Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds

Nature Communications
Marina Naval-SanchezJames Kijas

Abstract

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.

References

Sep 28, 2002·Nature·Helena Santos-RosaTony Kouzarides
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Dec 31, 2005·Nucleic Acids Research·A S HinrichsW J Kent
Jan 19, 2006·Nature Reviews. Genetics·J V ChamaryLaurence D Hurst
Feb 7, 2006·Trends in Genetics : TIG·Melinda A ZederDaniel G Bradley
Nov 7, 2006·Nature·Len A PennacchioEdward M Rubin
Dec 30, 2006·Genetics·Jennifer R S MeadowsJames W Kijas
Feb 17, 2007·Nature Reviews. Genetics·Gregory A Wray
May 12, 2007·Evolution; International Journal of Organic Evolution·Hopi E Hoekstra, Jerry A Coyne
Oct 24, 2007·Nature Genetics·Patrick SulemKari Stefansson
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Apr 25, 2009·Science·Bernardo ChessaMassimo Palmarini
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jan 1, 2010·BMC Genetics·Jonas Mengel-FromIan J Jackson
May 4, 2010·Nature Biotechnology·Cory Y McLeanGill Bejerano
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Feb 22, 2012·PLoS Biology·James W KijasUNKNOWN International Sheep Genomics Consortium Members
Mar 3, 2012·PloS One·Martin G ElferinkMartien A M Groenen
Apr 10, 2012·Animal Reproduction Science·F J McPherson, P J Chenoweth
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Genome Research·Marc A SchaubMichael Snyder
Nov 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Carl-Johan RubinLeif Andersson
Nov 16, 2012·Nature·Martien A M GroenenLawrence B Schook
Mar 30, 2013·Genome Research·Hunter B Fraser
Apr 16, 2013·Seminars in Cell & Developmental Biology·Monika Reissmann, Arne Ludwig
May 3, 2013·PLoS Genetics·Samantha WilkinsonPamela Wiener
Jun 14, 2013·BMC Genomics·Holly R RameyJeremy F Taylor
Dec 21, 2013·Reproduction : the Official Journal of the Society for the Study of Fertility·H M BrownR J Scaramuzzi
Mar 5, 2014·Nature Reviews. Genetics·Diego VillarDuncan T Odom
Apr 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Linus Girdland FlinkGreger Larson
Apr 24, 2014·Proceedings of the National Academy of Sciences of the United States of America·Greger LarsonDorian Q Fuller

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Citations

Mar 8, 2018·Nature Communications·Florian J AlbertoFrançois Pompanon
Oct 30, 2019·Journal, Genetic Engineering & Biotechnology·Mohammed Baqur S Al-ShuhaibThamer R S Aljubouri
Feb 6, 2020·Frontiers in Genetics·Saber Qanbari
Jan 9, 2019·Frontiers in Genetics·Martin Johnsson
Jun 26, 2020·Cell Research·Ming-Shan WangYa-Ping Zhang
Oct 13, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Chunlin LiFangyin Dai
Nov 8, 2020·Molecular Genetics and Genomics : MGG·Anna LetkoSandra Scholes
Jan 25, 2021·Science China. Life Sciences·Yongzhen HuangYu Jiang
Jan 26, 2021·Frontiers in Genetics·Alisha T MassaStephen N White
May 1, 2021·Animals : an Open Access Journal From MDPI·Michael N RomanovDarren K Griffin
Jun 8, 2021·Frontiers in Genetics·Kimberly M DavenportUNKNOWN Ovine FAANG Project Consortium
Sep 8, 2021·Frontiers in Genetics·Zhong-Huang WangMeng-Hua Li
Sep 23, 2021·Genome Biology·Pâmela A AlexandreAntonio Reverter
Jan 6, 2022·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Alberto CesaraniNicolò P P Macciotta

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Datasets Mentioned

BETA
PRJEB14685
PRJEB3139
ERP001583

Methods Mentioned

BETA
ChIP-Seq
PCA
immunoprecipitation
chip

Software Mentioned

RoadMap
VCFtools
SAMTOOLS
BWA aligner
Bioconductor package
Epigenome Roadmap
ensembl
liftOver
PLINK
CLCBIO

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