Showing papers by "United States Department of Energy published in 2016"

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

Abstract: Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.

Genome evolution in the allotetraploid frog Xenopus laevis

Abstract: To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

United States Data Center Energy Usage Report

Abstract: Author(s): Shehabi, Arman; Smith, Sarah; Sartor, Dale; Brown, Richard; Herrlin, Magnus; Koomey, Jonathan; Masanet, Eric; Horner, Nathaniel; Azevedo, Ines; Lintner, William

JBrowse: a dynamic web platform for genome visualization and analysis

Abstract: JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

Abstract: Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

The Global Ocean Data Analysis Project version 2 (GLODAPv2) – an internally consistent data product for the world ocean

Abstract: . Version 2 of the Global Ocean Data Analysis Project (GLODAPv2) data product is composed of data from 724 scientific cruises covering the global ocean. It includes data assembled during the previous efforts GLODAPv1.1 (Global Ocean Data Analysis Project version 1.1) in 2004, CARINA (CARbon IN the Atlantic) in 2009/2010, and PACIFICA (PACIFic ocean Interior CArbon) in 2013, as well as data from an additional 168 cruises. Data for 12 core variables (salinity, oxygen, nitrate, silicate, phosphate, dissolved inorganic carbon, total alkalinity, pH, CFC-11, CFC-12, CFC-113, and CCl4) have been subjected to extensive quality control, including systematic evaluation of bias. The data are available in two formats: (i) as submitted but updated to WOCE exchange format and (ii) as a merged and internally consistent data product. In the latter, adjustments have been applied to remove significant biases, respecting occurrences of any known or likely time trends or variations. Adjustments applied by previous efforts were re-evaluated. Hence, GLODAPv2 is not a simple merging of previous products with some new data added but a unique, internally consistent data product. This compiled and adjusted data product is believed to be consistent to better than 0.005 in salinity, 1 % in oxygen, 2 % in nitrate, 2 % in silicate, 2 % in phosphate, 4 µmol kg−1 in dissolved inorganic carbon, 6 µmol kg−1 in total alkalinity, 0.005 in pH, and 5 % for the halogenated transient tracers. The original data and their documentation and doi codes are available at the Carbon Dioxide Information Analysis Center ( http://cdiac.ornl.gov/oceans/GLODAPv2/ ). This site also provides access to the calibrated data product, which is provided as a single global file or four regional ones – the Arctic, Atlantic, Indian, and Pacific oceans – under the doi:10.3334/CDIAC/OTG.NDP093_GLODAPv2 . The product files also include significant ancillary and approximated data. These were obtained by interpolation of, or calculation from, measured data. This paper documents the GLODAPv2 methods and products and includes a broad overview of the secondary quality control results. The magnitude of and reasoning behind each adjustment is available on a per-cruise and per-variable basis in the online Adjustment Table.

Advances and Promises of Layered Halide Hybrid Perovskite Semiconductors.

Abstract: Layered halide hybrid organic–inorganic perovskites (HOP) have been the subject of intense investigation before the rise of three-dimensional (3D) HOP and their impressive performance in solar cells. Recently, layered HOP have also been proposed as attractive alternatives for photostable solar cells and revisited for light-emitting devices. In this review, we combine classical solid-state physics concepts with simulation tools based on density functional theory to overview the main features of the optoelectronic properties of layered HOP. A detailed comparison between layered and 3D HOP is performed to highlight differences and similarities. In the same way as the cubic phase was established for 3D HOP, here we introduce the tetragonal phase with D4h symmetry as the reference phase for 2D monolayered HOP. It allows for detailed analysis of the spin–orbit coupling effects and structural transitions with corresponding electronic band folding. We further investigate the effects of octahedral tilting on the b...

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Abstract: Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceara or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

Warm spring reduced carbon cycle impact of the 2012 US summer drought

Abstract: The global terrestrial carbon sink offsets one-third of the world's fossil fuel emissions, but the strength of this sink is highly sensitive to large-scale extreme events. In 2012, the contiguous United States experienced exceptionally warm temperatures and the most severe drought since the Dust Bowl era of the 1930s, resulting in substantial economic damage. It is crucial to understand the dynamics of such events because warmer temperatures and a higher prevalence of drought are projected in a changing climate. Here, we combine an extensive network of direct ecosystem flux measurements with satellite remote sensing and atmospheric inverse modeling to quantify the impact of the warmer spring and summer drought on biosphere-atmosphere carbon and water exchange in 2012. We consistently find that earlier vegetation activity increased spring carbon uptake and compensated for the reduced uptake during the summer drought, which mitigated the impact on net annual carbon uptake. The early phenological development in the Eastern Temperate Forests played a major role for the continental-scale carbon balance in 2012. The warm spring also depleted soil water resources earlier, and thus exacerbated water limitations during summer. Our results show that the detrimental effects of severe summer drought on ecosystem carbon storage can be mitigated by warming-induced increases in spring carbon uptake. However, the results also suggest that the positive carbon cycle effect of warm spring enhances water limitations and can increase summer heating through biosphere-atmosphere feedbacks.

The Epigenomic Landscape of Prokaryotes

Abstract: DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.

A new global interior ocean mapped climatology: the 1° × 1° GLODAP version 2

Abstract: . We present a mapped climatology (GLODAPv2.2016b) of ocean biogeochemical variables based on the new GLODAP version 2 data product (Olsen et al., 2016; Key et al., 2015), which covers all ocean basins over the years 1972 to 2013. The quality-controlled and internally consistent GLODAPv2 was used to create global 1° × 1° mapped climatologies of salinity, temperature, oxygen, nitrate, phosphate, silicate, total dissolved inorganic carbon (TCO2), total alkalinity (TAlk), pH, and CaCO3 saturation states using the Data-Interpolating Variational Analysis (DIVA) mapping method. Improving on maps based on an earlier but similar dataset, GLODAPv1.1, this climatology also covers the Arctic Ocean. Climatologies were created for 33 standard depth surfaces. The conceivably confounding temporal trends in TCO2 and pH due to anthropogenic influence were removed prior to mapping by normalizing these data to the year 2002 using first-order calculations of anthropogenic carbon accumulation rates. We additionally provide maps of accumulated anthropogenic carbon in the year 2002 and of preindustrial TCO2. For all parameters, all data from the full 1972–2013 period were used, including data that did not receive full secondary quality control. The GLODAPv2.2016b global 1° × 1° mapped climatologies, including error fields and ancillary information, are available at the GLODAPv2 web page at the Carbon Dioxide Information Analysis Center (CDIAC; doi:10.3334/CDIAC/OTG.NDP093_GLODAPv2 ).

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

Abstract: The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant biomass and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite-repressed and are further regulated by a rich landscape of noncoding regulatory RNAs. Additionally, we identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.

High-resolution phylogenetic microbial community profiling

Abstract: Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.

Removal of TcO4− ions from solution: materials and future outlook

Abstract: Technetium mainly forms during artificial nuclear fission; it exists primarily as TcO4− in nuclear waste, and it is among the most hazardous radiation-derived contaminants because of its long half-life (t1/2 = 2.13 × 105 years) and environmental mobility. The high water solubility of TcO4− (11.3 mol L−1 at 20 °C) and its ability to readily migrate within the upper layer of the Earth's crust make it particularly hazardous. Several types of materials, namely resins, molecular complexes, layered double hydroxides, and pure inorganic and metal–organic materials, have been shown to be capable of capturing TcO4− (or other oxoanions) from solution. In this review, we give a brief description about the types of materials that have been used to capture TcO4− and closely related oxyanions so far and discuss the possibility of using metal–organic frameworks (MOFs) as next-generation ion-exchange materials for the stated application. In particular, with the advent of ultra-stable MOF materials, in conjunction with their chemical tunability, MOFs can be applied to capture these oxyanions under real-life conditions.

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at s =13 TeV using the ATLAS detector

Abstract: Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses proton-proton collision data corresponding to an inte ...

Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes

Abstract: Toxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from closely related parasites that typically have narrow, specialized host ranges. To elucidate the genetic basis for these differences, we compared the genomes of 62 globally distributed T. gondii isolates to several closely related coccidian parasites. Our findings reveal that tandem amplification and diversification of secretory pathogenesis determinants is the primary feature that distinguishes the closely related genomes of these biologically diverse parasites. We further show that the unusual population structure of T. gondii is characterized by clade-specific inheritance of large conserved haploblocks that are significantly enriched in tandemly clustered secretory pathogenesis determinants. The shared inheritance of these conserved haploblocks, which show a different ancestry than the genome as a whole, may thus influence transmission, host range and pathogenicity.

Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire: an expert assessment

Abstract: As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release w ...

Notes on Contributions to the Science of Rare Earth Element Enrichment in Coal and Coal Combustion Byproducts

Abstract: Coal and coal combustion byproducts can have significant concentrations of lanthanides (rare earth elements). Rare earths are vital in the production of modern electronics and optics, among other uses. Enrichment in coals may have been a function of a number of processes, with contributions from volcanic ash falls being among the most significant mechanisms. In this paper, we discuss some of the important coal-based deposits in China and the US and critique classification systems used to evaluate the relative value of the rare earth concentrations and the distribution of the elements within the coals and coal combustion byproducts.

Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities.

Abstract: Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.

Gate fidelity and coherence of an electron spin in an Si/SiGe quantum dot with micromagnet.

Abstract: The gate fidelity and the coherence time of a quantum bit (qubit) are important benchmarks for quantum computation. We construct a qubit using a single electron spin in an Si/SiGe quantum dot and control it electrically via an artificial spin-orbit field from a micromagnet. We measure an average single-qubit gate fidelity of ∼99% using randomized benchmarking, which is consistent with dephasing from the slowly evolving nuclear spins in the substrate. The coherence time measured using dynamical decoupling extends up to ∼400 μs for 128 decoupling pulses, with no sign of saturation. We find evidence that the coherence time is limited by noise in the 10-kHz to 1-MHz range, possibly because charge noise affects the spin via the micromagnet gradient. This work shows that an electron spin in an Si/SiGe quantum dot is a good candidate for quantum information processing as well as for a quantum memory, even without isotopic purification.

Identification of safety gaps for fusion demonstration reactors

Abstract: To assist in the development of nuclear fusion as a viable commercial power source, preparation is underway for the fusion demonstration reactor (DEMO), which will build on the work of ITER, the international experimental fusion reactor. Like other advanced nuclear energy systems, DEMO must satisfy several goals including a high level of public and worker safety, low environmental impact, high reactor availability, a closed fuel cycle and the potential to be economically competitive. Yet there are still large scientific and technological safety gaps between the on-going ITER project and DEMO that will need to be addressed. Here we review international fusion safety research and development relevant to DEMO, following the lessons learned so far from ITER. We identify the main scientific and technological safety gaps, drawing on knowledge from the development of fission energy, in particular Generation IV (Gen-IV) fission reactors. From this survey, we discuss the corresponding implications for the design and operation of DEMO. Following on from ITER, a fusion demonstration reactor will be needed to showcase the commercial viability of fusion energy. To guide preliminary design considerations, this Review explores safety gaps that must be filled between current fission reactors, ITER and future fusion reactors.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Abstract: Viruses represent the most abundant life forms on the planet Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools Here we present IMG/VR (https://imgjgidoegov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community

Placement of Remote-Controlled Switches to Enhance Distribution System Restoration Capability

Abstract: A smart distribution system should restore service to interrupted customers as quickly as possible after an outage. Upgrading manual switches to remote-controlled switches (RCSs) enhances restoration capability. The placement of RCSs should consider both functional and economic requirements. This paper presents a systematic method to determine the set of switches to be upgraded for an existing distribution system. The maximum restoration capability is achieved by upgrading a near-minimum number of manual switches to RCSs. The RCS placement problem is formulated as a weighed set cover (WSC) problem. A greedy algorithm with a polynomial-time computational efficiency is designed to generate a near-optimal solution for the WSC problem. A 3-feeder 9-node test system and a 4-feeder 1069-node unbalanced test system with microgrids are used to validate the effectiveness of the proposed method.

Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics

Abstract: The ‘Atribacteria’ is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the ‘Atribacteria’ inclusive of OP9 and JS1. Additional conserved features within the ‘Atribacteria’ were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the ‘Atribacteria’ are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.

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

Abstract: Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.