Multi-tissue transcriptome profiling of North American derived Atlantic salmon

The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing is enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analysed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from brain, pituitary, ovary and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors present in each tissue-specific gene cluster were identified. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation. The goal of this study is to catalogue gene expression in multiple tissues in Atlantic salmon. Key tissues important for understanding salmon biology and important traits related to their aquaculture industry were chosen namely; brain, pituitary gland, ovary and liver. RNA was isolated and 16 RNA-Seq libraries (4 tissues x 4 replicates) were sequenced on Illumina Nova-Seq sequencing platform. Samples were analysed to infer differential gene expression. Hierarchical clustering of those differentially expressed genes (DEGs) were performed and tissue-specific gene clusters were extracted and analysed for functional categories using the Gene Ontology database.