title: The salmonid MHC class I: more ancient loci uncovered.
abstract: An unprecedented level of sequence diversity has been maintained in the salmonid major histocompatibility complex (MHC) class I UBA gene, with between lineage AA sequence identities as low as 34%. The derivation of deep allelic lineages may have occurred through interlocus exon shuffling or convergence of ancient loci with the UBA locus, but until recently, no such ancient loci were uncovered. Herein, we document the existence of eight additional MHC class I loci in salmon (UCA, UDA, UEA, UFA, UGA, UHA, ULA, and ZE), six of which share exon 2 and 3 lineages with UBA, and three of which have not been described elsewhere. Half of the UBA exon 2 lineages and all UBA exon 3 lineages are shared with other loci. Two loci, UGA and UEA, share only a single exon lineage with UBA, likely generated through exon shuffling. Based on sequence homologies, we hypothesize that most exchanges and duplications occurred before or during tetraploidization (50 to 100 Ma). Novel loci that share no relationship with other salmonid loci are also identified (UHA and ZE). Each locus is evaluated for its potential to function as a class Ia gene based on gene expression, conserved residues and polymorphism. UBA is the only locus that can indisputably be classified as a class Ia gene, although three of the eight loci (ZE, UCA, and ULA) conform in three out of four measures. We hypothesize that these additional loci are in varying states of degradation to class Ib genes.
authors.affiliation: Pacific Biological Station, Fisheries and Oceans, Canada, 3190 Hammond Bay Rd., Nanaimo, B.C. V9T 6N7, Canada. Millerk@pac.dfo-mpo.gc.ca
authors.forename: Kristina M
authors.initials: KM
authors.lastname: Miller
authors.forename: Shaorong
authors.initials: S
authors.lastname: Li
authors.forename: Tobi J
authors.initials: TJ
authors.lastname: Ming
authors.forename: Karia H
authors.initials: KH
authors.lastname: Kaukinen
authors.forename: Angela D
authors.initials: AD
authors.lastname: Schulze
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D018388:Codon, Terminator / Q000235:genetics; D005091:Exons; D020440:Gene Duplication; D015870:Gene Expression; D008040:Genetic Linkage; D005838:Genotype; D015395:Histocompatibility Antigens Class I / Q000145:classification* / Q000235:genetics*; D006720:Homozygote; D008969:Molecular Sequence Data; D017686:Oncorhynchus mykiss / Q000235:genetics / Q000276:immunology*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D020317:Salmo salar / Q000235:genetics / Q000276:immunology*; D012487:Salmonidae / Q000235:genetics / Q000276:immunology; D012641:Selection, Genetic
chemical_list: D018388:Codon, Terminator; D015395:Histocompatibility Antigens Class I