ORIGINAL PAPER Structure of the catfish IGH locus: analysis of the region including the single functional IGHM gene E. Bengtén & S. Quiniou & J. Hikima & G. Waldbieser & G. W. Warr & N. W. Miller & M. Wilson Received: 15 February 2006 / Accepted: 13 June 2006 / Published online: 29 August 2006 # Springer-Verlag 2006 Abstract The catfish IGH locus is large (∼1 Mb) and complex, having undergone multiple internal duplications and transpositions. To define the structure of the locus that contains the single expressed IGHM gene, two overlapping bacterial-artificial-chromosome (BAC) clones spanning the most 3′ end of the channel catfish immunoglobulin heavy (IGH) chain locus have been completely sequenced. The analyses created a contig of 257,153 bp containing 55 VH, 6 D, 12 JH genes and the IGH constant region genes encoding the functional secreted and membrane forms of IgM and the membrane form of IgD. This analysis revealed three major features. First, no C-region genes were found aside from the previously described IGHM1 and IGHD1, with the latter gene being the most 3′ C-region gene of the catfish IGH locus. There was no evidence in the region sequenced for genes that could encode an Ig class similar to the IgZ/IgT described in zebrafish, trout and pufferfish. Second, there are a high number of VH pseudogenes, 28 out of 55 (51%). In contrast, the entire zebrafish IGH locus has 40 functional VH genes and eight pseudogenes (17%). Third, an internal duplication of a 52.4-kb block of VH genes has occurred. These observations suggest that the IGH locus of teleost fish varies significantly from species to species in the diversity of C-region genes as well as the numbers of genes encoding V regions. Keywords Immunoglobulin heavy chain locus . Catfish . Bacterial artificial chromosome Introduction Understanding the structure of the IGH locus of the channel catfish Ictalurus punctatus is of importance for several reasons. These include insight into the genetic basis of diversity in the antibody response of this species, and a better understanding of the evolutionary divergence of this important immune function locus in the vertebrates. Catfish are currently the most important species of fish raised commercially in the USA, comprising 68% of all aquacul- ture production, http://usda.mannlib.cornell.edu/reports/ nassr/other/pcf-bbc/. As a result, basic knowledge of catfish immunoglobulin genetics has practical relevance in terms of understanding infectious disease and mechanisms of host resistance, and the catfish has become one of the best models in which to study immune function at the phylogenetic level of the teleost fish (reviewed in Bengten et al. 2006; Clem et al. 1996; Magor et al. 1999; Miller et al. 1998; Shen et al. 2002). Catfish antibodies were first characterized serologically and biochemically, and the details of the structure/function relationships of the major antibody (IgM) have been known for many years (Getahun et al. 1999; Hayman and Lobb 1993; Lobb 1985, 1986a,b, 1987; Lobb and Clem 1983; Lobb and Hayman 1989; Lobb and Olson 1988; Plumb et Immunogenetics (2006) 58:831–844 DOI 10.1007/s00251-006-0139-9 E. Bengtén (*) : N. W. Miller : M. Wilson Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA e-mail: ebengten@microbio.umsmed.edu S. Quiniou : G. Waldbieser Catfish Genetics Research Unit, ARS, USDA, 141 Experimental Station Road, Stoneville, MS 38701, USA J. Hikima : G. W. Warr Marine Biomedicine and Environmental Sciences Center and Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA