Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies

Abstract

The rhesus macaque is a critically important animal model in biomedical research, most recently playing a key role in the development of vaccines against human immunodeficiency virus-1. Nevertheless, the immunoglobulin (Ig) loci of macaques are as yet incompletely determined and our understanding of differences between human and macaque humoral immunity remains deficient. We completed a high-coverage, high-quality whole genome sequencing and assembly project with a single rhesus macaque of Indian origin, and partial genome assemblies using genomic molecular targeting of the Ig loci in nine other rhesus macaques of Indian origin. These data indicate that the macaque Ig loci are substantially more diverse than those in humans, including greater sequence diversity and copy-number variation between individuals. It appears likely that such copy-number variation even occurs between allelic loci within individuals. Different Ig gene families in the macaque show distinct relationships to the corresponding human gene families and appear to evolve under different mechanisms. These results raise intriguing questions about the evolution of antigen receptors in primates but also have important practical implications for the design and interpretation of biomedical studies.

Slow delivery immunization enhances HIV neutralizing antibody and germinal center responses via modulation of immunodominance

“…No difference in IGHV gene use was identified due to the low number of V genes available in IMGT. Analyzing the data with a broader Ig database incorporating both genomic and RNA sequencing data (Corcoran et al, 2016; Ramesh et al, 2017; Sundling et al, 2012), use of IGLV3.15 (aka IGLV3-5) was again significantly higher among bolus immunized animals (q = 0.0003) ( Fig S4G ). E nv-specific B cells that used IGLV3.15 were phylogenetically diverse and could be found in both draining LNs within a single animal ( Fig 6C, S5A ).…”

“…Since the IMGT database (Lefranc and Lefranc, 2001) is lacking several V genes, a custom IgBLAST database was created for V genes using sequences from the genomic assembly in this study or by combining sequences from previously published studies (Corcoran et al, 2016; Lefranc and Lefranc, 2001; Ramesh et al, 2017; Sundling et al, 2012) and the sequences from the assembly in this study. The protein sequences for V genes from all these datasets were combined.…”

Systematic profiling of full-length immunoglobulin and T-cell receptor repertoire diversity in rhesus macaque through long read transcriptome sequencing

“…We suspect that our ability to identify hinge region variation was driven by the high heterogeneity of the alpha constant region [68] as well as its highest frequency among the Ig isotypes we recovered. Given the interspecies variability of IGHG between macaques and humans [72] and the heterogeneity of rhesus IGHC genes in general [16], it is imperative that future rhesus Ig gene analyses also consider this allotypic diversity to improve the translatability of NHP models.…”

“…Since Ig/TCR loci are among the most complex regions in the genome due to their duplicated and polymorphic nature, proper sequencing and assembly of these genomic regions requires sophisticated efforts [76]. Consequently, complete assemblies are only available for selected model organisms such as human and mouse; meanwhile, these loci still do not have complete assemblies for rhesus macaque despite recent efforts [16]. The PacBio Iso-Seq approach we used here sequences full-length Ig/TCR transcripts directly and in a high-throughput manner, bypassing transcript assembly issues.…”

“…Duplicated copies of these gene segments cluster into several large loci in the genome. As a result, correct assembly of their respective loci with highly repetitive sequences is a major technical challenge, one that has yet to be fully resolved in rhesus macaque despite significant improvements [16] and the recent release of a new genome assembly, rheMac10 (GCA_003339765.3). Standard databases (e.g.…”