Evolution and expression of the immune system of a facultatively anadromous salmonid

Vertebrates have evolved a complex immune system required for the identification of and coordinated response to harmful pathogens. For migratory species that spend periods of their life-cycle in more than one environment, a comprehensive immune gene repertoire is required to deal with a greater diversity of pathogenic challenges present across multiple environments. In facultatively anadromous salmonids, individuals may spend parts of their life-cycle in freshwater and marine environments. For species, such as the brown trout Salmo trutta, sexes differ in their life-histories with females more likely to migrate to sea while males stay and complete their life-cycle in their natal river. Salmonids have also undergone a lineage-specific whole genome duplication event, which may provide novel immune innovations but at present, our understanding of the salmonid immune gene repertoire, and how it is expressed, especially between the sexes, is limited. We characterized the brown trout immune gene repertoire, identifying a number of canonical immune genes in the zebrafish to be duplicated in S. trutta, with genes involved in innate and adaptive immunity. Through genome-wide transcriptional profiling (RNA-Seq) of male and female livers to investigate sex differences in gene expression amplitude and alternative splicing, we dentified immune genes as being generally male-biased in expression. Our study provides an important insight into the evolutionary consequences of whole genome duplication events on the salmonid immune gene repertoire, recent processes shaping their evolutionary history and how the sexes differ in constitutive immune expression.