LILRB1 and LILRB2 genomics and transcriptomics in macaque and baboon species: polymorphism, diversification, and extensive alternative splicing

We describe 71 <i>LILRB1</i> and 58 <i>LILRB2</i> alleles in the two macaque species, of which only one allele was previously published. In contrast, less polymorphism is observed in the Hamadryas baboon, with only six <i>LILRB1</i> and seven <i>LILRB2</i> alleles characterized. Phylogenetic analysis, including known human data, revealed extensive diversification of the <i>LILRB1</i> and <i>LILRB2</i> in macaques, with allelic variation clustering into nine and twelve distinct lineages, respectively. This contrasts with the more conserved repertoires observed in humans and Hamadryas baboons. Compared with our experience analyzing <i>MHC</i> and <i>KIR</i> transcriptome data, the <i>LILRB1</i> and <i>LILRB2</i> transcriptomes were dominated by alternatively spliced isoforms. Alternative 3' splice sites near exons 10 and 15 and/or skipping of exon 15, were encountered for most <i>LILRB1</i> alleles. In <i>LILRB2</i>, the deletion of exon 9 is the most prominent event, next to deletion of exon 10 and the use of alternative 3' splice sites near exons 10 and 15. The exons that encode the extracellular domains remain largely intact, suggesting that alternative splicing predominantly affects the stem region and the signaling capacity of the LILRB1 and LILRB2 receptors.