Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China.
School of Life Sciences, East China Normal University, Shanghai 200241 China.
Mol Phylogenet Evol. 2019 Oct;139:106565. doi: 10.1016/j.ympev.2019.106565. Epub 2019 Jul 18.
So far, the phylogenetic studies on ciliated protists have mainly based on single locus, the nuclear ribosomal DNA (rDNA). In order to avoid the limitations of single gene/genome trees and to add more data to systematic analyses, information from mitochondrial DNA sequence has been increasingly used in different lineages of ciliates. The systematic relationships in the subclass Scuticociliatia are extremely confused and largely unresolved based on nuclear genes. In the present study, we have characterized 72 new sequences, including 40 mitochondrial cytochrome oxidase c subunit I (COI) sequences, 29 mitochondrial small subunit ribosomal DNA (mtSSU-rDNA) sequences and three nuclear small subunit ribosomal DNA (nSSU-rDNA) sequences from 47 isolates of 44 morphospecies. Phylogenetic analyses based on single gene as well as concatenated data were performed and revealed: (1) compared to mtSSU-rDNA, COI gene reveals more consistent relationships with those of nSSU-rDNA; (2) the secondary structures of mtSSU-rRNA V4 region are predicted and compared in scuticociliates, which can contribute to discrimination of closely related species; (3) neither nuclear nor mitochondrial data support the monophyly of the order Loxocephalida, which may represent some divergent and intermediate lineages between the subclass Scuticociliatia and Hymenostomatia; (4) the assignments of thigmotrichids to the order Pleuronematida and the confused taxon Sulcigera comosa to the genus Histiobalantium are confirmed by mitochondrial genes; (5) both nuclear and mitochondrial data reveal that the species in the family Peniculistomatidae always group in the genus Pleuronema, suggesting that peniculistomatids are more likely evolved from Pleuronema-like ancestors; (6) mitochondrial genes support the monophyly of the order Philasterida, but the relationships among families of the order Philasterida remain controversial due to the discrepancies between their morphological and molecular data.
迄今为止，纤毛原生动物的系统发育研究主要基于单一基因座，即核核糖体 DNA（rDNA）。为了避免单基因/基因组树的局限性，并为系统分析增加更多数据，线粒体 DNA 序列信息已越来越多地用于纤毛动物的不同谱系中。基于核基因，Scuticociliatia 亚纲的系统发育关系极其混乱，很大程度上尚未解决。在本研究中，我们从 47 个形态种的 44 个分离物中，分别对 72 个新序列，包括 40 个线粒体细胞色素氧化酶 c 亚基 I（COI）序列、29 个线粒体小亚基核糖体 DNA（mtSSU-rDNA）序列和 3 个核小亚基核糖体 DNA（nSSU-rDNA）序列进行了特征描述。基于单基因和串联数据的系统发育分析显示：（1）与 mtSSU-rDNA 相比，COI 基因与 nSSU-rDNA 的关系更一致；（2）预测并比较了 scuticociliates 中线粒体 mtSSU-rRNA V4 区的二级结构，有助于鉴别密切相关的物种；（3）核基因和线粒体基因均不支持 Loxocephalida 目是单系的，它可能代表 Scuticociliatia 亚纲和 Hymenostomatia 之间的一些分歧和中间谱系；（4）纤毛原生动物的分类单元 Assignments 为 Pleuronematida 目，分类单元 Sulcigera comosa 为 Histiobalantium 属，这两个分类单元都通过线粒体基因得到确认；（5）核基因和线粒体基因都表明 Peniculistomatidae 科的物种总是属于 Pleuronema 属，这表明纤毛原生动物科更可能是从 Pleuronema 类似的祖先进化而来；（6）线粒体基因支持 Philasterida 目的单系性，但 Philasterida 目各科之间的关系仍存在争议，因为它们的形态学和分子数据存在差异。
