Abstract
BackgroundSalmonids are of major importance both as farmed and wild animals. With the changing environment comes changes in pathogenic pressures so understanding the immune system of all salmonid species is of essence. Major histocompatibility complex (MHC) genes are key players in the adaptive immune system signalling infection to responding T-cells populations. Classical MHC class I (MHCI) genes, defined by high polymorphism, broad expression patterns and peptide binding ability, have a key role in inducing immunity. In salmonids, the fourth whole genome duplication that occurred 94 million years ago has provided salmonids with duplicate MHCI regions, while Northern Pike, a basal sister clade to salmonids, represent a species which has not experienced this whole genome duplication.ResultsComparing the gene organization and evolution of MHC class I gene sequences in Northern pike versus salmonids displays a complex picture of how many of these genes evolved. Regional salmonid Ia and Ib Z lineage gene duplicates are not orthologs to the Northern pike Z lineage sequences. Instead, salmonids have experienced unique gene duplications in both duplicate regions as well as in the Salmo and Oncorhynchus branch. Species-specific gene duplications are even more pronounced for some L lineage genes.ConclusionsAlthough both Northern pike as well as salmonids have expanded their U and Z lineage genes, these gene duplications occurred separately in pike and in salmonids. However, the similarity between these duplications suggest the transposable machinery was present in a common ancestor. The salmonid MHCIa and MHCIb regions were formed during the 94 MYA since the split from pike and before the Oncorhynchus and Salmo branch separated. As seen in tetrapods, the non-classical U lineage genes are diversified duplicates of their classical counterpart. One MHCI lineage, the L lineage, experienced massive species-specific gene duplications after Oncorhynchus and Salmo split approximately 25 MYA. Based on what we currently know about L lineage genes, this large variation in number of L lineage genes also signals a large functional diversity in salmonids.
Highlights
Salmonids are of major importance both as farmed and wild animals
The results presented below are based on the NCBI genomes of the salmonids Atlantic salmon, brown trout, rainbow trout, sockeye salmon, coho salmon, chinook salmon and charr
To understand the evolution of genes, the salmonid data are compared against results from the Northern pike genome, a species that is basal to salmonids, but lacks the Unique salmonid fourth whole genome duplication (4WGD) [20] (Fig. 1)
Summary
Salmonids are of major importance both as farmed and wild animals. Major histocompatibility complex (MHC) genes are key players in the adaptive immune system signalling infection to responding T-cells populations. Classical MHC class I (MHCI) genes, defined by high polymorphism, broad expression patterns and peptide binding ability, have a key role in inducing immunity. Salmonids comprise many species that are of major importance both as farmed and wild animals on many continents. Major histocompatibility complex (MHC) molecules are involved in protection against invading pathogens. Classical MHCI molecules are defined by their polymorphic content, their expression in most tissues and their ability to bind and present peptides to CD8+ T-cells. Non-classical MHCI molecules have more restricted expression patterns, lower levels of polymorphism and most have non-peptide ligands
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