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  • Alneberg, Johannes, et al. (författare)
  • BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
  • 2018
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .
  • Beier, Sebastian, et al. (författare)
  • Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
  • 2017
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 4
  • Tidskriftsartikel (refereegranskat)abstract
    • Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. â € Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
  • Bennett, J. M., et al. (författare)
  • GloPL, a global data base on pollen limitation of plant reproduction
  • 2018
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant reproduction relies on transfer of pollen from anthers to stigmas, and the majority of flowering plants depend on biotic or abiotic agents for this transfer. A key metric for characterizing if pollen receipt is insufficient for reproduction is pollen limitation, which is assessed by pollen supplementation experiments. In a pollen supplementation experiment, fruit or seed production by flowers exposed to natural pollination is compared to that following hand pollination either by pollen supplementation (i.e. manual outcross pollen addition without bagging) or manual outcrossing of bagged flowers, which excludes natural pollination. The GloPL database brings together data from 2969 unique pollen supplementation experiments reported in 927 publications published from 1981 to 2015, allowing assessment of the strength and variability of pollen limitation in 1265 wild plant species across all biomes and geographic regions globally. The GloPL database will be updated and curated with the aim of enabling the continued study of pollen limitation in natural ecosystems and highlighting significant gaps in our understanding of pollen limitation.
  • Boke-Olén, Niklas, et al. (författare)
  • Data Descriptor : High-resolution African population projections from radiative forcing and socio-economic models, 2000 to 2100
  • 2017
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 4
  • Tidskriftsartikel (refereegranskat)abstract
    • For its fifth assessment report, the Intergovernmental Panel on Climate Change divided future scenario projections (2005-2100) into two groups: Socio-Economic Pathways (SSPs) and Representative Concentration Pathways (RCPs). Each SSP has country-level urban and rural population projections, while the RCPs are based on radiative forcing caused by greenhouse gases, aerosols and associated land-use change. In order for these projections to be applicable in earth system models, SSP and RCP population projections must be at the same spatial scale. Thus, a gridded population dataset that takes into account both RCP-based urban fractions and SSP-based population projection is needed. To support this need, an annual (2000-2100) high resolution (approximately 1km at the equator) gridded population dataset conforming to both RCPs (urban land use) and SSPs (population) country level scenario data were created.
  • Buck, Moritz, et al. (författare)
  • Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds
  • 2021
  • Ingår i: Scientific Data. - : NATURE RESEARCH. - 2052-4463. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.
  • Buetti-Dinh, Antoine, 1984-, et al. (författare)
  • Systems biology of acidophile biofilms for efficient metal extraction
  • 2020
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 7:1, s. 1-10
  • Tidskriftsartikel (refereegranskat)abstract
    • Society's demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput "omics" performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.
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