doi:10.1111/j.1365-2052.2010.02137.x A conserved segmental duplication within ELA C. L. Brinkmeyer-Langford*, W. J. Murphy † , C. P. Childers ‡ and L. C. Skow § *Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA. † Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA. ‡ Department of Biology, Georgetown University, Washington, DC, USA. § Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA Summary The assembled genomic sequence of the horse major histocompatibility complex (MHC) (equine lymphocyte antigen, ELA) is very similar to the homologous human HLA, with the notable exception of a large segmental duplication at the boundary of ELA class I and class III that is absent in HLA. The segmental duplication consists of a 710 kb region of at least 11 repeated blocks: 10 blocks each contain an MHC class I-like sequence and the helicase domain portion of a BAT1-like sequence, and the remaining unit contains the full-length BAT1 gene. Similar genomic features were found in other Perissodactyls, indicating an ancient origin, which is consistent with phylogenetic analyses. Reverse-transcriptase PCR (RT-PCR) of mRNA from peripheral white blood cells of healthy and chronically or acutely infected horses detected transcription from predicted open reading frames in several of the duplicated blocks. This duplication is not present in the sequenced MHCs of most other mammals, although a similar feature at the same relative position is present in the feline MHC (FLA). Striking sequence conservation throughout Perissodactyl evolution is consis- tent with a functional role for at least some of the genes included within this segmental duplication. Keywords equine lymphocyte antigen, horse, major histocompatibility complex, Seg- mented duplication. Introduction Many proteins of the innate and adaptive immune systems are encoded within the major histocompatibility complex (MHC) (Trowsdale 1995), and genetic variation among these genes is associated with predispositions to auto- immune diseases and susceptibility to various pathogens and parasites (Escayg et al. 1997; Thorsby 1997; Sharif et al.1998, 1999; Bailey et al. 2000; Kaufman 2000; Park et al. 2004; Dukkipati et al. 2006). The gene content and organization of the MHC have been described for human (MHC Sequencing Consortium 1999), mouse (Mouse Genome Sequencing Consortium 2002), dog (Wagner 2003), cat (Yuhki et al. 2008), pig (Renard et al. 2006), cow (Brinkmeyer-Langford et al. 2009), horse (Gustafson et al. 2003; Tallmadge et al. 2005) and opossum (Gouin et al. 2006). Overall, the structure of the MHC appears to be remarkably conserved among mammalian species. The genetic map of the horse equine lymphocyte antigen (ELA) shares the general structure of MHCs of other mammalian species (for review, see Bailey et al. 2000), but assembly of the horse genome sequence (EquCab2.0) predicted an unexpected segmental duplication of approximately 710 kb at the boundary of the class III and class I regions (Wade et al. 2009). Here, we describe a detailed analysis of the ELA segmental duplication, which revealed at least 11 duplicated units within the region, including ten that contain both class I-like and BAT1-like helicase domain sequences, flanked by a single unit with the full-length equine BAT1 gene. Evi- dence for each of the duplicated blocks was found in the genomes of other perissodactyls, and reverse-transcriptase PCR (RT-PCR) studies of mRNA from horse WBCs revealed several transcribed open reading frames (ORFs) in the duplication. The persistence of the segmental duplication in perissodactyl species separated by more than 55 million years of evolution suggests a functional role for genes contained within this region. Address for correspondence C. L. Brinkmeyer-Langford, Texas A & M University College of Vetinary Medicine, Dept. of Vetinary Integrative Biosciences, College Station, Texas 77 845-4458. E-mail: cbrinkmeyer@cvm.tamu.edu Nucleotide sequence data reported are available in the GenBank database under accession numbers HM195309–HM196011. Accepted for publication 21 September 2010 Ó 2010 The Authors, Journal compilation Ó 2010 Stichting International Foundation for Animal Genetics, 41 (Suppl. 2), 186–195 186