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.

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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

Register now for the EBI training course in Plant and Pathogen bioinformatics 13th-15th November 2017, Hinxton, UK

This course will provide an introduction to data resources, tools and essential bioinformatic techniques for biologists studying plants and their pathogens. It will be delivered using a mixture of lectures, practical computer sessions and include discussions based on relevant case studies and public domain data. For more details, go to http://www.ebi.ac.uk/training/events/2017/plant-and-pathogen-bioinformatics-0.

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).

Ensembl Plants Archive Site

Alongside release 32 we have launched a new archive site, where we will keep selected previous releases of Ensembl Plants publicly available. The first release available on the archive site is release 31, and includes the previous assemblies for wheat and maize.

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.

BBSRC logo

Past Funding

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

transPLANT logo The European flag

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. Click to see details of our funding.

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Acknowledgements

Ensembl Plants is a joint project of the European Bioinformatics Institute and the group of Doreen Ware at the Cold Spring Harbor Laboratory, who have developed the Gramene database [1,2], a resource for plant comparative genomics based on Ensembl technology [3,4]. A common set of databases are available through Ensembl Plants and Gramene, and the two groups are collaborating on the integration of content, quality control and the development of new features.

References

  1. Youens-Clark, K., et al., Gramene database in 2010: updates and extensions. Nucleic Acids Res. 2010. 39:D1085-94
    PubMed ID: 21076153
  2. Monaco MK., et al., Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. 2014. 42:D1193-9.
    PubMed ID: 24217918
  3. Hubbard, T., et al., The Ensembl genome database project. Nucleic Acids Res. 2002. 30:38-41
    PubMed ID: 11752248
  4. Kersey PJ., et al., Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2014. 42:D546-52.
    PubMed ID: 24163254