The chicken Ig-like receptor (CHIR) gene family is located on microchromosome 31, the orthologous region to the mammalian leukocyte receptor complex. CHIR are equally related to the mammalian killer Ig-like receptors and leukocyte Ig-like transcripts, but they occur in a much higher number and diversity. The chicken microchromosome 31 has been neglected in the genome sequence analysis. Here, we provide a first analysis of this region. For this purpose bacterial artificial chromosome (BAC) sequences originating from a single inbred red jungle fowl that served as basis for the chicken genome project were screened for the presence of CHIR sequences and eight BACs were identified as major CHIR containing regions. Since the sequences of these BACs that were available in the database were not complete, sequence gaps were further closed by novel data from the chicken genome project. The entire sequence was aligned into 26 contigs covering 875kbp that contained 84 functional CHIR and 46 CHIR pseudogenes that were hampered by different reasons such as premature stop codons. The 84 functional CHIR were further categorized into 35 activating (CHIRA), 26 inhibitory (CHIRB) and 23 bifunctional (CHIRAB) genes. A detailed comparison of the annotated sequence taking also into account the previously published CHIR BAC sequence originating from an Lohman selected leghorn chicken revealed that the CHIR locus seems to be a very active region with a high degree of gene reorganization that resembles a constant birth and death evolution. The present report provides a framework for the future completion of the CHIR locus. It further suggests that the entire microchromosome 31 may resemble a locus of extraordinary genomic diversity that is beneficial for the development of a large CHIR repertoire, but that has therefore lost all other genes, where such a diversification would be fatal.
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