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

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.

A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

“…in (Clark et al, 2017). Briefly, for each tissue a set of expression estimates, as transcripts per 177 million (TPM), were obtained using the alignment-free (technically, 'pseudo-aligning') 178…”

“…annotation genebuild pipeline used to assign gene names and symbols is conservative. Using 307 the annotation pipeline we described in (Clark et al, 2017) we were able to use the goat mini-308 atlas dataset to assign an informative gene name to 1114 previously un-annotated protein 309…”

“…These 334 functional classes were assigned based on GO term enrichment (Alexa and Rahnenfuhrer, 335 2010) for molecular function and biological process ( Supplementary Table S12). Assignment 336 of functional class was further validated by visual inspection of expression pattern and 337 comparison with functional groupings of genes observed in the sheep gene expression atlas 338 (Clark et al, 2017). 339…”

“…bacterial, parasitic and prion pathogens, including multiple potential zoonoses (Sherman,110 2011), but there have been few comparisons of relative susceptibility or pathology between 111 the species to the same pathogen, nor the nature of innate immunity. To reveal transcriptional 112 similarities and differences between sheep and goats we have performed a comparative 113 analysis of species-specific gene expression by comparing the goat mini-atlas dataset with a 114 comparable subset of data from the sheep gene expression atlas (Clark et al, 2017). We also 115 use the goat mini-atlas dataset to examine the expression of candidate genes associated with 116 functional traits in goats and link these with allele-specific expression (ASE) profiles across 117 tissues, using a robust methodology for ASE profiling .…”

“…To measure allele-specific expression (ASE), across tissues and cell-types from the 256 goat mini-atlas we used the method described in . Briefly, BAM files 257 from the RNA-Seq data, were mapped to the ARS1 top level DNA fasta track from Ensembl 258 v96, using HISAT2 as described in (Clark et al, 2017). Any reference mapping bias was 259 removed using WASP v0.3.1 (van de Geijn et al, 2015) and the resultant BAM files 260 processed using the Genome Analysis Tool Kit (GATK) to produce individual VCF files.…”