Immunoglobulin Genomics in the Guinea Pig Figure 10. The nucleotide sequences of DH genes. DH coding region nucleotide sequences are represented together the RSS elements (nonamer and heptamer sequences). doi:10.1371/journal.pone.0039298.g010 largest family, VH3, could be further divided into two subfamilies (Figure 6, Figure 7). We also performed Southern blotting to verify the multiple numbers of VH genes of different families in the guinea pig genome (Figure 8). We chose all potentially functional guinea pig VH sequences of and VH sequences that represented previously reported gene families from other mammalian species to construct a neighbor- joining phylogenetic tree [31,32] (Figure 9). The phylogenetic tree indicated that the mammalian VH gene families were classified into three clans [33]. The guinea pig VH families 1 and 2 belonged to clan II, and family 3 belonged to clan III. Analysis of the Guinea Pig DH and JH Gene Segments Approximately 504 kb downstream from the last VH segment (VH1-1), we identified 41 DH segments (i.e., DH1–DH41). They spanned a 660 kb region of DNA in scaffold 54 (Figure 1). Each Figure 11. The nucleotide sequences of JH genes. JH nucleotide sequences are represented together the RSS elements (nonamer and heptamer sequences) and RNA donor splicing site. doi:10.1371/journal.pone.0039298.g011 PLoS ONE | www.plosone.org 10 June 2012 | Volume 7 | Issue 6 | e39298