pig, in which Vk germline genes are more dominant than Vl (84 functional Vk genes vs. 58 functional Vl genes). It has been proposed that the priority of use of the light-chain gene isotypes at the protein level may be connected with the overall number of V gene segments [87]. It is possible that the k chain preponderates over the l chain at the protein level in guinea pigs. Also, multiple pseudogenes exist in the guinea pig VH (413), Vk (238), and Vl (84) loci, which may contribute to the Ig diversity in guinea pigs, similar to other species [47,88,89]. In conclusion, we have reported the characterization and annotation of the guinea pig Ig loci genomic maps for the first time. This information, together with the characterization of the guinea pig Ig germline gene repertoire currently being undertaken, should lay the foundations for further studies into the differenti- ation and structure of mammalian Ig genes, including those found in guinea pigs. Supporting Information Multiple sequence alignments of guinea pig Figure S1 VH genes. (DOC) Figure S2 Vk genes. (DOC) Figure S3 Vl genes. (DOC) Multiple sequence alignments of guinea pig Multiple sequence alignments of guinea pig Figure S4 Guinea pig immunoglobulin heavy chain constant region encoding gene amino acid sequences. Four guinea pig encoding gene amino acid sequences of constant region (IgM, IgG, IgE and IgA) are cloned by 39RACE. (TIF) Figure S5 Analysis results of the guinea pig Ig m, c, e and a genes in scaffold 54. Four guinea pig constant region encoding genes of tansmembrane type for IgM, IgG, IgE and IgA were identified by bioinformatics analysis. (TIF) Figure S6 Alignment of the IgG amino acid sequences of the guinea pig. Alignment of IgG1, IgG2 and IgG squence of References 1. Padilla-Carlin DJ, McMurray DN, Hickey AJ (2008) The guinea pig as a model of infectious diseases. Comp Med 58: 324–340. 2. 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Southern blotting analysis of guinea pig heavy chain constant region IgG genes. The genomic DNA was digested with BamH I (B), EcoR I (E), Hind III (H) and Xba I (X), and hybridized with probes for IgG-CH1 sequence. (TIF) Figure S8 Guinea pig germline DH segments. The nonamers (9-mer) and heptamers (7-mer) are displayed. Heptamer components that are different from the consensus (59: CACTGTG and 39: CACAGTG) are shadowed. The deduced amino acids of all three reading frames of the coding region of D segments are shown, all the DH segments were attached by 12 bp spacer. (RAR) Table S1 Primers were designed for amplify guinea pig four classes immunoglobulin M, E, A, and G genes. (DOC) Table S2 GenBank accession numbers or references of the gene sequences from other species. (RAR) Table S3 The guinea pig immunoglobulin heavy chain DNA segments location in scaffolds 54 and 75. (RAR) Table S4 The guinea pig immunoglobulin k light chain DNA segments location in scaffolds 37 and 24. 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PLoS ONE | www.plosone.org 16 June 2012 | Volume 7 | Issue 6 | e39298