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

doi:10.1186/s12915-020-0743-4

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 PitelJ Patrick Seiler, Tsuyoshi Shimmura, Chad Tomlinson, Alain Vignal, Robert G Webster, Takashi Yoshimura, Wesley C Warren, Jacqueline Smith

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	(2020) 18:14
Number of pages	18
Journal	BMC Biology
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s12915-020-0743-4
Publication status	Published - 12 Feb 2020

Keywords

Coturnix japonica
Quail
Genome
Influenza
Seasonality
Photoperiod
Bird flu
H5N1

Access to Document

10.1186/s12915-020-0743-4

The quail genome
© The Author(s). 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Final published version, 2.85 MBLicence: Creative Commons: Attribution (CC-BY)

1 Finished
1 Active

ISP 3 2017/22 Improving Animal Health and Welfare
Meddle, S.
BBSRC
1/04/17 → 31/03/22
Project: Research
Unravelling the networks that regulate seasonal rhythmicity in the epigenome
Meddle, S.
BBSRC
2/07/16 → 31/03/20
Project: Research

Jacqueline Smith
- Jacqueline.smith@roslin.ed.ac.uk
- Royal (Dick) School of Veterinary Studies - Group Leader
- Global Academy of Agriculture and Food Security
Person: Academic: Research Active (Research Assistant)

Cite this

Morris, K. M., Hindle, M. M., Boitard, S., Burt, D. W., Danner, A. F., Eory, L., Forrest, H. L., Gourichon, D., Gros, J., Hillier, L. W., Jaffredo, T., Khoury, H., Lansford, R., Leterrier, C., Loudon, A., Mason, A. S., Meddle, S. L., Minvielle, F., Minx, P., ... Smith, J. (2020). The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC Biology, 18(1), [(2020) 18:14]. https://doi.org/10.1186/s12915-020-0743-4

Morris, Katrina M ; Hindle, Matthew M ; Boitard, Simon ; Burt, David W ; Danner, Angela F ; Eory, Lel ; Forrest, Heather L ; Gourichon, David ; Gros, Jerome ; Hillier, LaDeana W ; Jaffredo, Thierry ; Khoury, Hanane ; Lansford, Rusty ; Leterrier, Christine ; Loudon, Andrew ; Mason, Andrew S ; Meddle, Simone L ; Minvielle, Francis ; Minx, Patrick ; Pitel, Frédérique ; Seiler, J Patrick ; Shimmura, Tsuyoshi ; Tomlinson, Chad ; Vignal, Alain ; Webster, Robert G ; Yoshimura, Takashi ; Warren, Wesley C ; Smith, Jacqueline. / The quail genome : insights into social behaviour, seasonal biology and infectious disease response. In: BMC Biology. 2020 ; Vol. 18, No. 1.

@article{869aa338278d44eaaabcba199c118b07,

title = "The quail genome: insights into social behaviour, seasonal biology and infectious disease response",

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.",

keywords = "Coturnix japonica, Quail, Genome, Influenza, Seasonality, Photoperiod, Bird flu, H5N1",

author = "Morris, {Katrina M} and Hindle, {Matthew M} and Simon Boitard and Burt, {David W} and Danner, {Angela F} and Lel Eory and Forrest, {Heather L} and David Gourichon and Jerome Gros and Hillier, {LaDeana W} and Thierry Jaffredo and Hanane Khoury and Rusty Lansford and Christine Leterrier and Andrew Loudon and Mason, {Andrew S} and Meddle, {Simone L} and Francis Minvielle and Patrick Minx and Fr{\'e}d{\'e}rique Pitel and Seiler, {J Patrick} and Tsuyoshi Shimmura and Chad Tomlinson and Alain Vignal and Webster, {Robert G} and Takashi Yoshimura and Warren, {Wesley C} and Jacqueline Smith",

year = "2020",

month = feb,

day = "12",

doi = "10.1186/s12915-020-0743-4",

language = "English",

volume = "18",

journal = "BMC Biology",

issn = "1741-7007",

publisher = "BioMed Central",

number = "1",

}

Morris, KM , Hindle, MM, Boitard, S, Burt, DW, Danner, AF, Eory, L, Forrest, HL, Gourichon, D, Gros, J, Hillier, LW, Jaffredo, T, Khoury, H, Lansford, R, Leterrier, C, Loudon, A, Mason, AS, Meddle, SL, Minvielle, F, Minx, P, Pitel, F, Seiler, JP, Shimmura, T, Tomlinson, C, Vignal, A, Webster, RG, Yoshimura, T, Warren, WC & Smith, J 2020, 'The quail genome: insights into social behaviour, seasonal biology and infectious disease response', BMC Biology, vol. 18, no. 1, (2020) 18:14. https://doi.org/10.1186/s12915-020-0743-4

The quail genome : insights into social behaviour, seasonal biology and infectious disease response. / Morris, Katrina M ; Hindle, Matthew M; Boitard, Simon; Burt, David W; Danner, Angela F; Eory, Lel; Forrest, Heather L; Gourichon, David; Gros, Jerome; Hillier, LaDeana W; Jaffredo, Thierry; Khoury, Hanane; Lansford, Rusty; Leterrier, Christine; Loudon, Andrew; Mason, Andrew S; Meddle, Simone L; Minvielle, Francis; Minx, Patrick; Pitel, Frédérique; Seiler, J Patrick; Shimmura, Tsuyoshi; Tomlinson, Chad; Vignal, Alain; Webster, Robert G; Yoshimura, Takashi; Warren, Wesley C; Smith, Jacqueline.

In: BMC Biology, Vol. 18, No. 1, (2020) 18:14, 12.02.2020.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - The quail genome

T2 - insights into social behaviour, seasonal biology and infectious disease response

AU - Morris, Katrina M

AU - Hindle, Matthew M

AU - Boitard, Simon

AU - Burt, David W

AU - Danner, Angela F

AU - Eory, Lel

AU - Forrest, Heather L

AU - Gourichon, David

AU - Gros, Jerome

AU - Hillier, LaDeana W

AU - Jaffredo, Thierry

AU - Khoury, Hanane

AU - Lansford, Rusty

AU - Leterrier, Christine

AU - Loudon, Andrew

AU - Mason, Andrew S

AU - Meddle, Simone L

AU - Minvielle, Francis

AU - Minx, Patrick

AU - Pitel, Frédérique

AU - Seiler, J Patrick

AU - Shimmura, Tsuyoshi

AU - Tomlinson, Chad

AU - Vignal, Alain

AU - Webster, Robert G

AU - Yoshimura, Takashi

AU - Warren, Wesley C

AU - Smith, Jacqueline

PY - 2020/2/12

Y1 - 2020/2/12

N2 - 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.

AB - 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.

KW - Coturnix japonica

KW - Quail

KW - Genome

KW - Influenza

KW - Seasonality

KW - Photoperiod

KW - Bird flu

KW - H5N1

U2 - 10.1186/s12915-020-0743-4

DO - 10.1186/s12915-020-0743-4

M3 - Article

C2 - 32050986

VL - 18

JO - BMC Biology

JF - BMC Biology

SN - 1741-7007

IS - 1

M1 - (2020) 18:14

ER -

The quail genome: insights into social behaviour, seasonal biology and infectious disease response

Abstract

Keywords

Access to Document

Fingerprint

Projects

ISP 3 2017/22 Improving Animal Health and Welfare

Unravelling the networks that regulate seasonal rhythmicity in the epigenome

Profiles

Jacqueline Smith

Cite this