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，有利于维持等位基因的多样性。蕈菌的交配型位点（mating type locus, MAT）可编码数十乃至数百个不相容等位基因；这类等位基因因负频率依赖选择（negative frequency selection）而难以从种群中丢失，由此形成序列高度分化的等位基因系统。本研究以5个亲缘关系紧密的广义异担子菌（Heterobasidion annosum sensu lato）根腐担子菌物种的MAT位点同源结构域（homeodomain, HD）编码基因的DNA序列为研究材料，结果表明：MAT等位基因的延长溯祖时间远早于该类群的物种形成事件。MAT位点的等位基因分化与物种系统发育一致性较低，呈现广泛的跨物种多态性（trans-species polymorphism），而MAT以外的位点其等位基因分化则大体与物种系统发育相符。我们观察到，MAT位点的谱系深度与多态性程度约为非MAT位点的6倍；基于分子钟校准的物种系统发育分析，这一结果表明平衡多态性的维持时长至少可达2400万年。与其他担子菌的HD基因类似，基于受选择密码子的鉴定以及该区域内无重组发生的结果，平衡选择似乎集中于蛋白质N端的特异性决定区域。然而，升高的多态性不仅延伸至非特异性决定区域，还波及邻近的非MAT位点基因——线粒体中间肽酶（mitochondrial intermediate peptidase, MIP）。此种情况下，等位基因间分化程度的提升会降低重组发生率，并附带产生功能性结构域的不相容性：这些结构域不参与等位基因识别，而是调控有性发育过程。