The characterization of Lactate Dehydrogenase genes in rainbow smelt (Osmerus mordax)

Lactate Dehydrogenase isozymes (LDH-A, LDH-B and LDH-C) represent the classical example of a multi-gene system derived by successive gene duplications. By investigating the genes encoding the LDH isozymes in rainbow smelt, a diploid out-group of the tetraploid salmonids, I sought to gain insight into the effect of a whole genome duplication superimposed upon more ancient gene duplications. I isolated rainbow smelt BAC clones containing the LDH-A, LDH-B and LDH-C genes, made shotgun libraries of three representative BACs and annotated the sequences. I characterized the smelt LDH genes with respect to structure, tissue expression and genome organization. This information was used for comparative genomic analyses with the LDH genes from Atlantic salmon. There was no evidence for positive selection, an expectation of neo-functionalization, but different rates of amino acid substitutions between and within lineages were evident in the LDH-A and LDH-B salmonid duplicates. LDH-B1 and LDH-B2 in salmonids have experienced sub-functionalization.