Stramenopiles are one of the major eukaryotic assemblages. This group comprises a wide range of species including photosynthetic unicellular and multicellular algae, fungus-like osmotrophic organisms and many free-living phagotrophic flagellates. However, the phylogeny of the Stramenopiles, especially relationships among deep-branching heterotrophs, has not yet been resolved because of a lack of adequate transcriptomic data for representative lineages. In this study, we performed multigene phylogenetic analyses of deep-branching Stramenopiles with improved taxon sampling. We sequenced transcriptomes of three deep-branching Stramenopiles: Incisomonas marina, Pseudophyllomitus vesiculosus and Platysulcus tardus. Phylogenetic analyses using 120 protein-coding genes and 56 taxa indicated that Pl. tardus is sister to all other Stramenopiles while Ps. vesiculosus is sister to MAST-4 and form a robust clade with the Labyrinthulea. The resolved phylogenetic relationships of deep-branching Stramenopiles provide insights into the ancestral traits of the Stramenopiles.

超视线虫是主要的真核生物组合之一。这一组包括各种各样的物种，包括光合作用的单细胞和多细胞藻类，真菌样渗透性生物和许多自由生活的吞噬性鞭毛虫。然而，由于缺乏足够的代表性谱系的转录组数据，因此尚未解决超大型蝶形目的系统发育，特别是深支异养生物之间的关系。在这项研究中，我们进行了改进的分类单元采样的深支Strameopiles多基因系统发育分析。我们测序了三个深分支Straneopiles的转录组：海滨Incomononas，Pseudophyllomitus vesiculosus和Tallusuldardus。使用120个蛋白质编码基因和56个分类单元的系统发育分析表明P1。Tardus是所有其他Stramenopiles的姐妹，而Ps。vesiculosus是MAST-4的姐妹，与Labyrinthulea形成牢固的分支。已解决的深分支扁线虫的系统发育关系提供了深入了解扁线虫的祖先特征的信息。