What’s coming in Ensembl 110 / Ensembl Genomes 57?

by ·Comments Off on What’s coming in Ensembl 110 / Ensembl Genomes 57?

Ensembl 110 and Ensembl Genomes 57 are expected to be released in May 2023 July 2023. Find out what’s coming in the new release, although we cannot guarantee everything listed here will make it into the final release.

Human

  • Human genome assembly version to be updated to the latest patch release GRCh38.p14
  • Genes on patches will appear on scaffold coordinates only
  • Y PAR genes are stand-alone genes and are no longer taken from X;
    MANE attributes remain on X PAR genes only
  • MANE and Ensembl canonical attributes to be added as tags in GFF3 files 

Vertebrates

Regulation data:

  • Regulatory annotation to be added in collaboration with the GENE-SWitCH and AQUA-FAANG consortia. These include annotation of open chromatin regions and promoters in Pig, Chicken, Atlantic salmon, Turbot, and European seabass.

Updated genomes:

  • Cricetulus griseus PICR  GCA_003668045.2 (Chinese hamster)
  • Heterocephalus glaber GCA_944319725.1 (male) and GCA_944319715.1 (female; Naked mole-rat)

New rat strains:

  • SHR/Utx RGD_8142385 GCA_023515785.1
  • WKY/Bbb RGD_1581635 GCA_023515805.1
  • SHRSP/BbbUtx GCA_021556685.1

Plants

Updated genomes:

  • Eragrostis tef GCA_024500355.1 (Teff)
  • Oryza sativa GCA_001433935.1 (Rice)
  • Populus trichocarpa GCA_000002775.4 (Black cottonwood)
  • Triticum aestivum cv. Renan GCA_937894285.1 (Common wheat)

New species:

  • Oryza sativa cv. ARC GCA_009831255.1
  • Oryza sativa cv. Azucena GCA_009830595.1
  • Oryza sativa cv. Chao Meo GCA_009831315.1)
  • Oryza sativa cv. Gobol Sail (Balam) GCA_009831025.1
  • Oryza sativa cv. IR64 GCA_009914875.1
  • Oryza sativa cv. Ketan Nangka GCA_009831275.1
  • Oryza sativa cv. Khao Yai Guang GCA_009831295.1
  • Oryza sativa cv. Larha Mugad GCA_009831355.1
  • Oryza sativa cv. Lima GCA_009831355.1
  • Oryza sativa cv. Liu Xu GCA_009829375.1
  • Oryza sativa cv. MH63 GCA_001618785.1
  • Oryza sativa cv. N22 GCA_001952365.2
  • Oryza sativa cv. Natel Boro GCA_009831335.1
  • Oryza sativa cv. PR106 GCA_009831045.1
  • Oryza sativa cv. ZS97 GCA_001618795.1
  • Triticum aestivum IWGSC RefSeq v2.1 GCA_018294505.1

Metazoa

Updated genomes:

  • Amphimedon queenslandica (Sponge)
  • Acyrthosiphon pisum (Pea aphid)
  • Drosophila melanogaster (Common fruit fly)
  • Lingula anatina (Lamp shell)
  • Phlebotomus perniciosus (Sand fly)

New assembly for existing species:

  • Athalia rosae (Turnip sawfly)
  • Bombus terrestris (Buff-tailed bumblebee)
  • Diabrotica virgifera virgifera (Western corn rootworm)
  • Lucilia cuprina (Australian sheep blowfly)
  • Melitaea cinxia (Glanville fritillary)

New species:

  • Amyelois transitella (Navel orangeworm)
  • Anthonomus grandis (Boll weevil)
  • Bicyclus anynana (Squinting bush brown)
  • Chelonus insularis (Parasitoid wasp)
  • Dermacentor andersoni (Rocky mountain wood tick)
  • Galleria mellonella (Greater wax moth)
  • Helicoverpa armigera (Cotton bollworm)
  • Helicoverpa zea (Corn earworm)
  • Homalodisca vitripennis (Glassy-winged sharpshooter)
  • Leguminivora glycinivorella (Moth)
  • Manduca sexta (Tobacco hornworm)
  • Neodiprion lecontei (Red-headed pine sawfly)
  • Neodiprion pinetum (White pine sawfly)
  • Nilaparvata lugens (Brown planthopper)
  • Pectinophora gossypiella (Pink bollworm)
  • Polistes canadensis (Red paper wasp)
  • Polistes dominula (European paper wasp)
  • Polistes fuscatus (Northern paper wasp)
  • Schistocerca americana (American bird grasshopper)
  • Sitophilus oryzae (Rice weevil)
  • Thrips palmi (Melon thrips)
  • Venturia canescens (Endoparasitoid wasp)
  • Zerene cesonia (Southern dogface)

Other updates and highlights

  • Re-annotation of the majority of genomes in Ensembl Bacteria in collaboration with MGnify.
  • Update of Compara REST API endpoints to require a species to be provided in addition to stable ID.
  • Removal of the Compara Perl API Compara::MemberAdaptor method fetch_by_stable_id, and its replacement by fetch_by_stable_id_GenomeDB, which accepts a Compara GenomeDB object in addition to a stable ID, and returns a corresponding gene or sequence member.
  • Update to Metazoa Compara gene trees via introduction of three species sets instead of one.
  • Removal of unused options from the Regulation BioMart filters: karyotype band, marker and ENCODE pilot regions.
  • New Variant Effect Predictor (VEP) plugin to integrate a number of phenotypic profiles in Geno2MP associated with rare variant genotypes (to be available on the web interface and via the REST API).
  • New transcript annotator VEP plugin to annotate variant-transcript pairs with custom data (only available for command-line VEP).
  • Enhanced mapping with AlphaFold protein structure database. Mapping to protein structures is available for species with UniParc annotations.
  • Ensembl 92 archive to be retired.