Data from: Extensive trans-specific polymorphism at the mating type locus of the root decay fungus Heterobasidion

Incompatibility systems in which individuals bearing identical alleles reject each other favor the maintenance of a diversity of alleles. Mushroom mating type loci (MAT) encode for dozens or hundreds of incompatibility alleles whose loss from the population is greatly restricted through negative frequency selection, leading to a system of alleles with highly divergent sequences. Here we use DNA sequences of homeodomain (HD) encoding genes the MAT locus of five closely related species of the root rot basidiomycete Heterobasidion annosum sensu lato to show that the extended coalescence time of MAT alleles greatly predates speciation in the group, contrasting loci outside of MAT that show allele divergences largely consistent with the species phylogeny with those of MAT which show rampant trans-species polymorphism. We observe a roughly six-fold greater genealogical depth and polymorphism of MAT compared to non-MAT which argues for the maintenance of balanced polymorphism for a minimum duration of 24 million years based on a molecular-clock calibrated species phylogeny. As with other basidiomycete HD genes, balancing selection appears to be concentrated at the specificity-determining region in the N-terminus of the protein based on identification of codons under selection and the absence of recombination within the region. However, the elevated polymorphism extends into the non-specificity determining regions as well as a neighboring non-MAT gene, the mitochondrial intermediate peptidase (MIP). In doing so, increased divergence should decrease recombination among alleles and as a by-product create incompatibilities in the functional domains not involved in allele recognition but in regulating sexual development.

携带相同等位基因的个体间相互排斥的不相容系统，有助于维持等位基因多样性。蘑菇交配型位点（Mating Type Locus, MAT）可编码数十乃至数百个不相容等位基因；这类等位基因通过负频率选择（negative frequency selection）极大限制了其在种群中的丢失，进而形成序列高度分化的等位基因系统。本研究针对5种近缘根腐担子菌异担子菌复合群（Heterobasidion annosum sensu lato），利用其MAT位点中编码同源结构域（Homeodomain, HD）的基因的DNA序列开展分析，结果显示MAT等位基因的延伸溯祖时间（coalescence time）远早于该类群的物种形成事件：MAT以外的位点其等位基因分化基本与物种种系统发育树一致，而MAT位点则呈现出广泛的跨物种多态性（trans-species polymorphism）。相较于非MAT位点，我们观测到MAT位点的谱系深度（genealogical depth）与多态性水平约高出6倍；基于分子钟校准的物种系统发育树推算，这类平衡多态性（balanced polymorphism）的维持时长至少可达2400万年。与其他担子菌HD基因一致，通过对受选择密码子的鉴定以及该区域内无重组现象的观测，我们发现平衡选择（balancing selection）主要集中在蛋白质N端的特异性决定区域。不过，升高的多态性不仅延伸至非特异性决定区域，还波及了邻近的非MAT位点基因——线粒体中间肽酶（mitochondrial intermediate peptidase, MIP）。此类序列分化程度的提升会降低等位基因间的重组频率，同时附带产生一类不相容效应：该效应作用于不参与等位基因识别、仅调控有性发育的功能结构域。