The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Katrina M. Morris,
Matthew M. Hindle,
Simon Boitard,
David W. Burt,
Angela F. Danner,
Lel Eory,
Heather L. Forrest,
David Gourichon,
Jerome Gros,
LaDeana W. Hillier,
Thierry Jaffredo,
Hanane Khoury,
Rusty Lansford,
Christine Leterrier,
Andrew Loudon,
Andrew S. Mason,
Simone L. Meddle,
Francis Minvielle,
Patrick Minx,
Frédérique Pitel,
J. Patrick Seiler,
Tsuyoshi Shimmura,
Chad Tomlinson,
Alain Vignal,
Robert G. Webster,
Takashi Yoshimura,
Wesley C. Warren,
Jacqueline Smith
Affiliations
Katrina M. Morris
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush
Matthew M. Hindle
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush
Simon Boitard
GenPhySE, Université de Toulouse
David W. Burt
The John Hay Building, Queensland Biosciences Precinct, 306 Carmody Road, The University of Queensland
Angela F. Danner
Virology Division, Department of Infectious Diseases, St. Jude Children’s Research Hospital
Lel Eory
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush
Heather L. Forrest
Virology Division, Department of Infectious Diseases, St. Jude Children’s Research Hospital
David Gourichon
PEAT Pôle d’Expérimentation Avicole de Tours, Centre de recherche Val de Loire, INRAE
Jerome Gros
Department of Developmental and Stem Cell Biology, Institut Pasteur
LaDeana W. Hillier
McDonnell Genome Institute, Washington University School of Medicine
Thierry Jaffredo
CNRS UMR7622, Inserm U 1156, Laboratoire de Biologie du Développement, Sorbonne Université, IBPS
Hanane Khoury
CNRS UMR7622, Inserm U 1156, Laboratoire de Biologie du Développement, Sorbonne Université, IBPS
Rusty Lansford
Department of Radiology and Developmental Neuroscience Program, Saban Research Institute, Children’s Hospital Los Angeles and Keck School of Medicine of the University of Southern California
Christine Leterrier
UMR85 Physiologie de la Reproduction et des Comportements, INRAE, CNRS, Université François Rabelais, IFCE, INRAE
Andrew Loudon
Centre for Biological Timing, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester
Andrew S. Mason
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush
Simone L. Meddle
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush
Abstract Background The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. Results We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1. Conclusions We have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species.
