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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

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Abstract

We report on the analyses of genes encoding immunoglobulin heavy and light chains in the rabbit 6.51× 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.

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Acknowledgments

This research was supported by the Intramural Research Programs of the NIH, NIAID, and NLM and by the Animal Genetics and Animal Physiology Divisions of INRA. We thank Dr. Josef Platzer, Roche Diagnostics, Penzberg, Germany for the gift of the 27 N5 BAC; Dr. Jessica Alföldi of the Broad Institute for rabbit RNASeq data; Drs. Christoph Rader, Nancy McCartney-Francis, and Michael Mage for suggestions to improve the manuscript; and Daniel Schäffer for assistance with the figures.

The UCSC rabbit Genome Browser was produced with the following acknowledgements: “sequencing/assembly was from The Broad Institute at MIT and Harvard, Cambridge, MA, USA; UCSC Rabbit Genome Browser (oryCun2) was from Hiram Clawsom and Antonio Coelho; Initial Genome Browser Annotations were from UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA”.

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Gertz, E.M., Schäffer, A.A., Agarwala, R. et al. 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. Immunogenetics 65, 749–762 (2013). https://doi.org/10.1007/s00251-013-0722-9

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