Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20

Abstract

We report analyses of genes encoding immunoglobulin heavy and light chains in the rabbit 6.51x whole genome assembly. This OryCun2.0 assembly confirms previous mapping of the duplicated IGK1 and IGK2 loci to chromosome 2 and the IGL lambda light chain locus to chromosome 21. The most frequently rearranged and expressed IGHV1 that is closest to IG DH and IGHJ genes encodes rabbit VHa allotypes. The partially inbred Thorbecke strain rabbit used for whole-genome sequencing was homozygous at the IGK but heterozygous with the IGHV1a1 allele in one of 79 IGHV-containing unplaced scaffolds and IGHV1a2, IGHM, IGHG and IGHE sequences in another. Some IGKV, IGLV and IGHA genes are also in other unplaced scaffolds. By fluorescence in situ hybridization, we assigned the previously unmapped IGH locus to the q-telomeric region of rabbit chromosome 20. An approximately 3 Mb segment of human chromosome 14 including IGH genes predicted to map to this telomeric region based on synteny analysis could not be located on assembled chromosome 20. Unplaced scaffold chrUn0053 contains some of the genes that comparative mapping predicts to be missing. We identified discrepancies between previous targeted studies and the OryCun2.0 assembly and some new BAC clones with IGH sequences that can guide other studies to further sequence and improve the OryCun2.0 assembly. Complete knowledge of gene sequences encoding variable regions of rabbit heavy, kappa and lambda chains will lead to better understanding of how and why rabbits produce antibodies of high specificity and affinity through gene conversion and somatic hypermutation.

From rabbit antibody repertoires to rabbit monoclonal antibodies

“…Although a potential pool of 200 VH genes are present for heavy-chain rearrangement, 66, 77 a majority of these are infrequently or not expressed. 78 There are 10–20 D genes and 4–5 JH genes.…”

“…The recent sequencing and annotation of the rabbit genome (OryCun2.0 assembly) has provided new insights into this unique antibody repertoire. 1, 65, 66 …”

Biology and Diseases of Rabbits

“…The assembly has 2.24 Gbp in 21 autosome and X chromosomes and 489 Mbp in 3219 unplaced scaffolds including mitochondria (Gertz et al, 2013). The annotated assembly is now available at the National Center for Biotechnology Information (NCBI), the University of California Santa Cruz (UCSC), and Ensembl.…”

Survey of genetic diversity of IgG in wild and domestic rabbits

“…IgG is the predominant serum immunoglobulin and has a wide range of functions. The European rabbit (O. cuniculus) has played an important role in immunological research (reviewed in Pinheiro et al, 2011) and is unique in having only one IGHG copy (Knight et al, 1985;Hamers, 1987;Ros et al, 2004;Gertz et al, 2013). The assessment of wild populations and domestic breeds' IgG genetic diversity was previously carried out by serological analyses based on two polymorphisms located to the hinge region (d11/d12) and CH2 domain (e14/e15) (Hamers & Hamers-Casterman, 1965;Dubiski, 1969;Mage, 1981;Esteves et al, 2002Esteves et al, , 2006.…”