Plants

Release Intentions

  • New genomes
  • Updated genomes
  • New data
    • New alignment based cross references to UniProt and RefSeq across all plants
    • New automatic ncRNA gene annotations across all plants
  • Updated data
    • Updated peptide comparative genomics including Jute, Cassava and Sorghum
    • Updated protein features
    • Updated BioMarts

Release Notes (Brief)

This release of Ensembl Plants adds one of the two recently sequenced Corchorus capsularis (jute) genomes (Nature 2017) and whole genome alignments between the latest Hordeum vulgare (barley) assembly and Oryza sativa (rice), summarised here, and Brachypodium distachyon, summarised here.

Did you know...?

The Track Hub Registry

You can search the Track Hub Registry to find more than 1,400 public RNA-Seq studies aligned to plants (read more)!

What's New in Release 37

Future Releases

New Ensembl Genomes Archive Sites

Ensembl Genomes now has archive sites for all divisions. These can be found at the following URLs:

http://oct2017-metazoa.ensembl.org

http://oct2017-plants.ensembl.org

http://oct2017-fungi.ensembl.org

http://oct2017-protists.ensembl.org

http://oct2017-bacteria.ensembl.org

The archive sites will allow researchers to access data from old releases in our web-based tools, and additionally will be able to display track hubs containing alignments and features located on older versions of genome assemblies that have since been upgraded in the live site. Archive sites will be searchable and BioMarts will be available where they were produced for the site when live. Schema and API versions for archive sites will be the same as when the data was released, i.e. archive sites will not be updated to use the most recent versions. Ensembl tools will not be active in the initial release, but we are hoping to enable these shortly. Major bugs (i.e. those impeding the usability of the site) will be fixed, but minor bugs will not be.

The first release of the archive sites contains content from release 37. New archive sites will be released at least once a year, under URLs indicating the date of first release of the data they contain. The previously existing archive for Ensembl Plants, http://archive.plants.ensembl.org, will continue to be available at this URL, but also as http://mar2016-plants.ensembl.org, in accordance with the new naming scheme. As previously, data from all recent releases will continue to be available for download at ftp://ftp.ensemblgenomes.org.

New barley genome

A ten-nation consortium has reported the first high-quality reference genome sequence of Hordeum vulgare (barley). The barley genome was sequenced and assembled using an array of state-of- the-art methods, taking ten years. For the first time, scientists can now locate all genes precisely in the genome and analyze complex gene families that play a key role in malting and resilience.

New Arabidopsis variation data from the 1001 Genomes Project

We have upgraded our representation of genetic variation in Arabidopsis thaliana, incorporating the full data set from the 1001 Genomes Project, covering more than 10 million variant loci across 1,135 samples (Cell 2016).

New bread wheat variation data

A total of 80,829 variation markers from the iSelect 90k array and 13.8 million Inter-Homoeologous Variants (IHVs) have been added to the new genome assembly of Triticum aestivum cv. Chinese Spring produced by the Earlham Institute.

This data is viewable alongside the existing Axiom 35k and 820k SNP marker sets provided by CerealsDB and located on the new assembly and the publicly available EMS mutant lines from tetraploid (cv. Kronos) and hexaploid (cv. Cadenza) TILLING populations (read more).

Funding

Ensembl Plants datasets are constructed in a direct collaboration with the Gramene resource, funded by the United States National Science Foundation award #1127112. Read more about our collaboration with Gramene.

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The development of resources for wheat is funded by the BBSRC-funded Designing Future Wheat ISP.

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Past Funding

transPLANT, funded by the European Commission within its 7th Framework Programme, under the thematic area "Infrastructures", contract number 283496.

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BBSRC funding for wheat (Triticeae Genomics For Sustainable Agriculture) and barley (UK barley genome sequencing project).

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.

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