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129 results for “Corylus”
Potential and realized distribution at 30m for Common hazel (Corylus avellana) in Europe for 2000 - 2020
<p>Probability and uncertainty maps showing the potential and realized distribution for the common hazel (<em>Corylus avellana, L.</em>) for Europe from the dataset prepared by <a href="http://doi.org/10.5281/zenodo.5818021">Bonannella et al. (2022)</a> and predicted using Ensemble Machine Learning (EML). Potential distribution map cover the period 2018 - 2020; realized distribution cover the period 2000 - 2020, split in the following time periods:</p> <ul> <li>2000 - 2002,</li> <li>2002 - 2006,</li> <li>2006 - 2010,</li> <li>2010 - 2014,</li> <li>2014 - 2018,</li> <li>2018 - 2020.</li> </ul> <p>Files are named according to the following naming convention, e.g:</p> <ul> <li>veg_corylus.avellana_anv.eml_md_30m_0..0cm_2000..2002_eumap_epsg3035_v0.3</li> </ul> <p>with the following fields:</p> <ul> <li>theme: e.g. <strong>veg</strong>,</li> <li>species code: e.g. <strong>corylus.avellana</strong>,</li> <li>species distribution type: e.g. <strong>anv</strong> (= actual natural vegetation),</li> <li>species estimation method: e.g. <strong>eml</strong>,</li> <li>species estimation type: e.g. <strong>md</strong> ( = model deviation),</li> <li>resolution in meters e.g. <strong>30m</strong>,</li> <li>reference depths (vertical dimension): e.g. <strong>0..0cm</strong>,</li> <li>reference period begin end: e.g. <strong>2000..2002</strong>,</li> <li>reference area: e.g. <strong>eumap</strong>,</li> <li>coordinate system: e.g. <strong>epsg3035</strong>,</li> <li>data set version: e.g. <strong>v0.3</strong>.</li> </ul> <p>For each species is then easy to identify probability and uncertainty distribution maps:</p> <ul> <li>veg_corylus.avellana_<strong>anv</strong>.eml_<strong>md</strong>: model uncertainty for realized distribution</li> <li>veg_corylus.avellana_<strong>anv</strong>.eml_<strong>p</strong>: probability for realized distribution</li> <li>veg_corylus.avellana_<strong>pnv</strong>.eml_<strong>md</strong>: model uncertainty for potential distribution</li> <li>veg_corylus.avellana_<strong>pnv</strong>.eml_<strong>p</strong>: probability for potential distribution</li> </ul> <p>Files are provided as <a href="https://gdal.org/drivers/raster/cog.html">Cloud Optimized GeoTIFFs</a> and projected in the Coordinate Reference System ETRS89 / LAEA Europe (= EPSG code 3035). Styling files are provided in both <em>SLD</em> and <em>QML</em> format.</p> <p>If you would like to know more about the creation of the maps and the modeling:</p> <ul> <li><strong>watch</strong> the talk at Open Data Science Workshop 2021 (<a href="https://doi.org/10.5446/55256">TIB AV-PORTAL</a>)</li> <li><strong>access </strong>the repository with our R/Python scripts and follow the instructions (<a href="https://gitlab.com/geoharmonizer_inea/spatial-layers/-/tree/master/veg_mapping">GitLab</a>)</li> <li><strong>access </strong>the repository with the training dataset (<a href="https://doi.org/10.5281/zenodo.5818021">Zenodo</a>)</li> <li><strong>read </strong>the tutorial with executable code on our <a href="https://opengeohub.github.io/spatial-prediction-eml/spatiotemporal-ml.html#spatiotemporal-distribution-of-fagus-sylvatica">GitBook</a></li> </ul> <p>A publication describing, in detail, all processing steps, accuracy assessment and general analysis of species distribution maps is available on <a href="https://doi.org/10.7717/peerj.13728">PeerJ</a>. To suggest any improvement/fix use <a href="https://gitlab.com/geoharmonizer_inea/spatial-layers/-/issues">https://gitlab.com/geoharmonizer_inea/spatial-layers/-/issues</a>.</p>
Genome assembly and annotation files for Corylus americana accessions 'Rush' and 'Winkler'
<p>The native shrub American hazelnut (<em>Corylus americana</em>) is currently used in breeding programs that are aiming to develop commercially viable hazelnut varieties for the U.S. Upper Midwestern U.S. This species provides significant ecological benefits as it is a perennial crop and well-adapted to this region. Breeding cycles for perennial species are long, and may benefit from the use of predictive methods such as genomic selection to reduce cycle time and increase the efficiency of field trials.</p> <p>High-quality reference genome assemblies are very useful for the implementation marker-assisted selection and genomic prediction, and we therefore developed the first chromosome-scale reference assemblies for <em>C. americana</em>, using the accessions 'Rush' and 'Winkler'. Initial draft assemblies were created using HiFi PacBio reads and Arima Hi-C sequencing to assemble genomes into 11 pseudomolecules. We then utilized Oxford Nanopore reads and a high-density genetic map in order to perform error correction. N50 scores were calculated to be 31.9 Mb and 35.3 Mb for 'Rush' and 'Winkler', respectively, while 97.1% (for 'Winkler') and 90.2% (for 'Rush') of the total genome was assembled into the 11 pseudomolecules. Gene prediction was performed using both RNAseq libraries as well as protein homology data. 'Rush' had a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while 'Winkler' had corresponding scores of 96.9 and 96.5, indicating extremely high-quality assemblies.</p> <p>These two independent, de novo assemblies enable unbiased assessment of structural variation across the genome, as well as patterns of syntenic relationships within C. americana and the <em>Corylus</em> genus. These assemblies are also an important first step in providing a resource for using next-generation sequencing data in the improvement of <em>C. americana</em>. We demonstrate this utility through the generation of high-density SNP marker sets from genotyping-by-sequencing data for 1,343 <em>C. americana</em>, <em>C. avellana</em>, and <em>C. americana</em> x <em>C. avellana</em> hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published <em>Corylus</em> genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing further evidence of unique molecular pathways governing self-incompatibility in Corylus not exhibited in other well-studied SSI systems. We hope these assemblies will aide in the application of modern breeding methods to the development of commercially viable hazelnut varieties for the U.S. Upper Midwest.</p>
Corylus americana (Betulaceae) - leaf - whole upper surface
Image of Corylus americana (Betulaceae) - leaf - whole upper surface
Corylus americana (Betulaceae) - inflorescence - whole - unspecified
Image of Corylus americana (Betulaceae) - inflorescence - whole - unspecified
Corylus americana (Betulaceae) - leaf - showing orientation on twig
Image of Corylus americana (Betulaceae) - leaf - showing orientation on twig
Corylus avellana L. (BR0000011825920)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011826538)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000014437076)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011826514)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011825234)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011827283)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011826750)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011825081)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000014437168)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011827146)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000014436925)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000005337736)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011824879)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000011825869)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Corylus avellana L. (BR0000014436918)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
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