Analysis of the Elephant Immunoglobulin Genes Figure 10. Phylogenetic analysis of the 58 elephant Vk genes. A phylogenetic tree of the nucleotide sequences of 58 elephant Vk segments was constructed. The eight Vk gene families are labeled with Arabic numerals. The credibility value for each node is shown. doi:10.1371/journal.pone.0016889.g010 mammalian VH families can be further classified into three clans: I, II, and III, which have co-existed in the genome for more than 400 Myr [79]. Similar to those of humans, the elephant VH families also conform to three clans: families 1, 5, and 7 form clan I, families 2, 4, and 6 form clan II, and family 3 forms clan III. The largest group of elephant VH genes is the VH4 family of clan II. It has been demonstrated that the unique VH family identified in cattle belonged to clan II [75,77]. In sheep, most VH genes are also categorized into clan II [80]. Based on a recent report, clan II also appeared to be the largest group in the horse [41], indicating that the herbivore animals may prefer to use the clan II VH genes. Close attention should also be paid to the elephant DH locus, where at least 87 germline D segments could be mapped to a 450-kb DNA region; the largest number in mammals examined so far. The presence of more DH segments may greatly increase the Ig diversity generated through DNA rearrangement. The size of the elephant DH coding regions ranges from 10 to 37 bp, similar to that of human (11 to 37 bp) [57]. Further inspection revealed that the elephant DH segments were translated in three reading frames abundant in polar/hydrophobic amino acids, which is different to dog [78], horse [41], mouse [81], rabbit [82], and chicken [83], which show preferences for neutral (polar/hydrophilic) amino acids. For the light chain genes, elephant Vk germline genes are more abundant than Vl (53 functional Vk genes vs. 2 functional Vl genes). Different mammalian species possess different ratios of Vk and Vl. In humans, roughly 60% of the variable light chain PLoS ONE | www.plosone.org 10 February 2011 | Volume 6 | Issue 2 | e16889