Analysis of the Elephant Immunoglobulin Genes Figure 4. Dot plot comparison of the elephant CH (m and c) region. A dot matrix representing repetitive sequences of elephant CH (m and c) genes. Switch regions are indicated by black-squared boxes and marked with arrowheads, and gaps are indicated by grey-squared boxes. Positions of CH genes are indicated as vertical lines. The dots represent homologies with a search length of 30 bp and maximum of 9 bp mismatches. doi:10.1371/journal.pone.0016889.g004 S3), which contain 2, 31, 2, 102, 1, 1, 2, and 1 members, respectively. The remaining 11 Vk pseudogenes could not be assigned to any family because they share less than 70% nucleotide similarity with any other Vk gene segment. A phylogenetic tree of the elephant Vk functional genes is shown in Fig.10. The six elephant Vk families (Vk1,Vk6) correspond to the six human Vk gene families. In addition, scaffold 86 includes 24 Vk segments showing the same transcriptional orientation as the Jk and Ck, and 18 Vk segments showing a reverse transcriptional direction. Three Jk segments and one Ck gene on scaffold 86 are displayed in Figure S5. In addition, Vk segments located on scaffolds 202 and 50 also possess two different transcriptional directions. l chain. Scaffold 68 was determined to contain the elephant l light gene complex (Fig. 9). Sequences analysis revealed that the 12 elephant Vl gene segments belonged to six families (Fig. 11), which were homologous with the human Vl 1, 3, 4, 7, 9 and 10 families. The remaining three Vl pseudogenes could not be assigned to any family because they share less than 70% nucleotide similarity with any other Vl gene segment. The three elephant Vl families consists of seven members. In contrast to Vk, all the Vl segments possess an identical transcriptional polarity to the downstream Jl segments. In addition, only Vl3-3 and Vl3-7 are identified as potentially functional genes. At the 39 end of the locus, three constant region genes are organized in tandem, where both Cl2 and Cl3 are preceded by a Jl. The Jl segment before Cl1 is missing because of a sequence gap. Three Cl genes show approximately 90% amino acid identity. The sequences of two Jl segments and three Cl genes are presented in Figure S5. Discussion In this study, we have made a preliminary analysis of the immunoglobulin genes in the elephant using the recently released elephant genome, revealing that the elephant IgH locus conforms PLoS ONE | www.plosone.org 5 February 2011 | Volume 6 | Issue 2 | e16889