Abstract
Passerine birds belong to the most species rich bird order and are found in a wide range of habitats. The extremely polymorphic adaptive immune system of passerines, identified through their major histocompatibility complex class I genes (MHC-I), may explain some of this extreme radiation. Recent work has shown that passerines have higher numbers of MHC-I gene copies than other birds, but little is currently known about expression and function of these gene copies. Non-passerine birds have a single highly expressed MHC-I gene copy, a pattern that seems unlikely in passerines. We used high-throughput sequencing to study MHC-I alleles in siskins (Spinus spinus) and determined gene expression, phylogenetic relationships and sequence divergence. We verified between six and 16 MHC-I alleles per individual and 97% of these were expressed. Strikingly, up to five alleles per individual had high expression. Out of 88 alleles 18 were putatively non-classical with low sequence divergence and expression, and found in a single phylogenetic cluster. The remaining 70 alleles were classical, with high sequence divergence and variable degrees of expression. Our results contradict the suggestion that birds only have a single dominantly expressed MHC-I gene by demonstrating several highly expressed MHC-I gene copies in a passerine.
Highlights
Passerine birds belong to the most species rich bird order and are found in a wide range of habitats
major histocompatibility complex class I genes (MHC-I) in siskins was initially characterized by Sanger-sequencing exon 2 to 4 in a single siskin individual
The retrieved siskin alleles were aligned against other bird Major Histocompatibility Complex (MHC)-I sequences and sites known to be conserved across vertebrates were present in the MHC-I of siskins (Supplementary Fig. 1)
Summary
Passerine birds belong to the most species rich bird order and are found in a wide range of habitats. O’Connor et al.[48] performed a comprehensive study of MHC-I using HTS across a large number of species from the parvorder Passerida within the order Passeriformes These species had between seven and 37 MHC-I alleles, i.e. at least four to 19 MHC-I gene copies per individual (classical and non-classical alleles combined). The highest number of MHC-I gene copies reported in any passerine species to date is in the sedge warbler where 65 MHC-I alleles have been identified in a single individual[8]. The exact purpose of this high number of MHC-I gene copies in passerines is not known and only limited efforts have been made to distinguish between classical and non-classical genes in passerines with even less research attention dedicated to studying MHC-I gene expression[33]
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