31 March 2010

From alpaca to zebra finch

A decade of cataloguing life's diversity

A male zebra finch, South Australia.

A male zebra finch, South Australia.

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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," explains Dr Paul Flicek, joint head of Ensembl and leader of the Vertebrate Genomics team at EMBL-EBI. "Without this annotation, the data gathered from sequencing projects would remain undecipherable."

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.

" In addition to helping us know more about evolutionary relationships and genetic diversity, genome annotation also provides the tools to tackle disease at the genetic level. "

Dr Steve Searle

"Genome analysis and comparison is key to linking genes to function and explaining why species differ from each other," says Dr Steve Searle, joint head of Ensembl and of Vertebrate Annotation at the Wellcome Trust Sanger Institute. "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."

"Over 10 years Ensembl has become part of the infrastructure of biological research," says Dr Tim Hubbard, Head of Informatics at the Wellcome Trust Sanger Institute. "Looking back it's hard to imagine research before genomes and genome browsers."

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

Publication details

  • The genome of a songbird.

    Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER and Wilson RK

    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
  • Related BBSRC press release
  • 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.
  • The European Bioinformatics Institute (EBI) is part of the European Molecular Biology Laboratory (EMBL) and is located on the Wellcome Trust Genome Campus in Hinxton near Cambridge (UK). The EBI grew out of EMBL's pioneering work in providing public biological databases to the research community. It hosts some of the world's most important collections of biological data, including DNA sequences (EMBL-Bank), protein sequences (UniProt), animal genomes (Ensembl), three-dimensional structures (the Protein Databank in Europe), data from gene expression experiments (ArrayExpress), protein-protein interactions (IntAct) and pathway information (Reactome). The EBI hosts several research groups and its scientists continually develop new tools for the biocomputing community.
  • The European Molecular Biology Laboratory is a basic research institute funded by public research monies from 20 member states (Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom) and associate member state Australia. Research at EMBL is conducted by approximately 80 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and Outstations in Hinxton (the European Bioinformatics Institute), Grenoble, Hamburg, and Monterotondo near Rome. The cornerstones of EMBL's mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and to actively engage in technology transfer activities. EMBL's International PhD Programme has a student body of about 170. The Laboratory also sponsors an active Science and Society programme. Visitors from the press and public are welcome.

The Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute, which receives the majority of its funding from the Wellcome Trust, was founded in 1992. The Institute is responsible for the completion of the sequence of approximately one-third of the human genome as well as genomes of model organisms and more than 90 pathogen genomes. In October 2006, new funding was awarded by the Wellcome Trust to exploit the wealth of genome data now available to answer important questions about health and disease.

Websites

The Wellcome Trust

The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.

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