Section for Molecular Ecology and Evolution, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
Methods Mol Biol. 2024;2809:275-295. doi: 10.1007/978-1-0716-3874-3_18.
The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.
主要组织相容性复合体 (MHC) 的基因在脊椎动物免疫系统中起着至关重要的作用，在进化生物学中引起了相当大的兴趣。虽然 MHC 在人类（人类白细胞抗原，HLA）和小鼠等模式生物中已经得到了详细的描述，但非模式生物的研究往往缺乏对该基因座结构、遗传变异性和进化特性的先验知识。非模式物种的 MHC 基因分型通常依赖于基于 PCR 的扩增子测序，尽管有几个已发表的方案有助于生成 MHC 序列数据，但缺乏用于下游数据分析的透明和标准化工具。在这里，我介绍了 MHCtools 版本 1.5 的 R 包，其中包含 15 个工具，（i）辅助从高通量扩增子测序数据中进行准确的 MHC 基因分型，并提供标准化的方法来分析 (ii) MHC 多样性、(iii) MHC 超型和 (iv) MHC 单倍型。我希望 MHCtools 将有助于未来非模式物种 MHC 的研究，并有助于增进我们对 MHC 在生态学和进化中的重要作用的理解。
