Immunoglobulin Genomics in the Guinea Pig Figure 15. The guinea pig Igl locus. The guinea pig Igl locus is in scaffold 4, the potentially functional Vl gene segments are shown in filled bars, and pseudogenes are represented by open bars. doi:10.1371/journal.pone.0039298.g015 were identified that spanned 0.6 kb. Furthermore, approximately 4 kb downstream from the last Jk, a single Ck gene was identified. Guinea Pig Igl Locus Guinea pig Igl chain genes were identified in scaffold 4, and spanned an approximately 1,642 kb length (Figure 15, Table S5). Of 142 germline Vl genes identified, 58 segments were categorized as potentially functional genes, and the remaining 84 were differentiated as pseudogenes. Based on sequence similarity analysis, the potentially functional guinea pig Vl genes were assigned to twelve families (Figure 16), comprised of 3, 1, 13, 6, 6, 8, 1, 3, 2, 5, 3 and 7 member/s, respectively. In contrast to the Vk genes, all the Vl genes have the same transcriptional orientation as the downstream Jk and Ck regions. At the 39 end of this scaffold, 11 J segments and C segments were organized in tandem and spanned 44 kb, while the Cl2 exhibited less structural integrity owing to the presence of gaps. The sequence alignments of Jl and Cl gene segments are shown in Figure 17. Discussion Rodents are a ubiquitous group of species worldwide, repre- senting nearly half of all mammalian species, which evolved from a common ancestor shared with the lagomorphs approximately 62– 100 million years ago [34,35]. The classification of the guinea pig within the family Caviidae and genus Cavia is somewhat controversial because the origin of this rodent is poorly known, with current classification data mostly relying on fossils or genetic relationships [36,37,38,39,40,41,42,43,44]. We therefore analyzed the Ig genes sequences of the guinea pig, not only to better understand the immune system of this species, but also to provide data for comparative studies of mammalian Ig genes. The IgH locus of mammals is arranged in a ‘‘translocon’’ configuration [32,45,46,47,48,49,50,51,52]. In the present study, we characterized the guinea pig Ig genes based on recently released genomic data and our experimental results. The guinea pig IgH locus in a configuration of VH (507)-DH (41)-JH (6)-Cm- yd-Cc2-Ce-Ca spanning at least 6,480 kb in two scaffolds may be largest in all mammalian species studied so far. On the basis of sequence analysis, we identified a single m, c, e and a gene within the guinea pig genome. We also found three fragments of d gene in an opposite direction downstream from the m gene. Due to sequence gaps, it is not certain if an additional functional d gene also exists in this species. We have also tried to confirm the sequence and orientation of the d gene fragments by genomic PCR to eliminate assembly error. The sequences of the d gene fragments were verified. Because two genomic fragments (approximately two kb and six kb) between m and d gene can not be successfully amplified, so the orientation of the d gene fragments remains a question. Many placental mammals, such as human, cow, sheep, horse and dog, have a single functional d gene. Except for a functional d gene which consists of ten CH domains, a reverse d pseudogene was previously observed in the platypus IgH locus [53], while in the elephant genome, only one Cd3 remnant fragment was identified [51]. In camelids, Cd3 exon appears to be highly mutated [54]. In the rabbit [24] and opossum (marsupial) [25], the d gene has clearly been shown to be missing in their genomes, indicating that the d gene might be not as essential as the m gene in the humoral immunity. PLoS ONE | www.plosone.org 13 June 2012 | Volume 7 | Issue 6 | e39298