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337 results for “Fraxinus”
Ash (Fraxinus excelsior L.) in vitro survival data for the UKs Living Ash Project
<p><em>In-vitro</em> propagation and survival data sets (including nursery survival) of the ash plants generated i.e. <em>Fraxinus excelsior</em> L., plus the PCR primers used and conditions applied.</p> <p>Surveyed from a range of ash seed material taken from across the UK, and held at the UK ash collection hosted by the Earth Trust in Oxfordshire, UK.</p> <p>A more detailed analysis of this data is currently expected to be be published in the <em>Annals of Forest Science</em>, and which has already provisionally accepted this work for publication, subject to the underlying data being made available i.e. here</p> <p>The data deposited here represents the underlying data that will be presented in graphical form in the forthcoming paper by Fenning et al., plus the associated metadata and statistical analyses, along with the original .jpg of the photos used.</p>
Gene annotation files for Fraxinus excelsior (European ash) genome assembly BATG-0.5
<p>Gene annotation files for <em>Fraxinus excelsior</em> genome assembly v. BATG-0.5, published in Nature (doi:10.1038/nature20786). These files were previously hosted on the Ash Tree Genomes website (http://www.ashgenome.org/transcriptomes) and first made available for download via that site on 2016-02-08.</p> <p>The following annotation files are available:</p> <p>### GFF file of all gene models (all isoforms)<br> Fraxinus_excelsior_38873_TGAC_v2.gff3</p> <p>### FASTA file of all cDNA sequences (all isoforms)<br> Fraxinus_excelsior_38873_TGAC_v2.gff3.cdna.fa</p> <p>### FASTA file of all CDS DNA sequences (all isoforms)<br> Fraxinus_excelsior_38873_TGAC_v2.gff3.cds.fa</p> <p>### FASTA file of all peptide sequences (all isoforms)<br> Fraxinus_excelsior_38873_TGAC_v2.gff3.pep.fa</p> <p>### Functional annotation for each gene model (all isoforms)<br> Fraxinus_excelsior_38873_TGAC_v2.gff3.functional_annotation.tsv</p> <p>### GFF file of all gene models (longest isoform only)<br> Fraxinus_excelsior_38873_TGAC_v2.longestCDStranscript.gff3</p> <p>### FASTA file of all cDNA sequences (longest isoform only)<br> Fraxinus_excelsior_38873_TGAC_v2.longestCDStranscript.gff3.cdna.fa</p> <p>### FASTA file of all CDS DNA sequences (longest isoform only)<br> Fraxinus_excelsior_38873_TGAC_v2.longestCDStranscript.gff3.cds.fa</p> <p>### FASTA file of all peptide sequences (longest isoform only)<br> Fraxinus_excelsior_38873_TGAC_v2.longestCDStranscript.gff3.pep.fa</p> <p>### GFF file for gene models identified as probable transposable element related sequences (excluded from the other files)<br> Fraxinus_excelsior_38873_TGAC_v2.transposable_elements.gff3</p> <p><br> NB: The annotation files include preliminary annotations for genes within the organellar scaffolds (gene models FRAEX38873_v2_000400370-FRAEX38873_v2_000401330), which were not reported in the publication of the BATG0.5 assembly (doi:10.1038/nature20786).</p>
Herbarium specimen image of Fraxinus platycarpa Michx., part of the collection of Meise Botanic Garden
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.
Herbarium specimen image of Fraxinus excelsior L., part of the collection of Royal Botanic Gardens, Kew
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.
Fraxinus pennsylvanica genome assembly and annotation
<p>We report the first chromosome-level assembly for green ash (<em>Fraxinus pennsylvanica</em>) to assist in ash breeding efforts to propagate resistance to the emerald ash borer. The final haploid assembly consists of 23 chromosomes and 87 unplaced scaffolds of 10 kb or more. Over 99% of the bases anchored to the chromosomes. The assembly spans 757 Mb and consists of 49.43% repetitive DNA. Gene annotation yielded 35,470 high-confidence gene models, all located on the chromosomes and assigned to 22,976 Asterid Orthogroups.</p>
Worldwide Fraxinus Genome Assemblies, Annotations, and Gene Families v0.2
<p>The worldwide <em>Fraxinus</em> genome project was conducted to assess the pathogenic resistance of 34 Ash tree species to Ash Dieback and Emerald Ash Borer. The project is led by Dr. Richard Buggs. v0.1 genomes are available at ashgenome.org and on ENA. As part of Josiah Seaman's PhD thesis, he improved the assembly of 13 genomes included here as v0.2. New de novo annotations, gene families, and all associated files are included for future studies and reproducibility. </p> <p>Annotations are done with GeMoMa using F. excelsior as a reference (Keilwagen et al. 2016). Gene families are defined as genes originating from a single copy at the last common ancestor with Solanum. Orthofinder outputs reconciled gene trees, aligned CDS, and gene families (Emms and Kelly 2015; Tekaia 2016). Species tree was calibrated based on fossil evidence using r8s, RAxML across 25,182,399 sites (SpeciesTreeAlignment.fa). More methods details can be found in the full Chapter two of Josiah Seaman's PhD thesis (2021).</p> <p>I'd be happy to talk with you if you'd like any additional information or help visualizing your genomic data. You can find the tools used to browse this data at https://fluentdna.com/ and http://graphgenome.org/ Contact me at josiah@newline.us</p>
Fraxinus quadrangulata (Oleaceae) - whole tree (or vine) - general
Image of Fraxinus quadrangulata (Oleaceae) - whole tree (or vine) - general
Fraxinus quadrangulata (Oleaceae) - fruit - lateral or general close-up
Image of Fraxinus quadrangulata (Oleaceae) - fruit - lateral or general close-up
Fraxinus quadrangulata (Oleaceae) - fruit - as borne on the plant
Image of Fraxinus quadrangulata (Oleaceae) - fruit - as borne on the plant
Fraxinus americana (Oleaceae) - fruit - lateral or general close-up
Image of Fraxinus americana (Oleaceae) - fruit - lateral or general close-up
Fraxinus americana (Oleaceae) - fruit - as borne on the plant
Image of Fraxinus americana (Oleaceae) - fruit - as borne on the plant
Fraxinus quadrangulata (Oleaceae) - bark - of a medium tree or large branch
Image of Fraxinus quadrangulata (Oleaceae) - bark - of a medium tree or large branch
Fraxinus pennsylvanica (Oleaceae) - inflorescence - whole - male
Image of Fraxinus pennsylvanica (Oleaceae) - inflorescence - whole - male
Fraxinus pennsylvanica (Oleaceae) - inflorescence - whole - unspecified
Image of Fraxinus pennsylvanica (Oleaceae) - inflorescence - whole - unspecified
Fraxinus biltmoreana (Oleaceae) - inflorescence - whole - male
Image of Fraxinus biltmoreana (Oleaceae) - inflorescence - whole - male
Fraxinus biltmoreana (Oleaceae) - inflorescence - whole - unspecified
Image of Fraxinus biltmoreana (Oleaceae) - inflorescence - whole - unspecified
Fraxinus pennsylvanica (Oleaceae) - twig - winter overall
Image of Fraxinus pennsylvanica (Oleaceae) - twig - winter overall
Fraxinus pennsylvanica (Oleaceae) - twig - close-up winter leaf scar/bud
Image of Fraxinus pennsylvanica (Oleaceae) - twig - close-up winter leaf scar/bud
Fraxinus pennsylvanica (Oleaceae) - bark - of a small tree or small branch
Image of Fraxinus pennsylvanica (Oleaceae) - bark - of a small tree or small branch
Fraxinus pennsylvanica (Oleaceae) - whole tree (or vine) - view up trunk
Image of Fraxinus pennsylvanica (Oleaceae) - whole tree (or vine) - view up trunk
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International Brain Laboratory public data
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OpenNeuro
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