Comparative analysis of salmonid non-classical MHC class I L lineage genes

Non-classical MHC class I molecules, which are encoded by a diverse gene family, have a wide range of functions that can be immune- or non-immune related. From an evolutionary perspective, different non-classical MHC class I genes are typically specific to smaller phylogenetic groups and are often not well conserved among species within these groups rendering non-classical MHC phylogeny difficult to establish. Here we perform a comparative analysis spanning non-classical MHC class I L lineage gene content, organization, phylogeny and variability across divergent salmonid species, providing insight into L lineage immune system variation and species-specific adaptations. Based on evolutionary relationships and sequence analysis, salmonid L lineage genes can be classified into three clades, each with distinct features. Clade I gene sequences exhibit significant variation within species, comprising multiple haplotypes and null alleles, as well as notable variations between species, including highly flexible gene numbers and patterns of pseudogenization. Clade I genes comprise eleven subclades, each displaying separate evolutionary patterns, characteristic phylogenetic marker motifs and subclade specific promoter regions, indicative of unique regulatory patterns and subclade specific functional roles. Our study reveals two distinct phylogenetic patterns among these genes: some subclades display a high degree of flexibility, as demonstrated by species specific expansions and contractions, whereas others have been maintained as monogenic subfamilies with remarkably few changes in their nucleotide sequence across divergent species. Comparably, clade II L lineage genes consist of four subclades, among which LIA and LLA genes are full length genes with species specific pseudogenization patterns. We report compelling evidence that the LIA gene lineage is highly conserved and present in all 23 Salmonidae species examined as well as in representative Esociformes. This suggests that genes belonging to the LIA subclade have a conserved and likely biologically important role. This is in stark contrast to clade III genes, consisting of LAA1 and LAA2 gene sequences, which have been rendered non-functional in most species.