Physical mapping and germline genomic characterization of the giant panda immunoglobulin light chain κ and λ

Although four versions of the giant panda genome sequence have already been released, the fine structural characterization of antibody genes and the annotation of variable region gene clusters remain incomplete. This has hindered subsequent studies on the immune repertoire, vaccine development, and antibody discovery. At the root of this issue lie the complex repetitive sequences and fragmented architecture of antibody genes, which make it extremely difficult for genome assembly algorithms to correctly piece them together, leading to frequent assembly errors. Here, we present a comprehensive analysis of the germline genomic landscape of the giant panda immunoglobulin light chains, adopting a BAC-based physical mapping and targeted sequencing approach. We targeted 34 BAC clones that map to the chromosome-level genome assembly GPv1, span the entire locus, and unambiguously anchor each repeat-containing segments and gap, for sequencing and annotation. The light chain κ comprises 22 IGKV, 5 IGKJ and 1 IGKC genes, whereas the light chain λ comprises 187 IGLV, 17 IGLJ and 16 IGLC genes. Furthermore, the profile of the antibody repertoire and the preferential usage of V and J genes were investigated in blood from adult giant pandas. These results provide fundamental resources for monitoring giant panda’s health, analyzing the immune repertoire, and developing derived giant panda antibodies, thus improving the ex-situ conservation of the species.