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78 results for “Norway spruce”
Data from: The extended consequences of genetic conductivity: mating distance affects community phenotypes in Norway spruce
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Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as genotyping platform in Norway spruce
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Data from: Genome-wide exon-capture approach identifies genetic variants of Norway spruce genes associated with susceptibility to Heterobasidion parviporum infection
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Data from: Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)
A novel set of SNPs was derived from transcriptome data of ten Norway spruce (Picea abies) trees from the Bavarian Forest National Park in Germany (BaFoNP). SNPs were identified by mapping against a de-novo transcriptome assembly and against pre-mRNAs of predicted genes of the reference genome assembly. This resulted in 111,849 and 366,577 SNPs, respectively. Out of these, 311 were either randomly selected or chosen because of their pronounced divergence between sampling sites and genotyped in 218 trees with an Illumina Infinium HD iSelect BeadChip.
Dataset used in the paper 'Blue stain development on Norway spruce (Picea abies (L.) H. Karst.) logs under alpine conditions'
<p>The research material is open to support transparency in science.</p>
Phenotypic and genotypic data of genomic selection study of spring frost tolerance of Norway spruce
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Load-Displacement History Data and Video Recording of Norway Spruce Compression Experiment Perpendicular to Grain Direction
<p>This dataset contains load-displacement history of Norway Spruce compression experiments perpendicular to grain direction and the video recordings. The experiment utilized the Zwick RK 250/50 <em>Universal Testing Machine</em> (UTM) with HBM U2A load cell set at 200kN capacity, while video was recorded by Canon EOS 5DS R mounted on a tripod. Unfortunately the recording failed while recording specimen 3, hence only part of the beginning of the experiment is available.</p>
Fig. 2 in Effects Of Leaf-Litter Addition On Carabid Beetles In A Non-Native Norway Spruce Plantation
Fig. 2. The mean numbers (± S. E.) of the five dominant carabid species in the control and leaf-litter plots. Note different scales in the vertical axes
Field data for article "Root rot increases the vulnerability of Norway spruce trees to Ips typographus infestation"
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Data from: The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)
To evaluate the usefulness of Reduced Representation Libraries (RRL) in species with large and highly repetitive genomes such as conifers, we employed Hypomethylated Partial Restriction (HMPR) on the genome of Norway spruce (Picea abies). The HMPR method preferentially removes the repetitive fraction of the genome, which is commonly hypermethylated. Hence, RRLs should be enriched for the hypomethylated gene space. For comparison a standard shotgun library was constructed and samples of the respective libraries were obtained through Sanger sequencing. We obtained a nine-fold gene enrichment, a value which is slightly higher than for other plant species. The higher relative efficiency of HMPR is probably a consequence of the large Norway spruce genome size since the probability of finding genes in a standard shotgun library is very small. The amount of repetitive DNA was reduced by 45% in the RRLs, demonstrating the ability to efficiently remove hypermethylated DNA. Annotating sequences in an uncharacterized genome remains challenging and a large number of sequences could not be classified as either repetitive DNA or as belonging to the gene space. Upon further investigation, we found that some of these uncharacterized fragments were expressed, and in most cases the expression was spatially differentiated, indicating that they might have a function. Full-length transcripts of a subset of expressed fragments also revealed that these could be long non-coding RNAs. Long non-coding RNAs have been shown to be involved in gene regulation and deserve future attention. In conclusion, our study shows that the HMPR method is effective in constructing libraries enriched for the genic fraction of the genome, while simultaneously reducing the repetitive fraction, in P. abies and may prove a valuable tool for the discovery, validation and assessment of genetic markers in population studies when combined with next generation sequencing technology.
Data from: Accumulation rates and sources of external nitrogen in decaying wood in a Norway spruce dominated forest
Microbial respiration in dead wood contributes substantially to the long-lived forest carbon (C) pool and has a significant role in the forest nitrogen (N) cycle. Wood N content has been found to increase during the decay process; however, temporal dynamics and the sources of this external N remain unclear. To examine N dynamics at various stages of decomposition, we combined high variety of analytical methods on Norway spruce logs, including wood δ15N, N%, 14C-dating, fungal composition and N2 fixation rate. For N2 fixation rate, we also determined its dependency on ambient temperature and decay class, when estimating annual N2 fixation rates for our study site. N2 fixation was observed to have a major role in increasing wood N content during decay. For the most decayed wood, it accounted for 60% of the total N accumulation. Compared to other reports, where the annual temperature was similar to our site, the calculated annual fixation rate of 85 g N ha−1 year−1 is a low estimate. However, previous studies have not taken appropriately into account the dependency of N2 fixation rate on ambient temperature and decay class. Our δ15N model describing the sources of external N, statistical analysis and the fungal DNA composition of decayed wood suggest that other sources of external N accumulating in wood were soil-foraging wood-decay fungi and mycorrhizal fungi. Our study improves knowledge of the temporal dynamics of N accumulation in wood with advancing wood decay, the potential sources of external N and their relative significance. All of these factors are important for nitrogen as well as carbon models dealing with ecosystem responses to climate change.
Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms
BACKGROUND: A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now simultaneously identify the transcribed part of a species genome and estimate levels of gene expression. RESULTS: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads, together with publicly available expressed sequence tag (EST) data from Norway spruce, was used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 83.5% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression differences between samples collected under dark and light conditions. CONCLUSIONS: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 x 10-09 and 1.1 x 10-09) is an order of magnitude smaller than values reported for angiosperm herbs. However, if one takes generation time into account, most of this difference disappears. The estimates of the dN/dS ratio (non-synonymous over synonymous divergence) reported here are in general much lower than 1 and only a few genes showed a ratio larger than 1.
Sap flow in Norway spruce trees during the growing season 2015
<p>Primary data on the sap flow of Norway spruce trees growing on the southern border of their range in 2015 are presented. Coordinates N55.834715, E48.829725. The measurements were carried out from May 14 to August 31 with the help of instruments EMS51А (EMS, Brno, CZ). Measurement interval 10 minutes. At the same time, meteorological<br> observations.</p>
Data from: Accumulation rates and sources of external nitrogen in decaying wood in a Norway spruce dominated forest
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Data from: The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)
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Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms
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Data from: Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)
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Norway Spruce Cultured Cells Chitosan & C.polonica Stress
GEO Series GSE10771. Picea; Picea abies. 24 samples. Type: Expression profiling by array.
Profiling of small RNA in Norway spruce embryonic calli and male gametophytes
GEO Series GSE129413. Picea abies. 10 samples. Type: Non-coding RNA profiling by high throughput sequencing.
PARE libraries for the identification of miRNA target genes in Norway spruce
GEO Series GSE65248. Picea abies. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.