Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains

Abstract

The light chain immunoglobulin genes of biomedically relevant mouse strains are poorly documented in current germline gene databases. We previously showed that IGH loci of wild-derived mouse strains representing the major mouse subspecies contained 247 germline IGHV sequences not curated in the international ImMunoGeneTics (IMGT) information system, which is the most commonly used database that curates the germline repertoires used for sequence alignment in AIRR-seq analysis. Despite containing levels of polymorphism similar to the IGH locus, the germline gene content and diversity of the light chain loci have not been comprehensively cataloged. To explore the extent of germline light chain repertoire diversity across mouse strains commonly used in the biomedical sciences, we performed AIRR-seq analysis and germline gene inference for 18 inbred mouse strains, including the four wild-derived strains with diverse sub-species origins. We inferred 1582 IGKV and 63 IGLV sequences, representing 459 and 22 unique IGKV and IGLV sequences. Of the unique inferred germline IGKV and IGLV sequences, 67.8% and 59%, respectively, were undocumented in IMGT. Across strains we observed germline IGKV sequences shared by three distinct IGK haplotypes and a more conserved IGLV germline repertoire. In addition, J gene inference indicated a novel IGK2 allele shared between PWD/PhJ and MSM/MsJ and a novel IGLJ1 allele for LEWES/EiJ and IGLJ2 allele for MSM/MsJ. Finally, a combined IGHV, IGKV, and IGLV phylogenetic analysis of wild-derived germline repertoires displayed reduced germline diversity for the light chain repertoire compared to the heavy chain repertoire, suggesting potential evolutionary differences between the two chains.

Immunoglobulin genes, reproductive isolation and vertebrate speciation

“…Exact matches to the CAST/EiJ sequences were only seen in 5 of 92 V gene sequences from the M. m. musculus –derived PWD/PhJ strain, and in 2 of 78 V gene sequences from the M. m. domesticus –derived LEWES/EiJ strain 39 . Some divergence was also seen in the heavy‐chain D and J gene sets, while single‐nucleotide polymorphism analysis and our unpublished data suggest that the sets of light‐chain genes of the three subspecies are also highly divergent 36,40 …”

“…39 Some divergence was also seen in the heavy-chain D and J gene sets, while single-nucleotide polymorphism analysis and our unpublished data suggest that the sets of light-chain genes of the three subspecies are also highly divergent. 36,40 The loci of common inbred mouse strains are also highly divergent both from one another and from the loci of the wild-derived inbred strains, for as a consequence of their early breeding histories, the heavy and light chain loci of classical inbred mouse strains seem to be mosaics of genes derived from each of the different mouse sub-species. 39,41 For example, just 4 of the 109 expressed IG heavy-chain V genes of the C57BL/6 mouse are found among the 162 expressed V gene sequences identified in the BALB/c mouse.…”

Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta and beta loci

“…At present, the impact that these missing germline genes and alleles has on the analysis and interpretation of TCR repertoire sequencing studies is not clear, but would be expected to have profound effects on germline gene/allele assignment efforts, similar to what has been noted for IG repertoires. As observed in the IG loci(36–39), it will be interesting to understand whether the inter-individual diversity uncovered in the human TR loci will extend to non-human species as well.…”

Molecular basis for differential Igk versus Igh V(D)J joining mechanisms

“…For all other rearrangement analysis, primary pre-B cells and v-Abl cells used are from 129SV background. Since there is almost no difference in the Igk locus between C57BL/6 and 129SV genomic backgrounds 44 , the data were aligned to the AJ851868/mm9 hybrid (mm9AJ) genome 6 except: data from Igh-Igk hybrid-Vκ-JκRSS and Igh-Igk hybrid-Vκ-JκRSS-PKO v-Abl lines were aligned to the mm9AJ_ J H 1toJκ5RSS genome, data from single Jκ5-single Igh-J H RSS v-Abl line were aligned to the mm9AJ_Jκ5toJ H 1RSS genome, and data from Igh-Igk hybrid-D-VκRSS v-Abl line were aligned to the mm9AJ_DQ52uptoVκRSS genome. To show the absolute level of V(D)J recombination, each HTGTS-V(D)J-seq library was down-sampled to 500,000 total reads ( junctions + germline reads); to show the relative Vκ usage pattern across the Vκ locus, individual Vκ usage levels were divided by the total Vκ usage level in each HTGTS-V(D)J-seq library to obtain the relative percentage.…”