ABSTRACT
Networks of co-expressed genes produce complex phenotypes that are associated with sexual dimorphism, tissue-specificity, and functional novelty. Modules of potentially co-regulated genes can be compared across individuals to identify differences associated with phenotypic divergence. Here we use RNA-sequencing in the paleopolyploid salmonid Brook Charr Salvelinus fontinalis to characterize sex-specific co-expression networks within the liver of 100 full-sib offspring. Module conservation in each sex-specific network was tested in the alternate sex and in the congener Arctic Charr Salvelinus alpinus. Modules were further characterized by functional and chromosomal enrichment, hub gene identification, and correlation with 15 unique growth, reproductive and stress-related phenotypes. The majority of modules were conserved between sexes and species, including those involved in conserved cellular processes (e.g. translation, immune pathways). The few identified sex-specific modules may contribute to sexual dimorphism and resolution of sexual antagonism through gene regulation, including male-specific modules correlated with fish size or enriched for transcription factor activity. Most modules, including sex-specific modules, contained genes randomly dispersed throughout the genome, although several were overrepresented on specific chromosomes, suggesting an infrequent, but existing, chromosomal-based co-regulation. This comprehensive analysis provides network and chromosomal context to give insight into the transcriptome regulatory architecture of the paleopolyploid salmonids.