基于三代测序的食蟹猴Mafa-B等位基因共表达与进化分析

Co-expression and evolution of Mafa-B alleles in Macaca fascicularis based on third-generation sequencing

摘要:

【背景】主要组织相容性复合体(major histocompatibility complex，MHC)的多态性在很大程度上会影响生物医学实验的结果，而且特定的MHC-B等位基因与多种疾病的发展进程密切相关。食蟹猴(Macaca fascicularis，Mafa)是一种开展生物医学研究的重要实验动物，与人类相比，目前尚缺乏对食蟹猴Mafa-B等位基因的综合表征。【目的】获得全面的食蟹猴Mafa-B等位基因信息，鉴定Mafa-B等位基因共表达与进化关系。【方法】基于三代测序获得的食蟹猴MHC-B基因组信息，设计特异性引物扩增33只越南食蟹猴群体中的Mafa-B序列，并结合多种生物信息学方法进行分析。【结果】基于92个Mafa-B等位基因信息，鉴定了65个新的Mafa-B等位基因。其中，8个Mafa-B等位基因与其他地理来源的食蟹猴群体中已报道的序列相同，32个Mafa-B等位基因与其他猕猴物种中已报道的序列相同。此外，鉴定了7个高频Mafa-B谱系和7对共表达的Mafa-B等位基因，并检测到了一个潜在的重组事件。进化分析表明不同地理来源的食蟹猴群体Mafa-B序列具有很高的相似性。【结论】越南食蟹猴群体中共表达的Mafa-B等位基因经历了某些抗原的选择，不同地理来源的食蟹猴群体可能微调其Mafa-B序列以适应病原体的选择压力，本文为食蟹猴MHC遗传背景研究奠定了基础。

Abstract:

[Background] Major histocompatibility complex (MHC) is highly polymorphic, thus influencing the outcome of biomedical experiments. Particularly, specific MHC-B alleles are closely related to the development of various diseases. Macaca fascicularis (Mafa) is an important animal model for conducting biomedical research. Currently, Mafa-B alleles in Mafa have not been comprehensively characterized. [Objective] To explore the comprehensive information on Mafa-B alleles in Mafa and to identify co-expression and evolution of Mafa-B alleles. [Methods] Through third-generation sequencing, the genomic information of MHC-B of Mafa was obtained. Then, we designed specific primers to amplify Mafa-B alleles in a cohort of 33 Vietnamese Mafa individuals and characterized Mafa-B alleles with multiple bioinformatics methods. [Results] On the basis of information of 92 Mafa-B alleles, we identified 65 novel Mafa-B alleles. Among them, 8 alleles were identical to sequences previously reported in Mafa of other geographical origins and 32 were also found in macaque populations. In addition, we identified 7 high-frequency Mafa-B lineages and 7 pairs of co-expressed Mafa-B alleles, and detected one potential recombination event. Evolutionary analysis revealed the high similarity of Mafa-B sequences in Mafa from different geographical origins.[Conclusion] These co-expressed Mafa-B alleles in Vietnamese populations have undergone selection pressure by certain antigens, and Mafa populations of different geographical origins may fine-tune the Mafa-B sequences in response to pathogens. This study lays a foundation for elucidating the genetic background of MHC in Mafa.