Sequence analysis of MHC class I α2 from sockeye salmon (Oncorhynchus nerka)

Most studies assessing adaptive MHC diversity in salmon populations have focused on the classical class II DAB or DAA loci, as these have been most amenable to single PCR amplifications due to their relatively low level of sequence divergence. Herein, we report the characterization of the classical class I UBA α2 locus based on collections taken throughout the species range of sockeye salmon (Oncorhynchus nerka). Through use of multiple lineage-specific primer sets, denaturing gradient gel electrophoresis and sequencing, we identified thirty-four alleles from three highly divergent lineages. Sequence identity between lineages ranged from 30.0% to 56.8% but was relatively high within lineages. Allelic identity within the antigen recognition site (ARS) was greater than for the longer sequence. Global positive selection on UBA was seen at the sequence level (dN:dS = 1.012) with four codons under positive selection and 12 codons under negative selection.

► We sequence MHC class I UBA-α2 alleles sampled throughout the species range of sockeye salmon.
► Thirty-four unique alleles from three divergent lineages were identified.
► Positive selection was found at the sequence level across the locus.
► Four codons show evidence of positive selection and 12 of negative selection.