Title

The zebrafish reference genome sequence and its relationship to the human genome.

Authors

Kerstin Howe
Matthew D Clark
Carlos F Torroja
James Torrance
Camille Berthelot
Matthieu Muffato
John E Collins
Sean Humphray
Karen McLaren
Lucy Matthews
Stuart McLaren
Ian Sealy
Mario Caccamo
Carol Churcher
Carol Scott
Jeffrey C Barrett
Romke Koch
Gerd-Jörg Rauch
Simon White
William Chow
Britt Kilian
Leonor T Quintais
José A Guerra-Assunção
Yi Zhou
Yong Gu
Jennifer Yen
Jan-Hinnerk Vogel
Tina Eyre
Seth Redmond
Ruby Banerjee
Jianxiang Chi
Beiyuan Fu
Elizabeth Langley
Sean F Maguire
Gavin K Laird
David Lloyd
Emma Kenyon
Sarah Donaldson
Harminder Sehra
Jeff Almeida-King
Jane Loveland
Stephen Trevanion
Matt Jones
Mike Quail
Dave Willey
Adrienne Hunt
John Burton
Sarah Sims
Kirsten McLay
Bob Plumb
Joy Davis
Chris Clee
Karen Oliver
Richard Clark
Clare Riddle
David Eliott
Glen Threadgold
Glenn Harden
Darren Ware
Beverly Mortimer
Giselle Kerry
Paul Heath
Benjamin Phillimore
Alan Tracey
Nicole Corby
Matthew Dunn
Christopher Johnson
Jonathan Wood
Susan Clark
Sarah Pelan
Guy Griffiths
Michelle Smith
Rebecca Glithero
Philip Howden
Nicholas Barker
Christopher Stevens
Joanna Harley
Karen Holt
Georgios Panagiotidis
Jamieson Lovell
Helen Beasley
Carl Henderson
Daria Gordon
Katherine Auger
Deborah Wright
Joanna Collins
Claire Raisen
Lauren Dyer
Kenric Leung
Lauren Robertson
Kirsty Ambridge
Daniel Leongamornlert
Sarah McGuire
Ruth Gilderthorp
Coline Griffiths
Deepa Manthravadi
Sarah Nichol
Gary Barker
Siobhan Whitehead
Michael Kay
Jacqueline Brown
Clare Murnane
Emma Gray
Matthew Humphries
Neil Sycamore
Darren Barker
David Saunders
Justene Wallis
Anne Babbage
Sian Hammond
Maryam Mashreghi-Mohammadi
Lucy Barr
Sancha Martin
Paul Wray
Andrew Ellington
Nicholas Matthews
Matthew Ellwood
Rebecca Woodmansey
Graham Clark
James Cooper
Anthony Tromans
Darren Grafham
Carl Skuce
Richard Pandian
Robert Andrews
Elliot Harrison
Andrew Kimberley
Jane Garnett
Nigel Fosker
Rebekah Hall
Patrick Garner
Daniel Kelly
Christine Bird
Sophie Palmer
Ines Gehring
Andrea Berger
Christopher M Dooley
Zübeyde Ersan-Ürün
Cigdem Eser
Horst Geiger
Maria Geisler
Lena Karotki
Anette Kirn
Judith Konantz
Martina Konantz
Martina Oberländer
Silke Rudolph-Geiger
Mathias Teucke
Kazutoyo Osoegawa
Baoli Zhu
Amanda Rapp
Sara Widaa
Cordelia Langford
Fengtang Yang
Nigel P Carter
Jennifer Harrow
Zemin Ning
Javier Herrero
Steve M J Searle
Anton Enright
Robert Geisler
Ronald H A Plasterk
Charles Lee, The Jackson LaboratoryFollow
Monte Westerfield
Pieter J de Jong
Leonard I Zon
John H Postlethwait
Christiane Nüsslein-Volhard
Tim J P Hubbard
Hugues Roest Crollius
Jane Rogers
Derek L Stemple

Document Type

Article

Publication Date

4-25-2013

Keywords

Animals, Chromosomes, Conserved Sequence, Evolution, Molecular, Female, Genes, Genome, Genome, Human, Genomics, Humans, Male, Meiosis, Molecular Sequence Annotation, Pseudogenes, Reference Standards, Sex Determination Processes, Zebrafish, Zebrafish Proteins

JAX Source

Nature 2013 Apr 25; 496(7446):498-503.

PMID

23594743

Abstract

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination. Nature 2013 Apr 25; 496(7446):498-503.