Immunoglobulin Genomics in the Guinea Pig Figure 14. Phylogenetic analysis of the 111 guinea pig Vk genes. A phylogenetic tree of the nucleotide sequences of 111 guinea pig Vk segments were constructed. The six Vk gene families are labeled with Arabic numerals. doi:10.1371/journal.pone.0039298.g014 DH segment was flanked by conserved RSS elements composed of heptamers and nonamers separated by 12 bp spacers and existed within at last one alternative reading frame (Figure 10 and Figure S8), suggesting that they are potentially functional. JH region contained six genes (designated JH1 to JH6) spanning approximately 2 kb. Each JH gene had an upstream RSS element with a 22–23 bp spacer, ORF, and a downstream RNA donor- splicing site at the 39 end, suggesting that they are potentially functional (Figure 11). Guinea Pig Igk Locus The guinea pig Igk chain is located in scaffolds 37 and 24, and spans an approximately 4,029 kb genomic region (Figure 12, Figure 13 and Table S4). A total of 349 Vk genes were identified. Further analysis revealed that 111 Vk genes might be potentially functional genes, given that they contained an L sequence, ORF, RSS and V domain. The remaining 238 segments contain either in-frame stop codons or frameshifts, and are thus designated as pseudogenes. Based on sequence analysis, the 111 potentially functional Vk genes were divided into six families (Vk1–Vk6), which contained 69, 15, 7, 17, 2, and 1 member/s, respectively (Figure 14). In addition, 222 Vk genes were arranged in the same transcriptional orientation and exhibited downstream Jk and Ck, and 61 Vk segments and a reverse transcriptional direction in scaffold 37. Downstream of the Vk genes, three Jk gene segments PLoS ONE | www.plosone.org 12 June 2012 | Volume 7 | Issue 6 | e39298