A complete DNA sequence map of the ovine Major Histocompatibility Complex

Abstract

BackgroundThe ovine Major Histocompatibility Complex (MHC) harbors clusters of genes involved in overall resistance/susceptibility of an animal to infectious pathogens. However, only a limited number of ovine MHC genes have been identified and no adequate sequence information is available, as compared to those of swine and bovine. We previously constructed a BAC clone-based physical map that covers entire class I, class II and class III region of ovine MHC. Here we describe the assembling of a complete DNA sequence map for the ovine MHC by shotgun sequencing of 26 overlapping BAC clones.ResultsDNA shotgun sequencing generated approximately 8-fold genome equivalent data that were successfully assembled into a finished sequence map of the ovine MHC. The sequence map spans approximately 2,434,000 nucleotides in length, covering almost all of the MHC loci currently known in the sheep and cattle. Gene annotation resulted in the identification of 177 protein-coding genes/ORFs, among which 145 were not previously reported in the sheep, and 10 were ovine species specific, absent in cattle or other mammals. A comparative sequence analyses among human, sheep and cattle revealed a high conservation in the MHC structure and loci order except for the class II, which were divided into IIa and IIb subregions in the sheep and cattle, separated by a large piece of non-MHC autosome of approximately 18.5 Mb. In addition, a total of 18 non-protein-coding microRNAs were predicted in the ovine MHC region for the first time.ConclusionAn ovine MHC DNA sequence map was successfully assembled by shotgun sequencing of 26 overlapping BAC clone. This makes the sheep the second ruminant species for which the complete MHC sequence information is available for evolution and functional studies, following that of the bovine. The results of the comparative analysis support a hypothesis that an inversion of the ancestral chromosome containing the MHC has shaped the MHC structures of ruminants, as we currently observed in the sheep and cattle. Identification of relative large numbers of microRNAs in the ovine MHC region helps to provide evidence that microRNAs are actively involved in the regulation of MHC gene expression and function.

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

“…Two contigs containing the sheep major histocompatibility (MHC) loci (also designated as ovine lymphocyte antigen or OLA) generated with BAC-by-BAC sequencing 31 were used to search against the CHIR_1.0 for goat MHC loci. As expected, the goat MHC loci were located on chromosome 23 in our assembly.…”

“…5a). Based on a comparison to the sheep MHC, which contains 177 genes, we annotated 160 protein-coding genes ( Supplementary Table 17) using the same method as for the sheep MHC annotation 31 . Based on the annotation, we also analyzed conserved genes of MHC loci in sheep, goat and human.…”

Molecular characterization of Ovar-DRB1 exon2 gene in Garole sheep resilient to gastrointestinal nematodes

“…Primers used in this study were basically designed for BoLA (van Eijak et al, 1992). This shows that MHC genes are highly conserved across different species including human (Gao et al 2010). Major histocompatibility complex (MHC) class II molecules are glycoproteins composed of two non-covalently linked  and  chains.…”

A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA

“…) and sheep (Gao et al . ), the class II genes are distributed in two segments rather than a single segment as observed in humans (Vandiedonck & Knight ). The two segments, located about 20 c m apart, are known as class IIa and class IIb, with class IIa closely associated with the class I and class III regions.…”