School of Life Sciences, Shihezi University, Xinjiang 832007, China.
BMC Genomics. 2010 Aug 10;11:466. doi: 10.1186/1471-2164-11-466.
The 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.
DNA 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.
An 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.
绵羊主要组织相容性复合体（MHC）含有参与动物对传染性病原体的整体抗性/易感性的基因簇。然而，与猪和牛相比，绵羊 MHC 基因的数量有限，并且没有足够的序列信息。我们之前构建了基于 BAC 克隆的物理图谱，该图谱涵盖了绵羊 MHC 的 I 类、II 类和 III 类区域。在这里，我们描述了通过对 26 个重叠 BAC 克隆进行测序来组装绵羊 MHC 完整 DNA 序列图谱的过程。
DNA 测序生成了大约 8 倍基因组等效数据，这些数据成功地组装成绵羊 MHC 的完成序列图谱。该序列图谱长约 2434000 个核苷酸，几乎覆盖了绵羊和牛中目前已知的所有 MHC 基因座。基因注释确定了 177 个蛋白编码基因/ORF，其中 145 个在绵羊中以前没有报道过，10 个是绵羊特有基因，在牛或其他哺乳动物中不存在。人与绵羊和牛的比较序列分析表明，MHC 结构和基因座顺序高度保守，除了 II 类，绵羊和牛的 II 类分为 IIa 和 IIb 亚区，由大约 18.5Mb 的大片非 MHC 常染色体隔开。此外，首次在绵羊 MHC 区域预测到 18 个非蛋白编码 microRNA。
通过对 26 个重叠 BAC 克隆进行测序，成功组装了绵羊 MHC 的 DNA 序列图谱。这使得绵羊成为继牛之后，第二种完整 MHC 序列信息可用于进化和功能研究的反刍动物。比较分析的结果支持了一个假说，即包含 MHC 的祖先染色体的倒位塑造了反刍动物的 MHC 结构，正如我们目前在绵羊和牛中观察到的那样。在绵羊 MHC 区域鉴定出相对大量的 microRNA，有助于提供证据表明 microRNA 积极参与 MHC 基因表达和功能的调控。
