35

EMS-type variants from sequenced tetraploid (cv ‘Kronos’) and hexaploid (cv ‘Cadenza’) TILLING populations were added to Ensembl Plants.

Researchers and breeders can search this database online, identify mutations in the different copies of their target gene, and request seeds to study gene function or improve wheat varieties. Seeds can be requested from the UK SeedStor (https://www.seedstor.ac.uk/shopping-cart-tilling.php) or from the US-based Dubcovsky lab (http://dubcovskylab.ucdavis.edu/wheat-tilling).

A new assembly of Triticum aestivum cv. Chinese Spring (bread wheat) is now available in Ensembl Plants. The assembly and gene model annotation has been generated by The Earlham Institute, formerly The Centre for Genome Analysis (TGAC). Read more...

The fast protein sequence search of HMMER is now available for all divisions of Ensembl Genomes, via the 'HMMER' link in the menu at the top of every page (e.g. Ensembl Metazoa).

The previous wheat assembly (IWGSC CSS) and every other plant from release 31 is available in the new Ensembl Plants archive site: http://archive.plants.ensembl.org/

New track hubs have been created for more than 900 public RNA-Seq studies, totaling more than 16,000 tracks across 35 plant species (read more).

Division Content

Release Intentions

  • Release scheduled for 21st March 2017
  • Update to Ensembl 88 software
  • Removal of MySQL databases from release 26 from the public MySQL server

Release Notes Outline

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What's New in Release 35 (April 2017)

Ensembl Bacteria has been updated to include the latest versions of 44,039 genomes (43,552 bacteria and 494 archaea) from the INSDC archives.

In this release we include an updated gene set for Botrytis cinerea B05.10. This gene set was manually curated by the community using the WebApollo tool. A new strain of Puccinia striiformis was imported from JGI and other new genomes from ENA are also available.

Three species make their Ensembl Metazoa debut: a bdelloid rotifer arrives to represent the Rotifera phylum; the rather attractive (and destructive) Asian long-horned beetle joins our existing Coleoptera (one of which, the red flour beetle, was updated to the latest assembly and gene set in this release); and the Hessian fly, a crop pest, was lured in by all that lovely wheat in Ensembl Plants. The sponge, Amphimedon queenslandica, has also been updated to the latest gene set.

Ortholog metrics were calculated and used to determine a set of "high confidence" orthologs. The metrics included congruence with whole genome alignments and (for closely related species) gene order conservation.

This release of Ensembl Plants includes an updated version of the Sorghum genome and an updated gene build for Zea mays. Additionally EMS variation data has been added for wheat, and QTL data for rice.

This protists release includes new variation data for Phaeodactylum tricornutum generated from 10 ecotypes.