Data from: Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions

Background: Recent work suggests that gene duplications may play an important role in the evolution of immunity genes. Passerine birds, and in particular Sylvioidea warblers, have highly duplicated major histocompatibility complex (MHC) genes, which are key in immunity, compared to other vertebrates. However, reasons for this high MHC gene copy number are yet unclear. High-throughput sequencing (HTS) allows MHC genotyping even in individuals with extremely duplicated genes. This HTS data can reveal evidence of selection, which may help to unravel the putative functions of different gene copies, i.e. neofunctionalization. We performed exhaustive genotyping of MHC class I in a Sylvioidea warbler, the sedge warbler, Acrocephalus schoenobaenus, using the Illumina MiSeq technique on individuals from a wild study population. Results: The MHC diversity in 863 genotyped individuals by far exceeds that of any other bird species described to date. A single individual could carry up to 65 different alleles, a large proportion of which are expressed (transcribed). The MHC alleles were of three different lengths differing in evidence of selection, diversity and divergence within our study population. Alleles without any deletions and alleles containing a 6 bp deletion showed characteristics of classical MHC genes, with evidence of multiple sites subject to positive selection and high sequence divergence. In contrast, alleles containing a 3 bp deletion had no sites subject to positive selection and had low divergence. Conclusions: Our results suggest that sedge warbler MHC alleles that either have no deletion, or contain a 6 bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a 3 bp deletion may encode molecules with a different function. This study demonstrates that highly duplicated MHC genes can be characterised with HTS and that selection patterns can be useful for revealing neofunctionalization. Importantly, our results highlight the need to consider the putative function of different MHC genes in future studies of MHC in relation to disease resistance and fitness.

研究背景：近期研究表明，基因重复可能在免疫基因的演化过程中发挥关键作用。雀形目（Passerine）鸟类，尤其是莺下总科（Sylvioidea）的鸣禽，相较于其他脊椎动物，其主要组织相容性复合体（major histocompatibility complex, MHC）基因存在高度重复现象，而该复合体是机体免疫功能的核心组分。但目前这种高MHC基因拷贝数的成因仍未阐明。高通量测序（high-throughput sequencing, HTS）技术可实现存在高度重复基因的个体的MHC基因分型，相关HTS数据能够揭示选择压力的相关证据，有助于解析不同基因拷贝的潜在功能，即新功能化（neofunctionalization）。本研究针对莺下总科的鸣禽——芦莺（Acrocephalus schoenobaenus），采用Illumina MiSeq技术对野生研究种群中的个体开展了全面的MHC I类基因分型工作。

研究结果：本研究对863个个体进行基因分型后发现，其MHC多样性远超迄今已报道的所有鸟类物种。单个个体可携带多达65种不同的等位基因，其中大部分均存在表达（转录）现象。在本研究种群中，MHC等位基因存在三种不同长度，且在选择压力、多样性及序列分化程度上存在显著差异。无碱基缺失的等位基因与携带6 bp缺失的等位基因，均表现出经典MHC基因的特征：存在多个受正向选择的位点，且序列分化程度较高。与之相反，携带3 bp缺失的等位基因未检测到受正向选择的位点，且序列分化程度较低。

研究结论：本研究结果表明，芦莺中无碱基缺失或携带6 bp缺失的MHC等位基因，可编码经典的抗原呈递MHC分子；而携带3 bp缺失的MHC等位基因，或编码功能存在差异的其他分子。本研究证实，借助高通量测序技术可对高度重复的MHC基因进行分型，且选择模式可用于揭示新功能化过程。尤为重要的是，本研究结果凸显了在未来开展MHC与疾病抗性、适合度相关的研究时，需充分考虑不同MHC基因的潜在功能。