Functional Annotation of the Sheep (Ovis aries) Genome

Sheep are an important source of meat, milk and fibre globally. To support functional annotation of the sheep genome we have produced a high-resolution atlas of gene expression from a comprehensive set of tissues and cell types from Scottish Blackface x Texel crossbred individuals. RNA-Seq libraries were generated by Edinburgh Genomics from tissues and cells representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The dataset includes 352 medium depth mRNA-Seq libraries and 74 high depth total RNA-Seq libraries. The raw reads have been mapped using two pipelines, an alignment free method, Kallisto, and a conventional alignment based HiSat2-Stringtie pipeline. Of the protein coding genes currently annotated by Ensembl in the Oar_v3.1 reference genome, 96% are captured in the sheep atlas dataset. We have assigned gene names to hundreds of previously unannotated genes and are visualising the data as gene-gene network graphs in Miru (http://kajeka.com) to assign putative function to many of these genes. The sample metadata have been loaded into BioSamples and the sequence data are being deposited in the ENA. We intend to make the data available via the BioGPS gene annotation portal (http://biogps.org) in which the pattern of expression for each gene can be visualized across a range of tissues. The Sheep Gene Expression Atlas has the potential to inform future improvements in productivity, efficiency and health in sheep and other ruminants and is a valuable resource for the international Functional Annotation of Animal Genomes (FAANG) initiative.