454 screening of individual MHC variation in an endemic island passerine.
454 screening of individual MHC variation in an endemic island passerine.
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DOI：
10.1007/s00251-014-0822-1
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发表时间：
2015-03
期刊：
影响因子：
3.2
通讯作者：
Richardson, David S.
中科院分区：
文献类型：
--
作者：
Gonzalez-Quevedo, Catalina;Phillips, Karl P.;Spurgin, Lewis G.;Richardson, David S.
关键词：
主要组织相容性复合体(MHC)基因编码的受体是脊椎动物适应性免疫反应的核心。因此，这些基因是研究野生适应性遗传变异的重要遗传标记。在过去的十年里，下一代测序(NGS)越来越多地被用于MHC的基因分型。然而，NGS方法很容易出现测序错误，虽然已经提出了几种方法来处理这一问题，但直到最近还没有标准的指南来验证假定的MHC等位基因。在这项研究中，我们使用454NGS平台筛查了岛上特有的Berthelot‘s piit(Anthelot’s piit)种群中MHC I类外显子3的变异。我们能够对309名重复性很高的个体进行MHC基因分型。我们还能够确定具有低扩增效率的等位基因，因此其在个体内的识别可能不那么可靠。在种群水平上，我们发现Berthelot‘s piit的MHC多样性水平低于其广泛分布的大陆姊妹物种黄雀，并观察到跨物种的多态现象。利用测序数据，我们鉴定了基因转换的特征和贝塞洛特管道中保持功能差异的等位基因的证据。我们还在10个密码子上检测到正选择。因此，本研究表明，我们有一种有效的方法来筛选Berthelot‘s piit中的大型数据集中的单个MHC变异，并提供了可用于未来研究MHC选择的时空模式和尺度的数据。本文的在线版本(doi：10.1007/s00251-0140822-1)包含补充材料，可供授权用户使用。
Genes of the major histocompatibility complex (MHC) code for receptors that are central to the adaptive immune response of vertebrates. These genes are therefore important genetic markers with which to study adaptive genetic variation in the wild. Next-generation sequencing (NGS) has increasingly been used in the last decade to genotype the MHC. However, NGS methods are highly prone to sequencing errors, and although several methodologies have been proposed to deal with this, until recently there have been no standard guidelines for the validation of putative MHC alleles. In this study, we used the 454 NGS platform to screen MHC class I exon 3 variation in a population of the island endemic Berthelot’s pipit (Anthus berthelotii). We were able to characterise MHC genotypes across 309 individuals with high levels of repeatability. We were also able to determine alleles that had low amplification efficiencies, whose identification within individuals may thus be less reliable. At the population level we found lower levels of MHC diversity in Berthelot’s pipit than in its widespread continental sister species the tawny pipit (Anthus campestris), and observed trans-species polymorphism. Using the sequence data, we identified signatures of gene conversion and evidence of maintenance of functionally divergent alleles in Berthelot’s pipit. We also detected positive selection at 10 codons. The present study therefore shows that we have an efficient method for screening individual MHC variation across large datasets in Berthelot’s pipit, and provides data that can be used in future studies investigating spatio-temporal patterns and scales of selection on the MHC. The online version of this article (doi:10.1007/s00251-014-0822-1) contains supplementary material, which is available to authorized users.
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