Chang Liao, He Shiyang, Mao Danqing, Liu Yuanhong, Xiong Zijun, Fu Dongke, Li Bo, Wei Shuguang, Xu Xun, Li Shengbin, Yuan Hui
College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
BGI-Shenzhen, Shenzhen, Guangdong, China.
PLoS One. 2016 Dec 20;11(12):e0168744. doi: 10.1371/journal.pone.0168744. eCollection 2016.
Whole-genome shotgun (WGS) sequencing has become a routine method in genome research over the past decade. However, the assembly of highly polymorphic regions in WGS projects remains a challenge, especially for large genomes. Employing BAC library constructing, PCR screening and Sanger sequencing, traditional strategy is laborious and expensive, which hampers research on polymorphic genomic regions. As one of the most highly polymorphic regions, the major histocompatibility complex (MHC) plays a central role in the adaptive immunity of all jawed vertebrates. In this study, we introduced an efficient procedure based on recombination screening and short-reads assembly. With this procedure, we constructed a high quality 488-kb region of crested ibis MHC that consists of 3 superscaffolds and contains 50 genes. Our sequence showed comparable quality (97.29% identity) to traditional Sanger assembly, while the workload was reduced almost 7 times. Comparative study revealed distinctive features of crested ibis by exhibiting the COL11A2-BLA-BLB-BRD2 cluster and presenting both ADPRH and odorant receptor (OR) gene in the MHC region. Furthermore, the conservation of the BF-TAP1-TAP2 structure in crested ibis and other vertebrate lineages is interesting in light of the hypothesis that coevolution of functionally related genes in the primordial MHC is responsible for the appearance of the antigen presentation pathways at the birth of the adaptive immune system.
在过去十年中，全基因组鸟枪法（WGS）测序已成为基因组研究中的常规方法。然而，WGS项目中高度多态性区域的组装仍然是一项挑战，尤其是对于大型基因组。采用BAC文库构建、PCR筛选和桑格测序，传统策略既费力又昂贵，这阻碍了对多态性基因组区域的研究。作为多态性最高的区域之一，主要组织相容性复合体（MHC）在所有有颌脊椎动物的适应性免疫中起着核心作用。在本研究中，我们引入了一种基于重组筛选和短读长组装的高效方法。通过该方法，我们构建了朱鹮MHC的一个高质量488 kb区域，该区域由3个超级支架组成，包含50个基因。我们的序列与传统桑格组装法的质量相当（同一性为97.29%），而工作量减少了近7倍。比较研究通过展示COL11A2-BLA-BLB-BRD2簇以及在MHC区域呈现ADPRH和嗅觉受体（OR）基因，揭示了朱鹮的独特特征。此外鉴于原始MHC中功能相关基因的共同进化导致了适应性免疫系统诞生时抗原呈递途径出现这一假说，朱鹮和其他脊椎动物谱系中BF-TAP1-TAP2结构的保守性很有意思。
