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 6bp 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 3bp 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 6bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a3bp 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.背景：现有研究表明，基因重复事件可能在免疫基因的演化进程中发挥关键作用。相较于其他脊椎动物，雀形目鸟类（尤以莺总科鸣禽为甚）的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MHC基因是机体免疫功能的核心组分。但此类MHC基因高拷贝数的形成机制至今仍不明确。高通量测序（high-throughput sequencing, HTS）技术可实现对存在极端基因重复的个体开展MHC基因分型工作。此类高通量测序数据能够揭示选择作用的相关证据，有助于阐明不同基因拷贝的潜在功能，即新功能化（neofunctionalization）。本研究针对野生研究种群中的个体，采用Illumina MiSeq测序技术，对莺总科鸣禽——芦莺（Acrocephalus schoenobaenus）的MHC I类基因开展了全面的基因分型。 结果：本研究共对863个个体完成MHC基因分型，其MHC多样性远超目前已报道的所有鸟类类群。单个个体最多可携带65种不同的等位基因，其中绝大多数均处于表达（转录）状态。本研究种群内的MHC等位基因存在3种不同的长度类型，且不同长度类型在选择作用证据、多样性水平及序列分化程度上均存在显著差异。无碱基缺失以及携带6bp碱基缺失的等位基因，均表现出经典MHC基因的特征：存在多个受正选择作用的氨基酸位点，且序列分化程度较高。与之相反，携带3bp碱基缺失的等位基因则未检测到受正选择作用的位点，序列分化程度较低。 结论：本研究结果表明，芦莺MHC等位基因中无碱基缺失或携带6bp碱基缺失的类型，均编码经典的抗原呈递MHC分子；而携带3bp碱基缺失的等位基因，可能编码功能迥异的分子。本研究证实，采用高通量测序技术可对高度重复的MHC基因进行分型鉴定，且选择作用模式可用于揭示新功能化过程。尤为重要的是，本研究结果提示，在未来开展MHC基因与疾病抗性及生存适合度相关的研究时，需充分考虑不同MHC基因的潜在功能差异。