From alpaca to zebra finch

A decade of cataloguing life's diversity

From alpaca to zebra finch

zebrafinch.jpg
A male zebra finch, South Australia. Annotation of the genetic code of the zebra finch has enabled researchers to identify genes that may be responsible for vocalising messages.

Today's publication in Nature of the genetic blueprint for the zebra finch marks 10 years of success for the Ensembl project in helping researchers to navigate the genomes of a Noah's Ark of species.

Ensembl, a genome annotation system co-developed and jointly run by the European Bioinformatics Institute (EMBL-EBI) and the Wellcome Trust Sanger Institute, played a major part in finding the genes and other functionally important features in the zebra finch genome. For zebra finch, only the second bird to have its genome fully sequenced after the chicken, this interpretation of the genetic code has enabled the sequencing consortium to identify genes expressed in the zebra finch brain that may be responsible for vocalising messages: zebra finches communicate by singing whereas chickens cannot.

"Trying to navigate a genome that has not been annotated with important features such as genes and regulatory regions is a little bit like trying to read a map missing all the labels. Without this annotation, the data gathered from sequencing projects would remain undecipherable."

Dr Paul Flicek, joint head of Ensembl and leader of the Vertebrate Genomics team at EMBL-EBI

Ensembl, which was originally created as a means of cataloguing the genes in the human genome, now contains the complete genetic codes of more than 50 animals. In addition to zebra finch, Ensembl has unravelled the genomes of organisms ranging in complexity from the humble nematode worm through the duck-billed platypus to ourselves.

"Genome analysis and comparison is key to linking genes to function and explaining why species differ from each other. In addition to helping us know more about evolutionary relationships and genetic diversity, it also provides the tools to tackle disease at the genetic level."

Dr Steve Searle, joint head of Ensembl and of Vertebrate Annotation at the Wellcome Trust Sanger Institute

"Over 10 years Ensembl has become part of the infrastructure of biological research. Looking back it's hard to imagine research before genomes and genome browsers."

Dr Tim Hubbard, Head of Informatics at the Wellcome Trust Sanger Institute

Combining information held in Ensembl with the related Ensembl Genomes resource for the genomes of bacteria, fungi, plants, metazoa and protists launched by EMBL-EBI last year, every sequenced genome provides another jigsaw piece in cataloguing the genetic diversity of life.

Notes to Editors
Publications
  • The genome of a songbird.

    Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW et al.

    Nature 2010;464;7289;757-62

Funding

This work was funded by the National Human Genome Research Institute (NHGRI) and grants from the Swedish Research Council, Knut and Alice Wallenberg Foundation, the Howard Hughes Medical Institute (HHMI), the National Institutes of Health (NIH) Directors Pioneer Award and the Biotechnology and Biological Sciences Research Council (BBSRC).

Participating Centres
  • The Genome Center, Washington University School of Medicine, St Louis, Missouri, USA
  • University of Illinois, Urbana-Champaign, Illinois, USA
  • Uppsala University, Institute for Evolution and Genetics Systems, Uppsala, Sweden
  • University of California-Los Angeles, Los Angeles, California, USA
  • EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
  • MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, UK
  • Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA
  • Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon, USA
  • Department of Biology & Biochemistry, University of Houston, Houston, Texas, USA
  • Department of Bioinformatics, Institute for Animal Health, Compton, Berks, UK
  • Department of Biosciences, University of Kent, Canterbury, Kent, UK
  • Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Oviedo, Spain
  • Crown Human Genome Center, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
  • Institute for Systems Biology, Seattle, Washington, USA
  • Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
  • Department of Biochemistry & Molecular Genetics, University of Colorado Health Sciences Cente, Aurora, Colorado, USA
  • University of Washington, Genome Sciences, Seattle, Washington, USA
  • Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
  • The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, Scotland, UK
  • Freie Universitaet Berlin, Institut Biology, Berlin, Germany
  • Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
  • Department of Organismic and Evolutionary Biology, Harvard University, Cambridge Massachusetts, USA
  • Monsanto Company, St. Louis, Missouri, USA
  • Neuroscience Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
Selected Websites
  • Zebra finch genome in Ensembl
  • Ensembl is a joint project between EMBL-EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl receives major funding from the Wellcome Trust.
Selected Websites
Contact the Press Office

Emily Mobley, Media Manager

Tel +44 (0)1223 496 851

Dr Samantha Wynne, Media Officer

Tel +44 (0)1223 492 368

Dr Matthew Midgley, Media Officer

Tel +44 (0)1223 494 856

Wellcome Sanger Institute,
Hinxton,
Cambridgeshire,
CB10 1SA,
UK

Mobile +44 (0) 7748 379849

Recent News

Appointments and changes to the Genome Research Limited Board
At the GRL Board meeting on 2 December 2019, David Willetts announced his intention to step down as Chair because of his extensive commitments across the academic and science sectors. Wellcome's Director, Jeremy Farrar, will take over the Chair of GRL Board from 1 January 2020.
Researchers identify new possibilities for the treatment of inflammatory bowel disease
Two molecular pathways found to be integral to maintaining balance in the digestive system
Root of childhood kidney cancer discovered
Pre-cancerous signatures found in healthy tissue point the way towards new treatment options