Data and analysis for: A Comprehensive Analysis of Atlantic Salmon Gonad and Pituitary Transcriptomes Identifies Novel Players in Sexual Maturation

Understanding the mechanisms that drive variation in sexual maturation is crucial for advancing reproductive biology and elucidating how life history traits are encoded in the genome. In this study, we used Atlantic salmon (Salmo salar) as a model to investigate transcriptional changes in reproductive tissues—specifically the gonads and pituitary during sexual maturation. We analyzed samples from two age cohorts of Atlantic salmon reared under common garden hatchery conditions with natural photoperiods and temperature regimes. RNA sequencing was performed on polyadenylated RNA extracted from eight pituitary samples of 4-year-old immature males, and 90 gonadal samples from 1-year-old individuals, including immature ovaries, immature testis, and mature testis. Our systematic transcriptome analysis included the identification of novel putative protein-coding genes and long intergenic non-coding RNAs (lincRNAs) from intergenic regions. By integrating differential gene expression, tissue-specificity profiling, and gene co-expression network analysis, we uncovered key regulatory pathways and candidate functional lncRNAs associated with sexual maturation.