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Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria

Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria | MycorWeb Plant-Microbe Interactions | Scoop.it

Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor(Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell–cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.

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Genome of Phyllosticta citriasiana (Dothideomycetes)

Genome of Phyllosticta citriasiana (Dothideomycetes) | MycorWeb Plant-Microbe Interactions | Scoop.it

Phyllosticta is an Ascomycete fungus in the Dothideomycetes clade. Dothideomycetes is the largest and most diverse class of ascomycete fungi. It comprises 11 orders 90 families, 1300 genera and over 19,000 known species.
Phyllosticta citricarpa (Synonym: Guignardia citricarpa) is a plant pathogen, some strains of which cause a leaf condition called black spot on citrus plants. This fungus affects citrus plants throughout subtropical climates, causing a reduction in both fruit quantity and quality. Symptoms include both fruit and leaf lesions, the latter being critical to inter-tree dispersal.
This genome was sequenced as part of the 1000 Fungal Genomes Project.

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Genome of Clathrospora elynae (Dothideomycetes)

Genome of Clathrospora elynae (Dothideomycetes) | MycorWeb Plant-Microbe Interactions | Scoop.it

Clathrospora is a genus of fungi in the family Diademaceae (Dothideomycetes). Dothideomycetes is the largest and most diverse class of ascomycete fungi. It comprises 11 orders 90 families, 1300 genera and over 19,000 known species.
Clathrospora elynae was found growing on Carex curvula (curved sedge) in St. Moritz, Corviglia, Switzerland. This genome was sequenced as part of the 1000 Fungal Genomes Project.

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Auriscalpium vulgare FP105234-Sp v1.0

Auriscalpium vulgare FP105234-Sp v1.0 | MycorWeb Plant-Microbe Interactions | Scoop.it

As part of the 1000 Fungal Genomes Project, we have sequenced the genome of Auriscalpium vulgare, a species commonly found in pine forests decomposing pine cones. The genus Auriscalpium belongs to the order Russulales, a diverse order with a very interesting early evolution – exemplified by a high diversity of both morphology and nutritional mode in early diverging groups, which converges onto a mostly ectomycorrhizal lifestyle and agaricoid morphology in more derived groups. Auriscalpium is one of the genera that make the early evolution of this order so interesting to mycologists. Both its habitat specialization and its morphology made it an important target for genome sequencing. It inhabits pine cones, a rare and remarkable habitat for fungi because of its extractive composition and fungitoxic compounds – probably requiring a unique set of genes for neutralizing harmful decomposition intermediates.

Fruiting bodies of Auriscalpium have a lateral stipe, which represents an important stepping-stone towards the well-known agaricoid morphology, i.e. fruiting bodies with cap and stipe. Further, the spore-bearing surface (hymenium) of this species is composed of cylindrical pointed teeth (see inlet picture), a hymenium conformation that is relatively rarely seen in fungi. The genome of this species fills an important gap in studying the evolutionary development of fruiting body morphologies and that of the spore-producing surface in Fungi.

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Towards the unification of sequence-based classification and sequence-based identification of host-associated microorganisms

Towards the unification of sequence-based classification and sequence-based identification of host-associated microorganisms | MycorWeb Plant-Microbe Interactions | Scoop.it

Plants interact with a wide assortment of microbial organisms – taking the role of pathogens, mutualists, and commensals. Our knowledge of plant-associated microorganisms has traditionally been based on macroscopic and microscopic structures. In recent decades, the use of both DNA and RNA sequence data derived directly from the environment has been used to study both the taxonomic and functional diversity of host-associated microorganisms. More recently, an explosion of data derived from a shift in nucleotide sequencing technologies has revealed an astonishing diversity of microorganisms (Hibbett & Taylor, 2013). To elucidate taxonomic and functional microbial diversity, researchers employ distinct but not mutually exclusive techniques when using molecular data – Sequence-based Classification (SBC) and Sequence-based Identification (SBI). Those who utilize SBC are predominantly concerned with the discovery and categorization of microbial organisms on the basis of phylogenetic relationships. Researchers who engage in SBI utilize databases as references, often using similarity-based (as opposed to phylogeny-based) approaches, to taxonomically and/or functionally identify the composition of microbial communities. Together, SBC and SBI encompass a range of activities using sequence data – predominantly from nucleic acids – to identify, describe, and functionally characterize microorganisms from the plant-based environment. Marker-based and metagenomic studies, in particular, have sequenced nucleotides from thousands to millions of unidentified species and underscore the need for resources developed for taxonomic and functional characterization of microbial diversity (Hibbett et al., 2011). Perhaps most importantly, new analysis techniques and resources need to integrate with existing taxonomic and systematic knowledge that is based traditionally on cultures and type-material (Lindahl et al., 2013). There is a dire need to develop unified community-based resources and analysis standards for the integration of SBC and SBI of fungi and other microorganisms.

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Marc-André Selosse

Marc-André Selosse | MycorWeb Plant-Microbe Interactions | Scoop.it

Although I grew up in the city, in Paris, my grandfather walked with me daily in the forests surrounding the city and I spent my holidays in the familial island in Brittany, so as a child I spent a lot of time in nature. At 13, I began a life-long love affair with fungi, spending hours identifying and drawing them. I was very attracted to mutualistic symbioses and in 1985, when I was 17, I attended a talk by Bernard Boullard, who had once been the only mycorrhizal specialist in France; he was speaking on Juniperus mycorrhizas. I was fascinated by such an intimate mix of two partners, so much so that I later went on to apply for a PhD with François Le Tacon at the l'Institut national de la recherche agronomique (INRA) in Nancy, focusing on the survival of ectomycorrhizal Laccaria bicolor inoculated in forests. When I was 19 I began to pay more attention to flowering plants, first of all for my studies, and very soon afterwards as a hobby too. What was most fascinating to me was the similarities between different species from the same family, and this observation was something that inspired me to undertake the study of evolution. As I began to work on my PhD thesis, however, it became clear that taxonomy was not functional enough for me.

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Improving the reference eucalyptus (E. grandis) genome

Improving the reference eucalyptus (E. grandis) genome | MycorWeb Plant-Microbe Interactions | Scoop.it
A team of French researchers developed an array that allowed them to produce high-resolution genetic maps of two eucalyptus species. Comparing these maps to the E. grandis reference genome of eucalyptus produced by a team including DOE JGI researchers in June 2014 led to an improvement in the reference genome assembly.
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eLIFE: Antibacterial gene transfer across the tree of life

eLIFE: Antibacterial gene transfer across the tree of life | MycorWeb Plant-Microbe Interactions | Scoop.it

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group.


Via Stéphane Hacquard
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Belowground biodiversity and ecosystem functioning : Nature

Belowground biodiversity and ecosystem functioning : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Evidence is mounting that the immense diversity of microorganisms and animals that live belowground contributes significantly to shaping aboveground biodiversity and the functioning of terrestrial ecosystems. Our understanding of how this belowground biodiversity is distributed, and how it regulates the structure and functioning of terrestrial ecosystems, is rapidly growing. Evidence also points to soil biodiversity as having a key role in determining the ecological and evolutionary responses of terrestrial ecosystems to current and future environmental change. Here we review recent progress and propose avenues for further research in this field.
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What Goes “99-Thump?”

What Goes “99-Thump?” | MycorWeb Plant-Microbe Interactions | Scoop.it
A centipede with a wooden leg, of course. Laying aside for the moment the issue of whether any centipede does have 100 legs, this childish joke is an indicator of the special place that these creepy-crawliest of arthropods occupy in our collective psyche. Here's another one—a 150-year-old poem called the Centipede's Dilemma, usually attributed to Katherine Craster: “A centipede was happy—quite!/Until a toad in fun/Said, ‘Pray, which leg moves after which?’/This raised her doubts to such a pitch,/She fell exhausted in the ditch/Not knowing how to run.” This poem in turn gave its name to the Centipede Syndrome—the phenomenon whereby concentrating on a normally unconscious task compromises our ability to perform it.

The arthropods are one of Earth's real success stories—there are more species of arthropod than in any other animal phylum, but our knowledge of the genomic basis of arthropod biology is massively skewed towards insects. The phylum Arthropoda is conventionally subdivided into five subphyla, four of which are still with us. The hexapods (insects and their kin) scored the first arthropod genome sequence—that of the lab workhorse Drosophila melanogaster, published back in 2000—followed by many other insect genomes since. The chelicerates (spiders, scorpions, horseshoe crabs, etc.) and crustaceans (shrimps, crabs, barnacles, etc.) had to wait 11 more years for the publication of the sequences of Tetranychus urticae (red spider mite) and Daphnia pulex (water flea), respectively. Trilobites haven't been seen for a while now, so this just leaves the myriapods as the only extant arthropod subphylum with no sequenced genome.
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Spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases

Spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases | MycorWeb Plant-Microbe Interactions | Scoop.it

Symbiosis Receptor-like Kinase (SYMRK) is indispensable for the development of phosphate-acquiring arbuscular mycorrhiza (AM) as well as nitrogen-fixing root nodule symbiosis, but the mechanisms that discriminate between the two distinct symbiotic developmental fates have been enigmatic. In this study, we show that upon ectopic expression, the receptor-like kinase genes Nod Factor Receptor 1 (NFR1), NFR5, and SYMRK initiate spontaneous nodule organogenesis and nodulation-related gene expression in the absence of rhizobia. Furthermore, overexpressed NFR1 or NFR5 associated with endogenous SYMRK in roots of the legume Lotus japonicus. Epistasis tests revealed that the dominant active SYMRK allele initiates signalling independently of either the NFR1 or NFR5 gene and upstream of a set of genes required for the generation or decoding of calcium-spiking in both symbioses. Only SYMRK but not NFR overexpression triggered the expression of AM-related genes, indicating that the receptors play a key role in the decision between AM- or root nodule symbiosis-development. - See more at: http://elifesciences.org/content/3/e03891#sthash.7GMN2VZ5.dpuf

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Jean-Michel Ané's curator insight, November 25, 8:07 PM

That's a BIG paper in our field... a must read for all my lab members :-)

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Interspecific and host-related gene expression patterns in nematode-trapping fungi

Interspecific and host-related gene expression patterns in nematode-trapping fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host preferences. To provide insights into the genetic basis for this variation, we compared the transcriptome expressed by three species of nematode-trapping fungi (Arthrobotrys oligospora, Monacrosporium cionopagum and Arthrobotrys dactyloides, which use adhesive nets, adhesive branches or constricting rings, respectively, to trap nematodes) during infection of two different plant-pathogenic nematode hosts (the root knot nematode Meloidogyne hapla and the sugar beet cyst nematode Heterodera schachtii).
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Mycorrhizal phenotypes and the Law of the Minimum

Mycorrhizal phenotypes arise from interactions among plant and fungal genotypes and the environment. Differences in the stoichiometry and uptake capacity of fungi and plants make arbuscular mycorrhizal (AM) fungi inherently more nitrogen (N) limited and less phosphorus (P) limited than their host plants. Mutualistic phenotypes are most likely in P-limited systems and commensal or parasitic phenotypes in N-limited systems. Carbon (C) limitation is expected to cause phenotypes to shift from mutualism to commensalism and even parasitism.
Two experiments compared the influence of fertilizer and shade on mycorrhizas in Andropogon gerardii across three naturally N-limited or P-limited grasslands. A third experiment examined the interactive effects of N and P enrichment and shade on A. gerardii mycorrhizas.
Our experiments generated the full spectrum of mycorrhizal phenotypes. These findings support the hypothesis that mutualism is likely in P-limited systems and commensalism or parasitism is likely in N-limited systems. Furthermore, shade decreased C-assimilation and generated less mutualistic mycorrhizal phenotypes with reduced plant and fungal biomass.
Soil fertility is a key controller of mycorrhizal costs and benefits and the Law of the Minimum is a useful predictor of mycorrhizal phenotype. In our experimental grasslands arbuscular mycorrhizas can ameliorate P-limitation but not N-limitation.
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Interplant signalling through hyphal networks

Interplant signalling through hyphal networks | MycorWeb Plant-Microbe Interactions | Scoop.it
Mycorrhizal fungi can form common mycelial networks (CMNs) that interconnect plants. Here, we provide an insight into recent findings demonstrating that CMNs can be conduits for interplant signalling, influencing defence against insect herbivores and foliar necrotrophic fungi. A likely mechanism is direct transfer of signalling molecules within hyphae. However, electrical signals, which can be induced by wounding, may also enable signalling over relatively long distances, because the biophysical constraints imposed by liquid transport in hyphae and interaction with soil are relieved. We do not yet understand the ecological, evolutionary and agronomic implications of interplant signalling via CMNs. Identifying the mechanism of interplant signalling will help to address these gaps.
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Genome of Pseudovirgaria hyperparasitica (Dothideomycetes)

Genome of Pseudovirgaria hyperparasitica (Dothideomycetes) | MycorWeb Plant-Microbe Interactions | Scoop.it

Pseudovirgaria is a genus of fungi in the family Capnodiales (Dothideomycetes). Dothideomycetes is the largest and most diverse class of ascomycete fungi. It comprises 11 orders 90 families, 1300 genera and over 19,000 known species.
The Pseudovirgaria hyperparasitica genome was sequenced as part of the 1000 Fungal Genomes Project.

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Genome of Tothia fuscella (Venturiaceae)

Genome of Tothia fuscella (Venturiaceae) | MycorWeb Plant-Microbe Interactions | Scoop.it

Tothia is a genus of fungi in the Venturiaceae family whose placement in the Dothideomycetes class is uncertain. Dothideomycetes is the largest and most diverse class of ascomycete fungi. It comprises 11 orders 90 families, 1300 genera and over 19,000 known species.
This is a monotypic genus, containing the single species Tothia fuscella. Its ascospores resemble Microthyrium in being one-septate, guttulate, and slightly asymmetrical but differ in their dilute brown color. This genome was sequenced as part of the 1000 Fungal Genomes Project.

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The unseen iceberg: plant roots in arctic tundra

The unseen iceberg: plant roots in arctic tundra | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant roots play a critical role in ecosystem function in arctic tundra, but root dynamics in these ecosystems are poorly understood. To address this knowledge gap, we synthesized available literature on tundra roots, including their distribution, dynamics and contribution to ecosystem carbon and nutrient fluxes, and highlighted key aspects of their representation in terrestrial biosphere models. Across all tundra ecosystems, belowground plant biomass exceeded aboveground biomass, with the exception of polar desert tundra. Roots were shallowly distributed in the thin layer of soil that thaws annually, and were often found in surface organic soil horizons. Root traits – including distribution, chemistry, anatomy and resource partitioning – play an important role in controlling plant species competition, and therefore ecosystem carbon and nutrient fluxes, under changing climatic conditions, but have only been quantified for a small fraction of tundra plants. Further, the annual production and mortality of fine roots are key components of ecosystem processes in tundra, but extant data are sparse. Tundra root traits and dynamics should be the focus of future research efforts. Better representation of the dynamics and characteristics of tundra roots will improve the utility of models for the evaluation of the responses of tundra ecosystems to changing environmental conditions.
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Twenty-first century mycology: a diverse, collaborative, and highly relevant science

In June 2014, over 250 researchers from a variety of national and international locations attended the annual meeting of the Mycological Society of America (MSA), which was held on the campus of Michigan State University in East Lansing, MI, USA. Talks, posters, and symposia covered an impressive breadth of fungal biology organized around four main research themes: cell biology/physiology, ecology/pathology, genetics/molecular biology, and systematics. The taxonomic diversity of the fungal kingdom was highlighted throughout the meeting, with presentations covering all of the major fungal lineages. While the core of the talks was on the fungi themselves, many emphasized interactions with other species, including a wide range of plants, animals, and bacteria. It was also clear that mycologists have adopted all the latest ‘–omics’ and next generation sequencing methodologies to ask cutting-edge questions about topics such as infectious disease, climate change, and bioremediation. At the same time, in the era where almost anyone can generate a fungal sequence, strong organism-based knowledge has become even more important (see in this issue of New Phytologist, Herr et al., pp. 27–31). Fortunately, this was on consistent display throughout the meeting and the MSA has long been a welcoming community to researchers from all disciplinary backgrounds. Below we summarize a handful of the many meeting highlights.

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High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly

High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly | MycorWeb Plant-Microbe Interactions | Scoop.it
Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences.
The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome.
The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy.
This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome.
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Long-read, whole-genome shotgun sequence data for five model organisms

Long-read, whole-genome shotgun sequence data for five model organisms | MycorWeb Plant-Microbe Interactions | Scoop.it
Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.
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Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes | MycorWeb Plant-Microbe Interactions | Scoop.it
Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
Francis Martin's insight:

A long-awaited comprehensive review!

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The genome sequence of the orchid Phalaenopsis equestris

The genome sequence of the orchid Phalaenopsis equestris | MycorWeb Plant-Microbe Interactions | Scoop.it

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

 
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The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima | MycorWeb Plant-Microbe Interactions | Scoop.it
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
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Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut

Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut | MycorWeb Plant-Microbe Interactions | Scoop.it

Sugarcane smut can cause losses in cane yield and sugar content that range from 30% to total crop failure. Losses tend to increase with the passage of years. Sporisorium scitamineum is the fungus that causes sugarcane smut. This fungus has the potential to infect all sugarcane species unless a species is resistant to biotrophic fungal pathogens. However, it remains unclear how the fungus breaks through the cell walls of sugarcane and causes the formation of black or gray whip-like structures on the sugarcane plants. 

Here, we report the first high-quality genome sequence of S. scitamineum assembled de novo with a contig N50 of 41 kb, a scaffold N50 of 884 kb and genome size 19.8 Mb, containing an estimated 6,636 genes. This phytopathogen can utilize a wide range of carbon and nitrogen sources. A reduced set of genes encoding plant cell wall hydrolytic enzymes leads to its biotrophic lifestyle, in which damage to the host should be minimized. As a bipolar mating fungus, a and b loci are linked and the mating-type locus segregates as a single locus. The S. scitamineum genome has only 6 G protein-coupled receptors (GPCRs) grouped into five classes, which are responsible for transducing extracellular signals into intracellular responses, however, the genome is without any PTH11-like GPCR. There are 192 virulence associated genes in the genome of S. scitamineum, among which 31 expressed in all the stages, which mainly encode for energy metabolism and redox of short-chain compound related enzymes. Sixty-eight candidates for secreted effector proteins (CSEPs) were found in the genome of S. scitamineum, and 32 of them expressed in the different stages of sugarcane infection, which are probably involved in infection and/or triggering defense responses. There are two non-ribosomal peptide synthetase (NRPS) gene clusters that are involved in the generation of ferrichrome and ferrichrome A, while the terpenes gene cluster is composed of three unknown function genes and seven biosynthesis related genes.

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Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases

Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases | MycorWeb Plant-Microbe Interactions | Scoop.it

This study shows that the genome of Sclerotinia sclerotiorum has a large number of copies of Tc1-Mariner transposons, and in silico analysis shows evidence that they were recently active. This finding was confirmed by expressed sequence tag (EST) analysis. Fourteen new Tc1-Mariner transposon families that were distributed throughout the genome were identified, and in some cases, due to the excision/retention of introns, different transcripts were observed for the same family, which might be the result of an efficient strategy to circumvent mutations that generate premature stop codons in the RNA sequence. In addition, the presence of these introns shows that the transposase protein has a flexible coding sequence and, consequently, conformation. No evidence for RIP-like gene silencing mechanisms, which are commonly found in fungi, was found in the identified Tc1-Mariner elements, and analysis of the genomic insertion sites of these elements showed that they were widely distributed throughout the genome with some copies located near the 3′ regions of genes. In particular, EST analysis demonstrated that one of these copies was co-expressed with a gene, which showed the potential for these elements to undergo exaptation.

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Partner selection in the mycorrhizal mutualism

Partner selection in the mycorrhizal mutualism | MycorWeb Plant-Microbe Interactions | Scoop.it
Partner selection in the mycorrhizal symbiosis is thought to be a key factor stabilising the mutualism. Both plant hosts and mycorrhizal fungi have been shown to preferentially allocate resources to higher quality partners. This can help maintain underground cooperation, although it is likely that different plant species vary in the spatial precision with which they can select partners. Partner selection in the mycorrhizal symbiosis is presumably context-dependent and can be mediated by factors like (relative) resource abundance and resource fluctuations, competition among mycorrhizas, arrival order and cultivation history. Such factors complicate our current understanding of the importance of partner selection and its effectiveness in stimulating mutualistic cooperation.
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