Abstract
Immune genes show remarkable levels of adaptive variation shaped by pathogen-mediated selection. Compared to humans, however, population polymorphism in animals has been understudied. To provide an insight into immunogenetic diversity in birds, we sequenced complete protein-coding regions of all Toll-like receptor (TLR) genes with direct orthology between mammals and birds (TLR3, TLR4, TLR5 and TLR7) in 110 domestic chickens from 25 breeds and compared their variability with a corresponding human dataset. Chicken TLRs (chTLRs) exhibit on average nine-times higher nucleotide diversity than human TLRs (hTLRs). Increased potentially functional non-synonymous variability is found in chTLR ligand-binding ectodomains. While we identified seven sites in chTLRs under positive selection and found evidence for convergence between alleles, no selection or convergence was detected in hTLRs. Up to six-times more alleles were identified in fowl (70 chTLR4 alleles vs. 11 hTLR4 alleles). In chTLRs, high numbers of alleles are shared between the breeds and the allelic frequencies are more equal than in hTLRs. These differences may have an important impact on infectious disease resistance and host-parasite co-evolution. Though adaptation through high genetic variation is typical for acquired immunity (e.g. MHC), our results show striking levels of intraspecific polymorphism also in poultry innate immune receptors.
Highlights
Domestic chickens and humans have a lot in common
We sequenced complete protein-coding DNA sequences (CDSs) for all Toll-like receptor (TLR) with direct orthologues between mammals and birds (TLR3, TLR4, TLR5 and TLR7) in 110 chickens (25 breeds) to compare variability with a corresponding set of 110 randomly-selected humans sampled from 25 populations around the world as part of the 1000 Genomes Project[43]
Unlike human TLRs (hTLRs), we found no sequences with internal STOP codons in Chicken TLRs (chTLRs)
Summary
Domestic chickens and humans have a lot in common. Given their joint history, the domestic chicken is an abundant and widespread species around the world. Domestic chicken breeds remain rarely studied from the perspective of evolutionary immunology This is despite Darwin himself pointed out that variation in domestic fowl populations provides an excellent system for investigating evolution through natural and artificial selection[1]. Several hundreds of breeds are recognised worldwide, many of which are only locally distributed, having been maintained as stable phenotypic forms for centuries[11] These traditional fowl breeds were originally domesticated from free-living red junglefowl subspecies, with possible admixture of other Gallus species, on multiple occasions in different regions of Asia[12]. Variation in innate immune receptor genes, which form a direct molecular interface between pathogens and their hosts, is appealing since major www.nature.com/scientificreports/. Human TLR7 and TLR8 are closely related, they slightly differ in their natural ligand preferences[31,32,33,34]
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