Chromosome‐level assembly of wild Bactrian camel genome reveals organization of immune gene loci

Abstract Camelids are characterized by their unique adaptive immune system that exhibits the generation of homodimeric heavy‐chain immunoglobulins, somatic hypermutation of T‐cell receptors, and low genetic diversity of major histocompatibility complex (MHC) genes. However, short‐read assemblies are typically highly fragmented in these gene loci owing to their repetitive and polymorphic nature. Here, we constructed a chromosome‐level assembly of wild Bactrian camel genome based on high‐coverage long‐read sequencing and chromatin interaction mapping. The assembly with a contig N50 of 5.37 Mb and a scaffold N50 of 76.03 Mb, represents the most contiguous camelid genome to date. The genomic organization of immunoglobulin heavy‐chain locus was similar between the wild Bactrian camel and alpaca, and genes encoding for conventional and heavy‐chain antibodies were intermixed. The organizations of two immunoglobulin light‐chain loci and four T cell receptor loci were also fully deciphered using the new assembly. Additionally, the complete classical MHC region was resolved into a single contig. The high‐quality assembly presented here provides an essential reference for future investigations examining the camelid immune system.