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.
Highlights
Sheep (Ovis aries) represent an important livestock species globally and are a key source of animal products including meat, milk and fibre
Scope of the sheep gene expression atlas dataset. This sheep gene expression atlas dataset expands on the RNA-Seq datasets already available for sheep, merging a new set of 441 RNA-Seq libraries from the Texel x Scottish Blackface (TxBF) with 83 existing libraries from Texel [18]
The diversity of samples included in the sheep transcriptional atlas is the greatest from any mammalian species, including humans
Summary
Sheep (Ovis aries) represent an important livestock species globally and are a key source of animal products including meat, milk and fibre. They remain an essential part of the rural economy in many developed countries and are central to sustainable agriculture in developing countries. A better understanding of functional sequences, including transcribed sequences and the transcriptional control of complex traits such as disease resilience, reproductive capacity and feed conversion efficiency will enable further improvements in productivity with concomitant reductions in environmental impact. RNA-Sequencing (RNA-Seq) has transformed the analysis of gene expression from the single-gene to the genome-wide scale allowing visualisation of the transcriptome and re-defining how we view the transcriptional control of complex traits (reviewed in [5]). Large-scale gene expression atlas projects have defined the mammalian transcriptome in multiple species, initially using microarrays [6,7,8,9] and more recently by the sequencing of full length transcripts or of 5’ ends, for example in the horse [10], and in human and mouse by the FANTOM 5 Consortium [11,12,13], ENCODE project [14] and Genotype-Tissue Expression (GTEx) Consortium [15]
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