Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus

Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for S. brevipes and re-sequenced the whole genomes of 28 individuals from coastal and montane sites in California. We detected two clearly delineated coast and mountain populations with very low divergence. Genomic divergence was restricted to few regions, including a region of extreme divergence containing a gene encoding for a membrane Na+/H+ exchanger known for enhancing salt tolerance in plants and yeast. Our results are consistent with a very recent split between the montane and coastal S. brevipes populations, with few small genomic regions under positive selection and a pattern of dispersal and/or establishment limitation. Furthermore, we identify a putatively adaptive gene that motivates further functional analyses to link genotypes and phenotypes and shed light on the genetic basis of adaptive traits.真菌是一类分布广泛且多样性极高的生物类群，构成了真核生物多样性的重要组成部分。目前学界对真菌种群分化乃至后续物种分化的驱动因子尚缺乏深入认知，尤其是共生菌根真菌（mycorrhizal fungi）。本研究以与松树形成共生关系的风力传播型土壤真菌——短柄乳牛肝菌（Suillus brevipes (Peck) Kuntze）为对象，探究其种群结构与环境适应性。我们组装并注释了短柄乳牛肝菌的参考基因组，并对采自美国加利福尼亚州沿海与山地生境的28个个体开展了全基因组重测序。研究检测到两个界限清晰的沿海种群与山地种群，二者基因组分化程度极低。基因组分化仅局限于少数区域，其中一个高度分化的区域包含一个编码膜Na+/H+转运蛋白的基因，该类蛋白已知可提升植物与酵母菌的耐盐能力。本研究结果支持短柄乳牛肝菌的山地种群与沿海种群发生了极晚近的分化，仅有少量小型基因组区域受到正选择，且呈现出扩散限制或定植限制的分布模式。此外，本研究还鉴定出一个推定的适应性基因，该发现可为后续开展功能分析以关联基因型与表型、阐明适应性性状的遗传基础提供重要方向。