and their significance for future space exploration. These studies demonstrate that Antarctic RIF offer an excellent opportunity to investigate many basic, but also applicative areas of research on extremophily.
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An integrated functional approach to dissect systemic responses in maize to arbuscular mycorrhizal symbiosis

An integrated functional approach to dissect systemic responses in maize to arbuscular mycorrhizal symbiosis | MycorWeb Plant-Microbe Interactions | Scoop.it

Most terrestrial plants benefit from the symbiosis with arbuscular mycorrhizal fungi (AMF) mainly under nutrient-limited conditions. Here the crop plant Zea mays was grown with and without AMF in a bi-compartmented system separating plant and phosphate (Pi) source by a hyphae-permeable membrane. Thus, Pi was preferentially taken up via the mycorrhizal Pi uptake pathway while other nutrients were ubiquitously available. To study systemic effects of mycorrhizal Pi uptake on leaf status, leaves of these plants that display an increased biomass in the presence of AMF were subjected to simultaneous ionomic, transcriptomic and metabolomic analyses. We observed robust changes of the leaf elemental composition, that is, increase of P, S and Zn and decrease of Mn, Co and Li concentration in mycorrhizal plants. Although changes in anthocyanin and lipid metabolism point to an improved P status, a global increase in C versus N metabolism highlights the redistribution of metabolic pools including carbohydrates and amino acids. Strikingly, an induction of systemic defence gene expression and concomitant accumulation of secondary metabolites such as the terpenoids alpha- and beta-amyrin suggest priming of mycorrhizal maize leaves as a mycorrhiza-specific response. This work emphasizes the importance of AM symbiosis for the physiological status of plant leaves and could lead to strategies for optimized breeding of crop species with high growth potential.

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Rhizobium-legume symbiosis in the absence of Nod factors: two possible scenarios with or without the T3SS

The occurrence of alternative Nod factor (NF)-independent symbiosis between legumes and rhizobia was first demonstrated in some Aeschynomene species that are nodulated by photosynthetic bradyrhizobia lacking the canonical nodABC genes. In this study, we revealed that a large diversity of non-photosynthetic bradyrhizobia, including B. elkanii, was also able to induce nodules on the NF-independent Aeschynomene species, A. indica. Using cytological analysis of the nodules and the nitrogenase enzyme activity as markers, a gradient in the symbiotic interaction between bradyrhizobial strains and A. indica could be distinguished. This ranged from strains that induced nodules that were only infected intercellularly to rhizobial strains that formed nodules in which the host cells were invaded intracellularly and that displayed a weak nitrogenase activity. In all non-photosynthetic bradyrhizobia, the type III secretion system (T3SS) appears required to trigger nodule organogenesis. In contrast, genome sequence analysis revealed that apart from a few exceptions, like the Bradyrhizobium ORS285 strain, photosynthetic bradyrhizobia strains lack a T3SS. Furthermore, analysis of the symbiotic properties of an ORS285 T3SS mutant revealed that the T3SS could have a positive or negative role for the interaction with NF-dependent Aeschynomene species, but that it is dispensable for the interaction with all NF-independent Aeschynomene species tested. Taken together, these data indicate that two NF-independent symbiotic processes are possible between legumes and rhizobia: one dependent on a T3SS and one using a so far unknown mechanism.

Via Jean-Michel Ané
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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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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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Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat

Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat | MycorWeb Plant-Microbe Interactions | Scoop.it
Among the understudied fungi found in nature are those living in close association with social and solitary bees. The bee-specialist genera Bettsia, Ascosphaera and Eremascus are remarkable not only for their specialized niche but also for their simple fruiting bodies or ascocarps, which are morphologically anomalous in Pezizomycotina. Bettsia and Ascosphaera are characterized by a unicellular cyst-like cleistothecium known as a spore cyst, while Eremascus is characterized by completely naked asci, or asci not formed within a protective ascocarp. Before molecular phylogenetics the placement of these genera within Pezizomycotina remained tentative; morphological characters were misleading because they do not produce multicellular ascocarps, a defining character of Pezizomycotina. Because of their unique fruiting bodies, the close relationship of these bee-specialist fungi and their monophyly appeared certain. However, recent molecular studies have shown that Bettsia is not closely related to Ascosphaera.

In this study, I isolated the very rare fungus Eremascus fertilis (Ascomycota, Pezizomycotina) from the bee bread of honey bees. These isolates represent the second report of E. fertilis both in nature and in the honey bee hive. To establish the systematic position of E. fertilis and Bettsia alvei, I performed phylogenetic analyses of nuclear ribosomal LSU + SSU DNA sequences from these species and 63 additional ascomycetes.
Results

The phylogenetic analyses revealed that Eremascus is not monophyletic. Eremascus albus is closely related to Ascosphaera in Eurotiomycetes while E. fertilis belongs in Myxotrichaceae, a putative member of Leotiomycetes. Bettsia is not closely related to Ascosphaera and like E. fertilis apparently belongs in Leotiomycetes. These results indicate that both the naked ascus and spore cyst evolved twice in the Pezizomycotina and in distantly related lineages. The new genus Skoua is described to accommodate E. fertilis.
Conclusions

The naked ascus and spore cyst are both shown to have evolved convergently within the bee habitat. The convergent evolution of these unusual ascocarps is hypothesized to be adaptive for bee-mediated dispersal. Elucidating the dispersal strategies of these fungal symbionts contributes to our understanding of their interaction with bees and provides insight into the factors which potentially drive the evolution of reduced ascocarps in Pezizomycotina.
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The Plant Genome Integrative Explorer Resource: PlantGenIE.org - Sundell - 2015 - New Phytologist - Wiley Online Library

The Plant Genome Integrative Explorer Resource: PlantGenIE.org - Sundell - 2015 - New Phytologist - Wiley Online Library | MycorWeb Plant-Microbe Interactions | Scoop.it
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training.
We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo.
We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated.
The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
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Elsa Ballini's curator insight, July 22, 2015 2:00 AM

Waiting for rice !

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Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation

Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation | MycorWeb Plant-Microbe Interactions | Scoop.it

Understanding how developmental and functional complexity of organisms evolves is a longstanding challenge in biology. Genetic mutation has long been thought to be the cause of biological complexity. However, increasing evidence indicates that epigenetic variation provides a parallel path for the evolution of biological complexity. Cytosine DNA methylation, the addition of a chemical mark on DNA, is a conserved and essential gene regulatory mechanism. Recent studies have greatly advanced our understanding of the DNA methylation landscapes and key regulatory components across many species. In this review, I summarize recent advances in understanding DNA methylation from an evolutionary perspective. Using comparative approaches, I highlight the conservation and divergence of DNA methylation patterns and regulatory machinery in plants and other eukaryotic organisms.

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Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants - Annual Review of Plant Biology, 62(1):567

Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants - Annual Review of Plant Biology, 62(1):567 | MycorWeb Plant-Microbe Interactions | Scoop.it
All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) endosymbiotic events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence.
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Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism | MycorWeb Plant-Microbe Interactions | Scoop.it
White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
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Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis

Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis | MycorWeb Plant-Microbe Interactions | Scoop.it

Extracellular proteins play crucial roles in the interaction between mycorrhizal fungi and their environment. Computational prediction and experimental detection allowed identification of 869 proteins constituting the exoproteome of Hebeloma cylindrosporum. Small secreted proteins (SSPs) and carbohydrate-active enzymes (CAZymes) were the two major classes of extracellular proteins.Twenty-eight per cent of the SSPs were secreted by free-living mycelia and five of the 10 most abundant extracellular proteins were SSPs. By contrast, 63–75% of enzymes involved in nutrient acquisition were secreted.A total of 150 extracellular protein-coding genes were differentially expressed between mycorrhizas and free-living mycelia. SSPs were the most affected. External environmental conditions also affected expression of 199 exoproteome genes in mycorrhizas. SSPs displayed different patterns of regulation in response to presence of a host plant or other environmental signals. Several of the genes most overexpressed in the presence of organic matter encoded oxidoreductases.Hebeloma cylindrosporum has not fully lost its ancestral saprotrophic capacities but rather adapted them not to harm its hosts and to use soil organic nitrogen. The complex and divergent patterns of regulation of SSPs in response to a symbiotic partner and/or organic matter suggest various roles in the biology of mycorrhizal fungi.


Via Pierre-Marc Delaux
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