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A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

View ORCID ProfileEL Clark, View ORCID ProfileSJ Bush, MEB McCulloch, IL Farquhar, R Young, View ORCID ProfileL Lefevre, View ORCID ProfileC Pridans, View ORCID ProfileHG Tsang, C Wu, C Afrasiabi, View ORCID ProfileM Watson, View ORCID ProfileCB Whitelaw, View ORCID ProfileTC Freeman, View ORCID ProfileKM Summers, View ORCID ProfileAL Archibald, View ORCID ProfileDA Hume
doi: https://doi.org/10.1101/132696
EL Clark
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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  • For correspondence: emily.clark@roslin.ed.ac.uk
SJ Bush
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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MEB McCulloch
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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IL Farquhar
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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R Young
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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L Lefevre
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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C Pridans
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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HG Tsang
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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C Wu
2Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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C Afrasiabi
2Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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M Watson
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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CB Whitelaw
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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TC Freeman
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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KM Summers
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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AL Archibald
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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DA Hume
1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG
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Abstract

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.

Author Summary Sheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as disease resiliance. The sheep genome is however missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If for example a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.

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Posted June 08, 2017.
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A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
EL Clark, SJ Bush, MEB McCulloch, IL Farquhar, R Young, L Lefevre, C Pridans, HG Tsang, C Wu, C Afrasiabi, M Watson, CB Whitelaw, TC Freeman, KM Summers, AL Archibald, DA Hume
bioRxiv 132696; doi: https://doi.org/10.1101/132696
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A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
EL Clark, SJ Bush, MEB McCulloch, IL Farquhar, R Young, L Lefevre, C Pridans, HG Tsang, C Wu, C Afrasiabi, M Watson, CB Whitelaw, TC Freeman, KM Summers, AL Archibald, DA Hume
bioRxiv 132696; doi: https://doi.org/10.1101/132696

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