Biedrzycka Aleksandra, O'Connor Emily, Sebastian Alvaro, Migalska Magdalena, Radwan Jacek, Zając Tadeusz, Bielański Wojciech, Solarz Wojciech, Ćmiel Adam, Westerdahl Helena
Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland.
Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Ecology Building, Sölvegatan 37, 223 62, Lund, Sweden.
BMC Evol Biol. 2017 Jul 5;17(1):159. doi: 10.1186/s12862-017-0997-9.
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.
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.
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.
近期研究表明，基因复制可能在免疫基因的进化中发挥重要作用。与其他脊椎动物相比，雀形目鸟类，尤其是莺科鸟类，拥有高度复制的主要组织相容性复合体（MHC）基因，而MHC基因在免疫过程中起着关键作用。然而，MHC基因拷贝数如此之高的原因尚不清楚。高通量测序（HTS）即使对于基因极度复制的个体也能进行MHC基因分型。这些HTS数据能够揭示选择的证据，这可能有助于阐明不同基因拷贝的假定功能，即新功能化。我们使用Illumina MiSeq技术对来自野生研究群体的草甸鹀（Acrocephalus schoenobaenus）这一莺科鸟类的MHC I类基因进行了详尽的基因分型。
863个基因分型个体的MHC多样性远远超过了迄今所描述的任何其他鸟类物种。单个个体最多可携带65个不同的等位基因，其中很大一部分是表达的（转录的）。MHC等位基因有三种不同长度，在我们的研究群体中，它们在选择证据、多样性和分化方面存在差异。没有任何缺失的等位基因和含有6bp缺失的等位基因表现出经典MHC基因的特征，有多个位点受到正选择的证据且序列差异高。相比之下，含有3bp缺失的等位基因没有受到正选择的位点且差异低。
我们的结果表明，没有缺失或含有6bp缺失的草甸鹀MHC等位基因编码经典的抗原呈递MHC分子。相比之下，含有3bp缺失的MHC等位基因可能编码具有不同功能的分子。这项研究表明，高度复制的MHC基因可以通过HTS进行表征，并且选择模式有助于揭示新功能化。重要的是，我们的结果强调在未来关于MHC与抗病性和适应性的研究中，需要考虑不同MHC基因的假定功能。
