BMC Genomics Research article A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish Jennifer G Sambrook1, Felipe Figueroa2 and Stephan Beck*1 Address: 1Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK and 2Max-Planck-Institut für Biologie, Abteilung Immunogenetik, 72076 Tübingen, Germany Email: Jennifer G Sambrook - js8@sanger.ac.uk; Felipe Figueroa - felipe.figueroa@tuebingen.mpg.de; Stephan Beck* - beck@sanger.ac.uk * Corresponding author BioMed Central Open Access Published: 04 November 2005 BMC Genomics 2005, 6:152 doi:10.1186/1471-2164-6-152 This article is available from: http://www.biomedcentral.com/1471-2164/6/152 Received: 05 June 2005 Accepted: 04 November 2005 © 2005 Sambrook et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The genomic organisation of the Major Histocompatibility Complex (MHC) varies greatly between different vertebrates. In mammals, the classical MHC consists of a large number of linked genes (e.g. greater than 200 in humans) with predominantly immune function. In some birds, it consists of only a small number of linked MHC core genes (e.g. smaller than 20 in chickens) forming a minimal essential MHC and, in fish, the MHC consists of a so far unknown number of genes including non-linked MHC core genes. Here we report a survey of MHC genes and their paralogues in the zebrafish genome. Results: Using sequence similarity searches against the zebrafish draft genome assembly (Zv4, September 2004), 149 putative MHC gene loci and their paralogues have been identified. Of these, 41 map to chromosome 19 while the remaining loci are spread across essentially all chromosomes. Despite the fragmentation, a set of MHC core genes involved in peptide transport, loading and presentation are still found in a single linkage group. Conclusion: The results extend the linkage information of MHC core genes on zebrafish chromosome 19 and show the distribution of the remaining MHC genes and their paralogues to be genome-wide. Although based on a draft genome assembly, this survey demonstrates an essentially fragmented MHC in zebrafish. Background The human Major Histocompatibility Complex (MHC) is a gene-dense region on chromosome 6p21.3, and com- prises a group of genes that are involved functionally with the adaptive and innate immune system. From centro- mere to telomere, it is divided into five regions: extended class II, classical class II, class III, classical class I and extended class I. The classical MHC contains 224 genes, many of which are pseudogenes, and with every two in five expressed genes having a potential immune function and a role in disease resistance [1], this region has become a focal locus in comparative genomics. Antibody and T cell mediated immune responses against invading patho- gens are initiated through MHC class I and class II mole- cules [2]. These main components are not only missing from invertebrates, but are also not present in primitive jawless fish, such as hagfish and lamprey [3]. MHC class I and II molecules do, however, exist in all jawed verte- brates, including the cartilaginous fish. The gene loci in the class III region encode a variety of proteins with both immune and non-immune functions [4]. Page 1 of 10 (page number not for citation purposes)