No abstract

ForewordThe Pierre Auger Observatory has begun a major Upgrade of its already impressive capabilities, with an emphasis on improved mass composition determination using the surface detectors of the Observatory. Known as AugerPrime, the upgrade will include new 4 m 2 plastic scintillator detectors on top of all 1660 water-Cherenkov detectors, updated and more flexible surface detector electronics, a large array of buried muon detectors, and an extended duty cycle for operations of the fluorescence detectors.This Preliminary Design Report was produced by the Collaboration in April 2015 as an internal document and information for funding agencies. It outlines the scientific and technical case for AugerPrime 1 . We now release it to the public via the arXiv server. We invite you to review the large number of fundamental results already achieved by the Observatory and our plans for the future.The Pierre Auger Collaboration 1 As a result of continuing R&D, slight changes have been implemented in the baseline design since this Report was written. These changes will be documented in a forthcoming Technical Design Report. ix x Executive Summary Present Results from the Pierre Auger ObservatoryMeasurements of the Auger Observatory have dramatically advanced our understanding of ultra-high energy cosmic rays. The suppression of the flux around 5×10 19 eV is now confirmed without any doubt. Strong limits have been placed on the photon and neutrino components of the flux indicating that "top-down" source processes, such as the decay of superheavy particles, cannot account for a significant part of the observed particle flux. A largescale dipole anisotropy of ∼7% amplitude has been found for energies above 8×10 18 eV. In addition there is also an indication of the presence of a large scale anisotropy below the ankle. Particularly exciting is the observed behavior of the depth of shower maximum with energy, which changes in an unexpected, non-trivial way. Around 3×10 18 eV it shows a distinct change of slope with energy, and the shower-to-shower variance decreases. Interpreted with the leading LHC-tuned shower models, this implies a gradual shift to a heavier composition. A number of fundamentally different astrophysical model scenarios have been developed to describe this evolution. The high degree of isotropy observed in numerous tests of the small-scale angular distribution of UHECR above 4×10 19 eV is remarkable, challenging original expectations that assumed only a few cosmic ray sources with a light composition at the highest energies. Interestingly, the largest departures from isotropy are observed for cosmic rays with E > 5.8×10 19 eV in ∼20 • sky-windows. Due to a duty cycle of ∼15% of the fluorescence telescopes, the data on the depth of shower maximum extend only up to the flux suppression region, i.e. 4×10 19 eV. Obtaining more information on the composition of cosmic rays at higher energies will provide crucial means to discriminate between the model classes and to understand the origin of the observed flux suppre...

We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.

Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by Phaeodactylum tricornutum at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the Thalassiosira pseudonana genome that encode for components of iron capture and uptake mechanisms.genome ͉ metabalomics ͉ photosynthesis ͉ transcriptomics ͉ nutrients

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.

The a mating type locus of the phytopathogenic fungus U. maydis controls fusion of haploid cells and filamentous growth of the dikaryotic mycelium. The a locus exists in two alleles, termed a1 and a2, which are defined by nonhomologous DNA regions comprising 4.5 kb for a1 and 8 kb for a2, flanked by identical sequences. Based on functional assays, mutants, and sequencing, we demonstrate that the mating type in each allele is determined by a set of two genes. One encodes a precursor for a lipopeptide mating factor, and the other specifies the receptor for the pheromone secreted by cells of opposite mating type. Thus, U. maydis employs a novel strategy to determine its mating type by providing the primary determinants of cell-cell recognition directly from the mating type locus.