Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.

对土壤、木材等环境样本中的细胞核核糖体内转录间隔区（ITS）进行DNA测序，已发现大量全新的真菌支系。尽管对这些全新支系开展系统发育分析是揭示复杂群落结构与多样性的核心环节，但由于该基因座在差异显著的类群间难以实现序列比对，针对环境样本ITS数据的此类分析仍较为匮乏。针对该问题的一种可行方案是同步完成序列比对与系统发育树构建。我们以隶属于子囊菌门（Ascomycota）基干类群地舌菌纲（Geoglossomycetes）的地舌菌的差异较大的ITS序列为研究对象，评估兼具渐进式比对与系统发育树构建功能的新型软件SATé的性能。研究结果表明，SATé可高效生成高质量序列比对结果，并能准确推断地舌菌的系统发育关系。基于包含300条地舌菌序列及逐步演化疏远的真菌支系序列的数据集，我们将公共序列数据库中30条鉴定信息不足的ITS序列归类至地舌菌纲。长期以来，学界一直假设地舌菌与植物存在共生关联，但迄今尚未获得确凿证据。ITS系统发育分析显示，4株外生菌根分离菌株与地舌属（Geoglossum）聚为一支，而非与毛舌菌属（Trichoglossum）地舌菌聚类，这表明环境样本的生态数据挖掘具有可观的应用潜力。环境采样是解决真菌学诸多核心问题的关键，而SATé所实现的同步比对与树构建方法，可为该研究方向提供高效助力。