Sequence analysis of 0.5 Mb of the rabbit germline immunoglobulin heavy chain locus

Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire

“…172,126 high quality reads corresponding to 88,830 unique heavy chain sequences across the three rabbits were obtained (Table 1). Germline VH usage was determined with IgBLAST [33] alignments using a custom database that included NZW rabbit germline sequences compiled from a number of sources [8], [13], [23], [24], [25], [26], [27], [28], [29] (see Materials and Methods). For the VHa sequences in all three rabbits, >99% were of the a3 allotype, strongly indicating that the cohort of NZW rabbits examined here is homozygous a3/a3 at the IgH locus.…”

“…An IgBLAST database for germline annotation of the rabbit IgG sequences was constructed using the following sequences: the IMGT rabbit V germline reference set that includes the allotypic a2 sequences in BAC clones AY386694 and AY386697 [23], allotypic a2 sequences from an Alicia rabbit (AF176997 through AF177016) [24], potentially latent IGHV (M12180, M60121, M60336) [8], [25], [26], allotypic a1 sequences VH1-a1 (M93171), VH3-a1 (M93177), and VH4-a1 (M93181) [27], and the allotypic a3 sequences VH1-a3 through VH7-a3 (M93173, M93176, M93179, M93183, M93184, M93185, M93186) [13], [27]. In addition to the IMGT rabbit reference set, initial IgBLAST database included VH8-a3 through VH11-a3 (L27311, L27312, L27313, L27314) [28], VHx (L03846) [29], and VHy (L03890) [29].…”

Phylogeny and Comparative Physiology of Mucosal Immunoglobulins

“…Functional analysis of I α promoters upstream of the C α genes was consistent with a mechanism of cytokine-activated CSR for switching to the different IgA subclasses, and the finding of nonfunctional I α promoters upstream of the C α3 and C α8 genes explained the lack of expression of IgA3 and IgA8 (Spieker-Polet et al, 2002). Subsequent mapping of the IGH locus in rabbits revealed single copies of C μ , C γ , and C ε genes and the absence of a C μ gene (Lanning et al, 2003;Ros et al, 2004). The loss of IgD in rabbits seems to be unique among mammalian species, although it is a common feature of birds (see above).…”

Isotype analysis of gerbil–mouse heterohybridomas by RT-PCR

“…Therefore, the misattribution by the isotyping kit may be due to cross-reactivity of goat anti-mouse IgG3 pAb to gerbil IgG2. Another reason may be differences in the numbers of IgG subclasses among species: mouse has four Cγ genes (Shimizu et al, 1982); rat has four (Brüggemann, 1988); rabbit has only one (Ros et al, 2004); and panda has two (Zhao et al, 2007). Therefore, the misattribution may be due to the difference in the numbers of IgG subclasses between gerbil and mouse, although we do not know whether gerbil has any more than the two Cγ IGHCs determined in our previous study.…”