**2.2 The Ig loci in sharks and the chicken are differently organized**

Figure 3 illustrates examples of the organization of V-D-J-C segments in three different shark species which are organized as repeating cassettes rather than in translocon fashion. Interestingly, Figure 2A also shows that an apparent evolutionary remnant of this form of organization is still found in the lambda light chain locus of mammals. In the shark, an entire cassette is used for encoding an antibody; recombination among cassettes is unusual. Furthermore, segments within the cassettes of certain sharks are fused in the genome so recombination (Section 4) does not occur. It is believed that the tandem repeat system of sharks later evolved into the translocon system (Marchalonis et al., 1998). In the translocon system, recombination among the various V, D, and J segments can occur and the rearranged VDJ is later spliced to a C region exon (Fig. 4A).

Fig. 3. Organization of heavy chain loci in sharks and chicken. Three different types of clusters are shown for sharks, some in which VDJs are fused in the genome; n= number of repeating clusters. Modified from Dooley & Flajnik, 2006. In the diagram for chicken, the number (n) of gene segments of each type is indicated. Only VH1 of chicken is a functional VH gene.

The chicken also displays a translocon system but there is only one functional VH (and one V; not shown), multiple highly similar DH segments and only one JH. All VH genes upstream of VH1 in the chicken are pseudogenes (Fig. 3; Ratcliffe, 2006). These pseudo VH genes are used in SGC to create the chicken antibody repertoire (Reynaud et al., 1987; Ratcliffe, 2006).
