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.

脊椎动物演化出复杂的免疫系统，用以识别有害病原体并启动协同防御应答。对于生命周期需跨越多种环境的洄游物种而言，需具备全面的免疫基因库，以应对跨多个环境的多样病原挑战。兼性溯河产卵的鲑科鱼类，其个体可在生命周期中同时经历淡水与海洋环境。以褐鳟（Salmo trutta）为例，该物种存在性别特异性生活史：雌性更倾向于洄游至海洋，而雄性则留守出生河流完成整个生命周期。鲑科鱼类还经历了谱系特异性的全基因组复制（whole genome duplication）事件，这可能为其带来全新的免疫创新，但目前学界对鲑科免疫基因库及其表达模式，尤其是性别间的表达差异，仍了解有限。本研究对褐鳟的免疫基因库进行了系统表征，鉴定出斑马鱼中的多个经典免疫基因在褐鳟中发生了复制，这些基因涉及先天免疫与适应性免疫通路。通过对雌雄褐鳟肝脏开展全基因组转录组分析（RNA测序（RNA-Seq）），以探究基因表达幅度与可变剪接的性别差异，我们鉴定发现免疫基因整体呈现雄性偏向性表达。本研究为理解全基因组复制事件对鲑科免疫基因库的演化影响、塑造其演化历史的近期进程，以及性别间组成型免疫表达的差异提供了重要见解。