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A Menagerie of New Genomes Released by International Ensembl Project

Monday, March 16, 2020

The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP)

 

Meerkats, yaks, geese, and lots of flies — oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project

The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data.

Among them are 38 new species and two dog breeds (Great Dane and Basenji), as well as four updated genome assemblies. Many were created using PacBio sequencing data. 

 

Thirteen of the new assemblies have been produced by the Vertebrate Genome Project (VGP):

  • Canada lynx
  • Greater horseshoe bat
  • Golden eagle 
  • Kakapo 
  • Jewelled blenny (pictured, right)
  • Pinecone soldierfish
  • Live sharksucker
  • Orbiculate cardinalfish
  • Gilthead seabream 
  • River trout (also part of the Sanger 25 Genomes Project)
  • Zebra finch (updated assembly)
  • Asian bonytongue (updated assembly) 
  • Fugu (updated assembly) 

Part of Ensembl’s mission is to provide gene annotation for the genome assemblies produced by this long-term global collaboration.

 

The release also included six more mammalian genome assemblies: 

  • Siberian musk deer 
  • Chacoan peccary
  • Sperm whale
  • Meerkat (pictured, right)
  • Arabian camel
  • Domestic yak 

Nine more bird genome assemblies: 

  • Gouldian finch
  • Yellow-billed parrot
  • Burrowing owl
  • African ostrich (pictured, right)
  • Swan goose
  • Indian peafowl
  • Eurasian sparrowhawk
  • Golden pheasant
  • Ring necked pheasant

Ten fish: 

  • Golden-line barbel
  • Blind barbel (pictured, right)
  • Horned golden-line barbel
  • German mirror carp
  • Hebao red carp
  • Hunaghe carp
  • Atlantic salmon (also part of the AquaFAANG project
  • Blue tilapia
  • Round goby 
  • Nile tilapia (updated assembly)

And four new reptiles: 

  • Komodo dragon (pictured, right)
  • Common wall lizard
  • Eastern brown snake 
  • Three-toed box turtle

As for mice and human genomes, Ensembl 99 includes updated annotations with many new genes and changes to existing ones – GENCODE M24 and GENCODE 33, respectively. 

 

There are also 35 new metazoa genome assemblies, including:

  • 18 new Anopheles mosquito species
  • an update from the L3 to L5 assembly for Aedes aegypti
  • the vector of Zika virus Aedes albopictus
  • six Tsetse fly species
  • two Sand fly species
  • the freshwater snail vector of schistosomiasis (Biomphalaria glabrata)
  • the common bedbug (Cimex lectularius)
  • the Lyme disease tick (Ixodes scapularis)
  • common house fly (Musca domestica)
  • stable fly (Stomoxys calcitrans)

And there are some sweet additions to plant genomes:

  • Sweet cherry (Prunus avium)
  • Clementine (Citrus clementina)
  • Morning glory (Ipomoea triloba
  • Wild sugarcane (Saccharum spontaneum

Started in 1999 to annotate the human genome and make all data publicly and freely available via the web, the Ensembl project is based at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Genome Campus near Cambridge, UK, and now involves hundreds of scientists from around the world.

 

See the full list of all Ensembl genomes and learn more about plant and animal sequencing on the PacBio Systems.. 

 

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