Multitissue transcriptome profiling during onset of salmon maturation v1

Despite the importance of sexual maturation as a trait of interest it can be difficult to study, as the timing of onset varies widely in response to both genetics and environmental factors and occurs prior to measurable phenotypic change. To overcome this, we chose to investigate sexual maturation in Atlantic salmon where photoperiod manipulation in an experimental system can be used to synchronise animals and access tissues across the time period when animals first commit to the onset of puberty. We describe changes in genome-wide gene expression in pituitary gland, ovary and liver to identify transcriptional landscapes associated with maturation in salmon. We sequenced mRNA from four biological replicates of each tissue before (T1) and after the onset of maturation (T2, T3, T4). A total of 3.2 billion paired-end reads were mapped against the Atlantic salmon reference genome with 72% mapping efficiency to create an average depth of 50 million reads per library. The number of differentially expressed genes (DEGs) increased with elapsed time following the onset of the long light photoperiod for the two BPG axis tissues (pituitary and ovary). Of these, the ovary underwent the most dramatic remodelling over time with 403, 1709 and then 3497 DEGs observed at timepoints T2, T3 and T4 respectively. This increasing trajectory of differential ngene expression, coupled with the elevated GSI following the light stimuli, strongly suggests the experimental approach successfully initiated the onset of maturation. Next, we identified clusters of DEGs in each of the analysed tissues, which describe their physiological roles. The identity of the DEGs, in response to the onset of maturation, revealed the key players involved in the earliest triggers into maturation. Among these, upregulation of genes encoding specififc pituitary hormones such as gonadotropins along with genes encoding transcription factors (such as GATA2) are significant in controlling onset of maturation. To characterize the transcriptomic remodelling occurring in the ovary and liver, we assessed the DEG sets for GO enrichment. Upregulated genes in the ovary revealed processes related tocell adhesion, immune/inflammatory responseanddevelopment, while gene families involved inorganic acid metabolic processesandmitochondrial transportwere enriched among liver upregulated genes. This multitissue transcriptome paper provides novel insights into the transcriptional signature associated with onset of salmon maturation and is the basis of subsequent epigenetic studies aimed at understanding epigenetic mechanisms underlying maturation.