Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China.
Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
BMC Evol Biol. 2020 Jul 16;20(1):86. doi: 10.1186/s12862-020-01653-0.
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.
尽管系统基因组分析越来越多地用于揭示纤毛虫之间的进化关系，但很少有核蛋白编码基因标记被测试其是否适合作为推断该组内系统发育的候选标记。在这项研究中，我们研究了热休克蛋白 90 基因（Hsp90）作为推断纤毛虫系统发育关系的标记的适用性。
总共生成了 10 种 Hypotrich 纤毛虫的 87 个新的 Hsp90 基因序列。其中，85 个是独特的序列。基于这些数据的系统发育分析表明：（1）Hsp90 基因氨基酸树与小亚基 rDNA 树在类别的等级上恢复系统发育关系相当，但缺乏足够的系统发育信号来推断属级别的进化关系；（2）Hsp90 基因旁系同源物是最近的，因此不太可能对恢复纤毛虫进化枝造成重大问题；（3）一些纤毛虫目和科的定义需要修订，因为它们的单系性不被各种基因标记支持；（4）Sporadotrichida 目是并系的，但“核心”Urostylida 的单系性得到支持；（5）Oxytrichinae 亚科和 Urosoma 属似乎都不是单系的，但 AU 检验不拒绝 Urosoma 的单系性。
我们的结果首次表明，Hsp90 基因与 SSU rDNA 相当，可用于恢复类别的系统发育关系，其旁系同源物不太可能对恢复纤毛虫进化枝造成重大问题。本研究表明，对于纤毛虫的系统基因组分析，仔细选择基因标记具有重要价值。
