What’s coming in Ensembl 100 / Ensembl Genomes 47

Can you believe it? Our next release will be Ensembl 100! We are planning to release it along with Ensembl Genomes 47 in late March or beginning of April 2020. As with all releases, please note that these are intentions and are not guaranteed to make it into the releases. 

Major Data Updates

  • Update of Homo sapiens (Human) gene set to GENCODE 34
  • Update of Mus musculus (Mouse) gene set to GENCODE M25
  • Update of gnomAD genomic  allele frequencies on GRCh38 to version 3  

New Genomes

Mammals:

  • Delphinapterus leucas (Beluga whale)
  • Panthera leo (Lion)
  • Ursus thibetanus thibetanus (Asian black bear)

Fish:

  • Carassius auratus (Goldfish)
  • Dicentrarchus labrax (European seabass)
  • Oncorhynchus mykiss (Rainbow trout)
  • Oncorhynchus tshawytscha (Chinook salmon)
  • Oryzias javanicus (Javanese ricefish)
  • Oryzias sinensis (Chinese medaka)
  • Cyprinus carpio (Common carp reference)

Birds:

  • Anas platyrhynchos (Wild duck)
  • Camarhynchus parvulus (Small tree finch)
  • Cyanoderma ruficeps (Rufous-capped babbler)
  • Geospiza fortis (Medium ground finch)
  • Stachyris ruficeps (Rufous-capped babbler)
  • Zosterops lateralis melanops (Silvereye)

Reptiles:

  • Chelydra serpentina (Common snapping turtle)
  • Gopherus evgoodei (Goode’s thornscrub tortoise)
  • Laticauda laticaudata (Blue-lipped sea krait)
  • Pelusios castaneus (West African mud turtle) 

Metazoa:

  • Anopheles christyi

Plants:

  • Ananas comosus (Pineapple)
  • Chara braunii
  • Eragrostis curvula
  • Malus domestica (Golden Apple)
  • Olea europaea sylvestris (Wild olive)
  • Pistacia vera (Pistachio)
  • Prunus dulcis (Almond)
  • Matina and Criolllo cultivars of Theobroma cacao (Cacao tree) 

New Assemblies and/or Annotation

Mammals:

  • Ornithorhynchus anatinus (Platypus)

Fish:

  • Esox lucius (Northern pike)

Fungi:

  • Zymoseptoria tritici has an additional gene set from the Max Planck Institute and a revised gene set from Rothamsted Research 

The Gopherus evgoodei (Goode’s thornscrub tortoise) and the Ornithorhynchus anatinus (Platypus) genome are from the Vertebrate Genomes Project.

Other Updates and Highlights

  • Single exon genes for Sus scrofa (Pig)
  • Mitochondrial sequences and annotation for Macaca mulatta (Macaque)
  • Common name for Salmo trutta updated to Brown trout
  • New interface for configuration of multidimensional track hubs
  • The Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline has been parameterised and used to compute a multiple genome alignment of eleven Oryza taxa in Ensembl Plants.
  • Linkage disequilibrium display for Triticum aestivum (Wheat)
  • Addition of five pairwise genome alignments for Triticum turgidum (Durum wheat)
  • Discontinuation of dN/dS analysis for vertebrates and plants
  • BioMart  will no longer hold mappings of variants to transcripts with the biotypes lncRNA, processed_pseudogene and unprocessed_pseudogene. These data, including predicted functional consequences, will not be available for filtering and will not be reported as attributes.
  • Retirement of two archive sites, dec2014.archive.ensembl.org (Ensembl 78) and mar2015.archive.ensembl.org (Ensembl 79)

GRCh37

  • Removal of all data that is not for Homo sapiens (Human)
  • Updated RefSeq annotations
  • Updated Regulation data, including Regulatory Build and miRNA target features
  • Variation data updated to dbSNP version 153