Further analyses on the phylogeny of the subclass Scuticociliatia (Protozoa, Ciliophora) based on both nuclear and mitochondrial data

Tengteng Zhang; Xinpeng Fan; Feng Gao; Saleh A Al-Farraj; Hamed A El-Serehy; Weibo Song

doi:10.1016/j.ympev.2019.106565

Further analyses on the phylogeny of the subclass Scuticociliatia (Protozoa, Ciliophora) based on both nuclear and mitochondrial data

Mol Phylogenet Evol. 2019 Oct:139:106565. doi: 10.1016/j.ympev.2019.106565. Epub 2019 Jul 18.

Authors

Tengteng Zhang¹, Xinpeng Fan², Feng Gao³, Saleh A Al-Farraj⁴, Hamed A El-Serehy⁴, Weibo Song⁵

Affiliations

¹ 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.
² School of Life Sciences, East China Normal University, Shanghai 200241 China.
³ 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. Electronic address: gaof@ouc.edu.cn.
⁴ Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
⁵ 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; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China. Electronic address: wsong@ouc.edu.cn.

PMID: 31326515
DOI: 10.1016/j.ympev.2019.106565

Abstract

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.

Keywords: COI; Phylogeny; Scuticociliatia; Secondary structure; mtSSU-rDNA; nSSU-rDNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Nucleus / genetics*
DNA, Ribosomal / chemistry
DNA, Ribosomal / classification
DNA, Ribosomal / genetics
Electron Transport Complex IV / chemistry
Electron Transport Complex IV / classification
Electron Transport Complex IV / genetics
Mitochondria / genetics*
Nucleic Acid Conformation
Oligohymenophorea / classification*
Oligohymenophorea / genetics
Phylogeny
RNA, Ribosomal / chemistry
RNA, Ribosomal / classification
RNA, Ribosomal / genetics
Sequence Analysis, DNA

Substances

DNA, Ribosomal
RNA, Ribosomal
Electron Transport Complex IV