The repertoire of a West African chimpanzee population is characterized by limited gene, allele, and haplotype variation.

INTRODUCTION

The killer cell immunoglobulin-like receptors (KIR) play a pivotal role in modulating the NK cell responses, for instance, through interaction with major histocompatibility complex (MHC) class I molecules. Both gene systems map to different chromosomes but co-evolved during evolution. The human gene family is characterized by abundant allelic polymorphism and copy number variation. In contrast, our knowledge of the repertoire in chimpanzees is limited to 39 reported alleles, with no available population data. Only three genomic region configurations have been mapped, and seventeen additional ones were deduced by genotyping.

METHODS

Previously, we documented that the chimpanzee MHC class I repertoire has been skewed due to an ancient selective sweep. To understand the depth of the sweep, we set out to determine the full-length transcriptome - in our MHC characterized pedigreed West African chimpanzee cohort - using SMRT sequencing (PacBio). In addition, the genomic organization of 14 haplotypes was characterized by applying a Cas9-mediated enrichment approach in concert with long-read sequencing by Oxford Nanopore Technologies.

RESULTS

In the cohort, we discovered 35 undescribed and 15 already recorded alleles, and a novel hybrid gene. Some transcripts are subject to evolutionary conserved alternative splicing events. A detailed insight on the region dynamics (location and order of genes) was obtained, however, only five new region configurations were detected. The population data allowed to investigate the distribution of the MHC-C1 and C2-epitope specificity of the inhibitory lineage III KIR repertoire, and appears to be skewed towards C2.

DISCUSSION

Although the region is known to evolve fast, as observed in other primate species, our overall conclusion is that the genomic architecture and repertoire in West African chimpanzees exhibit only limited to moderate levels of variation. Hence, the ancient selective sweep that affected the chimpanzee MHC class I region may also have impacted the system.