Data from: Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast

In addition to genetic differences between individuals due to nucleotide sequence variation, epigenetic changes experienced by genotypes due to DNA methylation may also contribute to population niche width, an intriguing possibility that remains essentially untested. Using the nectar-living yeast Metschnikowia reukaufii as study subject, we examine the hypothesis that changes in genome-wide DNA methylation patterns underly the ability of this fugitive species to exploit a broad resource range in its heterogeneous patchy environment. Data on floral nectar characteristics and use by M. reukaufii in the wild were combined with laboratory experiments and methylation sensitive amplified polymorphism (MSAP) analyses designed to detect epigenetic responses of single genotypes to variations in sugar environment that mimicked those occurring naturally in nectar. Metschnikowia reukaufii exploited a broad range of resources, occurring in nectar of 48% of species and 52% of families surveyed, and its host plants exhibited broad intra- and interspecific variation in sugar-related nectar features. Under experimental conditions, sugar composition, sugar concentration, and their interaction influenced significantly the mean probability of MSAP markers experiencing a transition from unmethylated to methylated state. The methylation inhibitor 5-Azacytidine had strong inhibitory effects on M. reukaufii proliferation in sugar-containing media, and a direct relationship existed across sugar x concentration experimental levels linking inhibitory effect of 5-Azacytidine and mean per-marker probability of genome-wide methylation. DNA methylation polymorphisms induced by variable sugar environments allowed genotypes to grow successfully in extreme sugar environments, and the broad population niche width of M. reukaufii was largely made possible by environmentally-induced epigenetic changes enabling genotype plasticity in resource use.

除了由核苷酸序列变异导致的个体间遗传差异外，基因型因DNA甲基化（DNA methylation）产生的表观遗传变化（epigenetic changes），也可能对种群生态位宽度产生贡献——这一引人关注的可能性迄今基本未被验证。本研究以栖息于花蜜中的梅奇尼科夫酵母（Metschnikowia reukaufii）为研究对象，旨在检验如下假说：全基因组DNA甲基化模式的改变，是这一机会主义物种在异质斑块环境中利用宽泛资源范围的能力基础。本研究整合了野生环境中M. reukaufii的花蜜特征及其宿主利用情况的相关数据，结合实验室控制实验与旨在检测单一基因型对模拟自然花蜜糖环境变异的表观遗传响应的甲基化敏感扩增多态性（methylation sensitive amplified polymorphism, MSAP）分析。结果显示，M. reukaufii可利用宽泛的资源范围，在所调查的48%的物种与52%的科的花蜜中均可检出该酵母；其宿主植物在糖相关的花蜜特征上表现出广泛的种内与种间变异。在实验条件下，糖组成、糖浓度及其交互作用，均显著影响MSAP标记从未甲基化状态向甲基化状态转变的平均概率。甲基化抑制剂5-氮杂胞苷（5-Azacytidine）对含糖培养基中M. reukaufii的增殖具有强烈抑制作用，且在不同糖浓度实验梯度中，5-氮杂胞苷的抑制效应与全基因组甲基化的每标记平均概率之间存在直接关联。由可变糖环境诱导的DNA甲基化多态性，使得基因型能够在极端糖环境中顺利生长；而M. reukaufii宽泛的种群生态位宽度，在很大程度上得益于环境诱导的表观遗传变化，这些变化赋予了基因型在资源利用方面的可塑性。