Complexity of expressed CHIR genes.

The chicken leukocyte receptor complex (LRC) encodes an unprecedented number of chicken Ig-like receptor (CHIR) genes compared to the mammalian LRC. Although there are at least 100 CHIR genes in the LRC, only little information is available about the number and variability of expressed CHIR. Recently, we showed that CHIR with one Ig domain encode a variety of different affinity IgY receptors, which are highly variable in different chicken strains. The current report focused on expressed CHIR with two Ig domains. Oligonucleotides specific for conserved regions at the 5' end of Ig1 and 3' end of Ig2 were used on PBMC mRNA obtained from two individual chickens with different MHC haplotypes (M11, R11). Sequencing of 142 colonies of M11 and 117 of R11 yielded 98 and 70 different CHIR2D amino acid sequences, respectively. Comparing a total of 219 CHIR sequences, including also a genomic dataset from an LSL chicken, revealed a single amino acid sequence identical between all three chicken strains, and four sequence pairs either shared between M11 and R11 or between M11 and LSL. Calculating Wu-Kabat variability revealed three amino acid positions, which were highly variable and the analysis of synonymous/non-synonymous ratio indicated positive selection. This analysis of expressed CHIR genes in different chickens demonstrates an unusual polymorphism of expressed receptors, where only few are conserved between chickens.