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Department of Microbiology, University of Iowa, Iowa City, IA 52242
The expressed porcine VH genes belong to the VH3 family (clan), four of which, VHA, VHB, VHC, and VHE, alone comprise 
80% of the preimmune repertoire. However, so-called "hybrid" VH genes that use CDR1 of one VH gene and the CDR2 of another are frequently encountered. We studied >3000 cloned VDJs and found that such hybrids can contribute up to 10% of the preimmune repertoire. Based on the 1) recovery of hybrid VH genes from bacterial artificial chromosome clones, 2) frequency of occurrence of certain hybrids in the preimmune repertoire, and 3) failure to recover equal numbers of reciprocal hybrids, we concluded that some chimeric genes are present in the genome and are not PCR artifacts. Two chimeric germline genes (VHZ and VHY), together with VHF and the four genes mentioned above, constitute the major VH genes and these account for >95% of the preimmune repertoire. Diversification of the preimmune IgG and IgM repertoires after environmental exposure was mainly due to somatic hypermutation of major VH genes with no evidence of gene conversion. Somatic hypermutation was 3- to 10-fold higher in CDRs than in framework regions, most were R mutations and transversions and transitions equally contributed. Data were used to 1) develop an index to quantify the degree of VH repertoire diversification and 2) establish a library of 29 putative porcine VH genes. One-third of these genes are chimeric genes and their sequences suggest that the porcine VH genome developed by duplication and splicing from a small number of prototypic genes.
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
1 This work was supported by National Pork Board Grants 05-143 and 05-174 and by Cooperative Agreement 58-3625-4-155 with the U.S. Department of Agriculture-Agricultural Research Service (Ames, IA).
2 Address correspondence and reprint requests to Dr. John E. Butler, University of Iowa, Department of Microbiology, Interdisciplinary Immunology Program, 51 Newton Road, Iowa City, IA 52242. E-mail address: john-butler{at}uiowa.edu
3 Abbreviations used in this paper: SHM, somatic hypermutation; MLN, mesenteric lymph node; BAC, bacterial artificial chromosome; CSR, class switch recombination; FR, framework; LB, Luria-Bertani; GF, germfree; RDI, repertoire diversification index.
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