Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates. A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the “core” Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests. Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.

中文翻译：

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评估Hsp90基因在纤毛亚种Hypotricha（Protista，Ciliophora）内推断进化关系的效用。

尽管系统生物学分析越来越多地用于揭示纤毛虫之间的进化关系，但已经测试了相对较少的核蛋白编码基因标记物作为该类推论系统发育的候选者的适用性。在这项研究中，我们调查了热休克蛋白90基因（Hsp90）作为推断亚种纤毛纤毛虫之间系统发生关系的标志物的效用。总共产生了10个亚种的87个新的Hsp90基因序列。其中，有85个是不同的序列。根据这些数据进行的系统发育分析表明：（1）Hsp90基因氨基酸树与小亚基rDNA树具有相似的恢复树系关系的系统发育关系，但缺乏足够的系统发生信号来推断属水平的进化关系。（2）Hsp90基因旁系同源物是最近的，因此不太可能对恢复亚皮特枝形成重大问题；（3）由于某些单子叶植物没有得到各种基因标记的支持，因此需要修改一些亚纲的定义。（4）Sporadotrichida目是副生的，但支持“核心” Urostylida的单性；（5）氧化尿囊菌亚科和泌尿生殖瘤属似乎都不是一元的，但AU检验并未拒绝泌尿生殖的单亲性。我们的研究结果首次证明，Hsp90基因在恢复系统亲缘关系方面可与SSU rDNA媲美，并且其旁系同源物不太可能对恢复hypotrich进化枝构成重大问题。这项研究表明，仔细选择基因标记对于纤毛虫的系统生物学分析具有价值。