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Zhang Q, Xu J, Warren A, Yang R, Shen Z, Yi Z. Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora). BMC Evol Biol 2020; 20:86. [PMID: 32677880 PMCID: PMC7364784 DOI: 10.1186/s12862-020-01653-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 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. RESULTS 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. CONCLUSIONS 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.
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Affiliation(s)
- Qi Zhang
- 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
| | - Jiahui Xu
- 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
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Ran Yang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Zhuo Shen
- Institute of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Zhenzhen Yi
- 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.
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Zhang T, Wang C, Katz LA, Gao F. A paradox: rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata (Protista, Ciliophora). SCIENCE CHINA-LIFE SCIENCES 2018; 61:1071-1078. [DOI: 10.1007/s11427-018-9333-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
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Macronuclear Actin copy number variations in single cells of different Pseudokeronopsis (Alveolata, Ciliophora) populations. Eur J Protistol 2017; 59:75-81. [DOI: 10.1016/j.ejop.2017.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 02/01/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
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Yi Z, Huang L, Yang R, Lin X, Song W. Actin evolution in ciliates (Protist, Alveolata) is characterized by high diversity and three duplication events. Mol Phylogenet Evol 2015; 96:45-54. [PMID: 26721556 DOI: 10.1016/j.ympev.2015.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 11/02/2015] [Accepted: 11/16/2015] [Indexed: 01/13/2023]
Abstract
Ciliates possess two distinct nuclear genomes and unique genomic features, including highly fragmented chromosomes and extensive chromosomal rearrangements. Recent transcriptomic surveys have revealed that ciliates have several multi-copy genes providing an ideal template to study gene family evolution. Nonetheless, this process remains little studied in ciliated protozoa and consequently, the evolutionary patterns that govern it are not well understood. In this study, we focused on obtaining fine-scale information relative to ciliate species divergence for the first time. A total of 230 actin gene sequences were derived from this study, among which 217 were from four closely related Pseudokeronopsis species and 13 from other hypotrichous ciliates. Our investigation shows that: (1) At least three duplication events occurred in ciliates: diversification of three actin genes (Actin I, II, III) happened after the divergence of ciliate classes but before that of subclasses. And several recent and genus-specific duplications were followed within Actin I (Sterkiella, Oxytricha, Uroleptus, etc.), Actin II (Sterkiella), respectively. (2) Within the genus Pseudokeronopsis, Actin I gene duplication events happened after P. carnea and P. erythrina diverged. In contrast, in the morphologically similar species P. flava and P. rubra, the duplication event preceded diversification of the two species. The Actin II gene duplication events preceded divergence of the genus Pseudokeronopsis. (3) Phylogenetic analyses revealed that actin is suitable for resolving ciliate classes, but may not be used to infer lower taxon relationships.
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Affiliation(s)
- Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China.
| | - Lijuan Huang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Ran Yang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xiaofeng Lin
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China.
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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