Caullerya mesnili is a common and virulent parasite of the water flea, Daphnia. It was classified within the Haplosporidia (Rhizaria) for over a century. However, a recent molecular phylogeny based on the 18S rRNA gene suggested it belonged to the Ichthyosporea, a class of protists closely related to animals within the Opisthokonta clade. The exact phylogenetic position of C. mesnili remained uncertain because it appeared in the 18S rRNA tree with a very long branch and separated from all other taxa, suggesting that its position could be artifactual. A better understanding of its phylogenetic position has been constrained by a lack of molecular markers and the difficulty of obtaining a suitable quantity and quality of DNA from in vitro cultures, as this intracellular parasite cannot be cultured without its host. We isolated and collected spores of C. mesnili and sequenced genomic libraries. Phylogenetic analyses of a newly generated multi-protein data set (22 proteins, 4998 amino acids) and of sequences from the 18S rRNA gene both placed C. mesnili within the Ichthyophonida sub-clade of Ichthyosporea, as sister-taxon to Abeoforma whisleri and Pirum gemmata. Our study highlights the utility of metagenomic approaches for obtaining genomic information from intracellular parasites and for more accurate phylogenetic placement in evolutionary studies.

短毛锦鸡儿是水蚤水蚤的一种常见且有毒的寄生虫。一个多世纪以来，它一直被归类于Haplosporidia（Rhizaria）。然而，最近基于18S rRNA基因的分子系统发育研究表明，它属于鱼眼孢子体，这是一种与Opisthokonta进化枝中的动物密切相关的原生生物。介孢子虫的确切系统发育位置仍然不确定，因为它出现在18S rRNA树中，具有很长的分支，并与所有其他类群分开，表明它的位置可能是人为的。缺乏分子标记以及难以从体外获得合适数量和质量的DNA限制了对它系统发育位置的更好理解培养，因为如果没有宿主，就无法培养这种细胞内寄生虫。我们分离并收集了C. mesnili孢子并测序了基因组文库。对新生成的多蛋白质数据集（22个蛋白质，4998个氨基酸）和来自18S rRNA基因的序列进行系统进化分析，均将麦角隐孢子虫放在鱼眼孢子虫子亚科中，作为惠氏小Ab和皮鲁姆的姐妹分类单元。双子星。我们的研究突出了宏基因组学方法在从细胞内寄生虫获取基因组信息以及在进化研究中更准确地进行系统发育定位方面的实用性。