1
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Jiang C, Gu S, Pan T, Wang X, Qin W, Wang G, Gao X, Zhang J, Chen K, Warren A, Xiong J, Miao W. Dynamics and timing of diversification events of ciliated eukaryotes from a large phylogenomic perspective. Mol Phylogenet Evol 2024; 197:108110. [PMID: 38768875 DOI: 10.1016/j.ympev.2024.108110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Ciliophora, an exceptionally diverse lineage of unicellular eukaryotes, exhibits a remarkable range of species richness across classes in the ciliate Tree of Life. In this study, we have acquired transcriptome and genome data from 40 representative species in seven ciliate classes. Utilizing 247 genes and 105 taxa, we devised a comprehensive phylogenomic tree for Ciliophora, encompassing over 60 % of orders and constituting the most extensive dataset of ciliate species to date. We established a robust phylogenetic framework that encompasses ambiguous taxa and the major classes within the phylum. Our findings support the monophyly of each of two subphyla (Postciliodesmatophora and Intramacronucleata), along with three subclades (Protocruzia, CONTHREEP, and SAPML) nested within Intramacronucleata, and elucidate evolutionary positions among the major classes within the phylum. Drawing on the robust ciliate Tree of Life and three constraints, we estimated the radiation of Ciliophora around 1175 Ma during the middle of the Proterozoic Eon, and most of the ciliate classes diverged from their sister lineage during the latter half of this period. Additionally, based on the time-calibrated tree and species richness pattern, we investigated net diversification rates of Ciliophora and its classes. The global net diversification rate for Ciliophora was estimated at 0.004979 species/Ma. Heterogeneity in net diversification rates was evident at the class level, with faster rates observed in Oligohymenophorea and Spirotrichea than other classes within the subclades CONTHREEP and SAPML, respectively. Notably, our analysis suggests that variations in net diversification rates, rather than clade ages, appear to contribute to the differences in species richness in Ciliophora at the class level.
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Affiliation(s)
- Chuanqi Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Siyu Gu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Pan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xueyan Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weiwei Qin
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Guangying Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xinxin Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kai Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
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2
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Cedrola F, Senra MVX, Morales MJA, Fregulia P, Canesin L, Dias RJP, Solferini VN. Giants' cooperation: a draft genome of the giant ciliate Muniziella cunhai suggests its ecological role in the capybara's digestive metabolism. Microb Genom 2024; 10:001263. [PMID: 38953769 PMCID: PMC11316547 DOI: 10.1099/mgen.0.001263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Several hundred ciliate species live in animals' guts as a part of their microbiome. Among them, Muniziella cunhai (Trichostomatia, Pycnotrichidae), the largest described ciliate, is found exclusively associated with Hydrochoerus hydrochaeris (capybara), the largest known rodent reaching up to 90 kg. Here, we present the sequence, structural and functional annotation of this giant microeukaryote macronuclear genome and discuss its phylogenetic placement. The 85 Mb genome is highly AT rich (GC content 25.71 %) and encodes a total of 11 397 protein-coding genes, of which 2793 could have their functions predicted with automated functional assignments. Functional annotation showed that M. cunhai can digest recalcitrant structural carbohydrates, non-structural carbohydrates, and microbial cell walls, suggesting a role in diet metabolization and in microbial population control in the capybara's intestine. Moreover, the phylogenetic placement of M. cunhai provides insights on the origins of gigantism in the subclass Trichostomatia.
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Affiliation(s)
- Franciane Cedrola
- Laboratório de Diversidade Genética, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | | | - Millke Jasmine Arminini Morales
- Laboratório de Diversidade Genética, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Priscila Fregulia
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | | | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Vera Nisaka Solferini
- Laboratório de Diversidade Genética, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Center for Computational Engineering and Sciences, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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3
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Rotterová J, Pánek T, Salomaki ED, Kotyk M, Táborský P, Kolísko M, Čepička I. Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade. Mol Phylogenet Evol 2024; 191:107991. [PMID: 38092322 DOI: 10.1016/j.ympev.2023.107991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Anaerobes have emerged in several major lineages of ciliates, but the number of independent transitions to anaerobiosis among ciliates is unknown. The APM clade (Armophorea, Muranotrichea, Parablepharismea) represents the largest clade of obligate anaerobes among ciliates and contains free-living marine and freshwater representatives as well as gut endobionts of animals. The evolution of APM group has only recently started getting attention, and our knowledge on its phylogeny and genetics is still limited to a fraction of taxa. While ciliates portray a wide array of alternatives to the standard genetic code across numerous classes, the APM ciliates were considered to be the largest group using exclusively standard nuclear genetic code. In this study, we present a pan-ciliate phylogenomic analysis with emphasis on the APM clade, bringing the first phylogenomic analysis of the family Tropidoatractidae (Armophorea) and confirming the position of Armophorida within Armophorea. We include five newly sequenced single cell transcriptomes from marine, freshwater, and endobiotic APM ciliates - Palmarella salina, Anteclevelandella constricta, Nyctotherus sp., Caenomorpha medusula, and Thigmothrix strigosa. We report the first discovery of an alternative nuclear genetic code among APM ciliates, used by Palmarella salina (Tropidoatractidae, Armophorea), but not by its close relative, Tropidoatractus sp., and provide a comparative analysis of stop codon identity and frequency indicating the precedency to the UAG codon loss/reassignment over the UAA codon reassignment in the specific ancestor of Palmarella. Comparative genomic and proteomic studies of this group may help explain the constraints that underlie UAR stop-to-sense reassignment, the most frequent type of alternative nuclear genetic code, not only in ciliates, but eukaryotes in general.
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Affiliation(s)
- Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic; Department of Marine Sciences, University of Puerto Rico Mayagüez, Mayagüez, PR, USA.
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic; Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, Rhode Island, USA
| | - Michael Kotyk
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic.
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4
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McGowan J, Kilias ES, Alacid E, Lipscombe J, Jenkins BH, Gharbi K, Kaithakottil GG, Macaulay IC, McTaggart S, Warring SD, Richards TA, Hall N, Swarbreck D. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids. PLoS Genet 2023; 19:e1010913. [PMID: 37796765 PMCID: PMC10553269 DOI: 10.1371/journal.pgen.1010913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/10/2023] [Indexed: 10/07/2023] Open
Abstract
The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the "universal" genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel uncultured ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3'UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.
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Affiliation(s)
- Jamie McGowan
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Elisabet Alacid
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - James Lipscombe
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Iain C. Macaulay
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Seanna McTaggart
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Sally D. Warring
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
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5
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Wu T, Cheng T, Cao X, Jiang Y, Al-Rasheid KAS, Warren A, Wang Z, Lu B. On four epibiotic peritrichous ciliates (Protozoa, Ciliophora) found in Lake Weishan Wetland: morphological and molecular data support the establishment of a new genus, Parapiosoma gen. nov., and two new species. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:337-358. [PMID: 37637257 PMCID: PMC10449748 DOI: 10.1007/s42995-023-00184-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/21/2023] [Indexed: 08/29/2023]
Abstract
During a study on the diversity of ciliated protists in Lake Weishan Wetland, the largest wetland in northern China, four epibiotic sessilid peritrichs were isolated from aquatic host animals. Two of them, i.e., Epistylis cambari Kellicott, 1885 and Epistylis lwoffi Fauré-Fremiet, 1943, were known species whereas the other two, i.e., Parapiosoma typicum gen. nov., sp. nov. and Orborhabdostyla gracilis sp. nov., are new to science. The new genus Parapiosoma gen. nov. is characterized by its branched non-contractile stalk, everted peristomial lip, obconical macronucleus and transverse silverlines. Two species are assigned to the new genus, namely Parapiosoma typicum sp. nov. and Parapiosoma gasterostei (Fauré-Fremiet, 1905) comb. nov. Morphologically, P. typicum sp. nov. is recognized by its goblet-shaped zooids, single-layered peristomial lip, dichotomously branched stalk, and infundibular polykinety 3 (P3) containing three equal-length rows. Orborhabdostyla gracilis sp. nov. is characterized by its slender zooid, curved macronucleus, and three equal-length rows in infundibular P3. Improved diagnoses and redescriptions of E. cambari and E. lwoffi are provided including, for the first time, data on the ciliature of E. cambari. Phylogenetic analyses based on SSU rDNA, ITS1-5.8S rDNA -ITS2, and LSU rDNA sequence data strongly support the assertion that the family Epistylididae comprises morphospecies with different evolutionary lineages and indicate that Parapiosoma gen. nov. may represent a new taxon at family level.
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Affiliation(s)
- Tong Wu
- Marine College, Shandong University, Weihai, 264209 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Ting Cheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xiao Cao
- Weishan Fishery Development Service Center, Jining, 277600 China
| | - Yaohan Jiang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | | | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK
| | - Zhe Wang
- Marine College, Shandong University, Weihai, 264209 China
| | - Borong Lu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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6
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Li J, Li S, Su H, Yu M, Xu J, Yi Z. Comprehensive phylogenomic analyses reveal that order Armophorida is most closely related to class Armophorea (Protista, Ciliophora). Mol Phylogenet Evol 2023; 182:107737. [PMID: 36841269 DOI: 10.1016/j.ympev.2023.107737] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/12/2023] [Accepted: 02/19/2023] [Indexed: 02/27/2023]
Abstract
Ciliate species within the class Armophorea are widely distributed in various anaerobic environments, hence they are of great interest to researchers studying evolution and adaptation of eukaryotes to extreme habitats. However, phylogenetic relationships within the class remain largely elusive, most especially assignment of the order Armophorida and classification within the family Metopidae. In this study, we newly sequenced transcriptomes and the SSU rDNA of five armophorean species, Sulfonecta cf. uniserialis (order Armophorida), Nyctotheroides sp. (order Clevelandellida), and Metopus major, M. paraes, and Brachonella contorta (order Metopida). Comprehensive phylogenomic analyses revealed that Armophorea was most closely related to Muranotrichea and Parablepharismea. Our results indicate that the order Armophorida either belongs to Armophorea or represents a new class within APM (Armophorea-Parablepharismea-Muranotrichea). Analyses combining ecological niches and molecular trees showed that APM species might descend from an anaerobic free-living ciliate species. Existing molecular phylogenomic/phylogenetic and morphological evidence indicate that the family Metopidae is non-monophyletic and should be further classified with inclusion of additional lines of evidences. Our results provide new insights into the long-debated relationships within Armophorea.
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Affiliation(s)
- Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Song Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Minjie Yu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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7
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Jiang C, Wang G, Zhang J, Gu S, Wang X, Qin W, Chen K, Yuan D, Chai X, Yang M, Zhou F, Xiong J, Miao W. iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes. Mol Ecol Resour 2023. [PMID: 36912756 DOI: 10.1111/1755-0998.13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/25/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Ciliates are a large group of ubiquitous and highly diverse single-celled eukaryotes that play an essential role in the functioning of microbial food webs. However, their genomic diversity is far from clear due to the need to develop cultivation methods for most species, so most research is based on wild organisms that almost invariably contain contaminants. Here we establish an integrated Genome Decontamination Pipeline (iGDP) that combines homology search, telomere reads-assisted and clustering approaches to filter contaminated ciliate genome assemblies from wild specimens. We benchmarked the performance of iGDP using genomic data from a contaminated ciliate culture and the results showed that iGDP could recall 91.9% of the target sequences with 96.9% precision. We also used a synthetic dataset to offer guidelines for the application of iGDP in the removal of various groups of contaminants. Compared with several popular metagenome binning tools, iGDP could show better performance. To further validate the effectiveness of iGDP on real-world data, we applied it to decontaminate genome assemblies of three wild ciliate specimens and obtained their genomes with high quality comparable to that of previously well-studied model ciliate genomes. It is anticipated that the newly generated genomes and the established iGDP method will be valuable community resources for detailed studies on ciliate biodiversity, phylogeny, ecology and evolution. The pipeline (https://github.com/GWang2022/iGDP) can be implemented automatically to reduce manual filtering and classification and may be further developed to apply to other microeukaryotes.
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Affiliation(s)
- Chuanqi Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jing Zhang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Siyu Gu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueyan Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weiwei Qin
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Dongxia Yuan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaocui Chai
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Mingkun Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fang Zhou
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Wuhan, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming, China
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8
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Wang X, Jiang C, Gu S, Liu Z, Xiong J, Warren A, Miao W. Large-scale phylogenetic analysis provides insights into the diversification and evolution of sessilid peritrich ciliates (Protista: Ciliophora). J Eukaryot Microbiol 2023; 70:e12950. [PMID: 36177660 DOI: 10.1111/jeu.12950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/13/2022] [Accepted: 09/25/2022] [Indexed: 12/01/2022]
Abstract
The Peritrichia is a speciose and morphologically distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades, the phylogenetic relationships of this group have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions, mainly owing to limited sampling. In the present study, we performed expanded phylogenetic analyses of 152 sessilid peritrichs collected from 14 different provinces of China and 141 SSU rDNA peritrich sequences from GenBank. The results of the analyses revealed new divergent relationships between and within major clades that challenge the morphological classification of this group including, (1) the recovery of four major phylogenetically divergent clades in the monophyletic order Sessilida, (2) aboral structures such as the stalk and spasmoneme were evolutionary labile, (3) the stalk or/and spasmoneme was lost in each divergent clade indicating that parallel evolution occurred in sessilid peritrichs and (4) the life cycle and habit drive the diversity of aboral structures as well as diversification and evolution in peritrichs.
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Affiliation(s)
- Xueyan Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuanqi Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Siyu Gu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhencheng Liu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan, China.,CAS Center for Excellence in Animal Evolution and Genetics, Kunming, China
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9
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Wang Z, Feng X, Li L, Al-Rasheid KAS, Warren A, Wang C, Gu Z. New considerations on the phylogeny of Sessilida (Protista: Ciliophora: Peritrichia) based on multiple-gene information, with emphasis on colonial taxa. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:569-583. [PMID: 37078081 PMCID: PMC10077168 DOI: 10.1007/s42995-022-00155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/28/2022] [Indexed: 05/03/2023]
Abstract
The subclass Peritrichia, containing two orders Sessilida and Mobilida, is a major group of ciliates with worldwide distribution and high species diversity. Several studies have investigated the phylogeny of peritrichs; however, the evolutionary relationships and classification of some families and genera within the Sessilida remain unclear. In the present study, we isolated and identified 22 peritrich populations representing four families and six genera and obtained 64 rDNA sequences to perform phylogenetic analyses and assess their systematic relationships. Ancestral character reconstruction was also carried out to infer evolutionary routes within the Sessilida. The results indicate: (1) family Vaginicolidae is monophyletic and acquisition of the typical peritrich lorica represents a single evolutionary divergence; (2) core epistylidids evolved from a Zoothamnium-like ancestor and experienced spasmoneme loss during evolution; (3) Campanella clusters with species in the basal clade and shows stable morphological differences with other epistylidids, supporting its assignment to a separate family; (4) the structure of the peristomial lip may be a genus-level character rather than a diagnostic character for discriminating Epistylididae and Operculariidae, thus a redefinition of Operculariidae should be carried out when more species have been investigated; (5) some characters, such as lifestyle (solitary or colonial), spasmoneme and living habit (sessile or free-swimming), evolved repeatedly among sessilids indicating that species with non-contractile stalks or that are free-swimming have multiple evolutionary routes and might derive from any sessilid lineage without a lorica. The close phylogenetic relationships of some morphologically distinct sessilids imply that the diagnoses of some genera and families should be improved.
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Affiliation(s)
- Zhe Wang
- Marine College, Shandong University, Weihai, 264209 China
- College of Fisheries/Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaoting Feng
- College of Fisheries/Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070 China
| | - Lifang Li
- Marine College, Shandong University, Weihai, 264209 China
| | | | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK
| | - Chundi Wang
- Marine College, Shandong University, Weihai, 264209 China
| | - Zemao Gu
- College of Fisheries/Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070 China
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10
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Wang Z, Chi Y, Li T, Song W, Wang Y, Wu T, Zhang G, Liu Y, Ma H, Song W, Al-Rasheid KAS, Warren A, Lu B. Biodiversity of freshwater ciliates (Protista, Ciliophora) in the Lake Weishan Wetland, China: the state of the art. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:429-451. [PMID: 37078082 PMCID: PMC10077249 DOI: 10.1007/s42995-022-00154-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/20/2022] [Indexed: 05/02/2023]
Abstract
Ciliates are core components of the structure of and function of aquatic microbial food webs. They play an essential role in the energy flow and material circulation within aquatic ecosystems. However, studies on the taxonomy and biodiversity of freshwater ciliates, especially those in wetlands in China are limited. To address this issue, a project to investigate the freshwater ciliates of the Lake Weishan Wetland, Shandong Province, commenced in 2019. Here, we summarize our findings to date on the diversity of ciliates. A total of 187 ciliate species have been found, 94 of which are identified to species-level, 87 to genus-level, and six to family-level. These species show a high morphological diversity and represent five classes, i.e., Heterotrichea, Litostomatea, Prostomatea, Oligohymenophorea, and Spirotrichea. The largest number of species documented are oligohymenophoreans. A comprehensive database of these ciliates, including morphological data, gene sequences, microscope slide specimens and a DNA bank, has been established. In the present study, we provide an annotated checklist of retrieved ciliates as well as information on the sequences of published species. Most of these species are recorded in China for the first time and more than 20% are tentatively identified as new to science. Additionally, an investigation of environmental DNA revealed that the ciliate species diversity in Lake Weishan Wetland is higher than previously supposed. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00154-x.
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Affiliation(s)
- Zhe Wang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Yong Chi
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Tao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Wenya Song
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yunfeng Wang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Tong Wu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Gongaote Zhang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yujie Liu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Honggang Ma
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Weibo Song
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Marine College, Shandong University, Weihai, 264209 China
- Laoshan Laboratory, Qingdao, 266237 China
| | | | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK
| | - Borong Lu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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11
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Wang Z, Wu T, Mu C, Wang Y, Lu B, Warren A, Wang C. The taxonomy and molecular phylogeny of two epibiotic colonial peritrich ciliates (Ciliophora, Peritrichia). Eur J Protistol 2022; 86:125921. [PMID: 36126378 DOI: 10.1016/j.ejop.2022.125921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/03/2022]
Abstract
Two colonial sessilid peritrichs, Epistylis qingdaoensis n. sp. and Carchesium cyclopidarum Nenninger, 1948, were isolated from a marine crustacean and a freshwater mayfly, respectively. Morphological characters for each species were revealed by in vivo observations and silver staining methods. Epistylis qingdaoensis n. sp. is characterized by the apperance of the colony which is up to 250 μm high and usually contains fewer than eight zooids, the single-layered peristomial lip, the conspicuously conical peristomial disc, and the structure of infundibular polykinety 3 which comprises three isometric ciliary rows. Carchesium cyclopidarum is recognized by the colony height of about 600 μm, the small zooid size of 35-50 × 20-30 μm, and the low number of silverlines. Phylogenetic analyses based on small subunit ribosomal DNA sequences were performed to reveal their evolutionary relationships. Surprisingly, neither species clustered with its congeners. Epistylis qingdaoensis n. sp. nested within a clade of Zoothamnium species that was sister to a clade comprising core Epistylis species and several Zoothamnium species. Carchesium cyclopidarum nested within a clade comprising solitary peritrichs and was distantly related to the type species of Carchesium, C. polypinum. These findings imply for the first time that Carchesium is non-monophyletic.
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Affiliation(s)
- Zhe Wang
- Marine College, Shandong University, Weihai 264209, China
| | - Tong Wu
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Changjun Mu
- Weishan Special Aquaculture Base, Jining 277600, China
| | - Ya Wang
- Weishan Fishery Development Service Center, Jining 277600, China
| | - Borong Lu
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Chundi Wang
- Marine College, Shandong University, Weihai 264209, China.
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12
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Rotterová J, Edgcomb VP, Čepička I, Beinart R. Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments. J Eukaryot Microbiol 2022; 69:e12912. [PMID: 35325496 DOI: 10.1111/jeu.12912] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.
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Affiliation(s)
- Johana Rotterová
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roxanne Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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13
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Zheng W, Dou H, Li C, Al-Farraj SA, Byerly A, Stover NA, Song W, Chen X, Li L. Comparative Genome Analysis Reveals Cis-Regulatory Elements on Gene-Sized Chromosomes of Ciliated Protists. Front Microbiol 2022; 13:775646. [PMID: 35265055 PMCID: PMC8899921 DOI: 10.3389/fmicb.2022.775646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Gene-sized chromosomes are a distinct feature of the macronuclear genome in ciliated protists known as spirotrichs. These nanochromosomes are often only several kilobase pairs long and contain a coding region for a single gene. However, the ways in which transcription is regulated on nanochromosomes is still largely unknown. Here, we generated macronuclear genome assemblies for two species of Pseudokeronopsis ciliates to better understand transcription regulation on gene-sized chromosomes. We searched within the short subtelomeric regions for potential cis-regulatory elements and identified distinct AT-rich sequences conserved in both species, at both the 5’ and 3’ end of each gene. We further acquired transcriptomic data for these species, which showed the 5’ cis-regulatory element is associated with active gene expression. Gene family evolution analysis suggests nanochromosomes in spirotrichs may originated approximately 900 million years ago. Together our comparative genomic analyses reveal novel insights into the biological roles of cis-regulatory elements on gene-sized chromosomes.
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Affiliation(s)
- Weibo Zheng
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China.,School of Life Sciences, Ludong University, Yantai, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Huan Dou
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
| | - Chao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Adam Byerly
- Department of Computer Science, Bradley University, Peoria, IL, United States
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria, IL, United States
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, China
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14
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Chen L, Ren Y, Han K, Stoeck T, Jiang J, Pan H. Re-description and molecular phylogeny of the free-swimming peritrichs Hastatella radians and H. aesculacantha (Ciliophora, Peritrichia) from china. Eur J Protistol 2022; 84:125891. [DOI: 10.1016/j.ejop.2022.125891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 11/03/2022]
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15
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Wu T, Wang Z, Lu B, Lei J, Al‐Rasheid KA, Sheng Y. New contribution to the peritrichous genus
Ophrydium
(Protista, Ciliophora) with notes on the morphology, taxonomy and phylogeny of a well‐known species
Ophrydium crassicaule
Penard, 1922. J Eukaryot Microbiol 2022; 69:e12900. [DOI: 10.1111/jeu.12900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tong Wu
- Guangdong Key Laboratory of Subtropical Biodiversity and Biomonitoring School of Life Sciences South China Normal University Guangzhou 510631 China
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao 266003 China
| | - Zhe Wang
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao 266003 China
| | - Borong Lu
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao 266003 China
| | - Jingtao Lei
- Weishan Fishery Development Service Center Jining 277600 China
| | | | - Yalan Sheng
- Guangdong Key Laboratory of Subtropical Biodiversity and Biomonitoring School of Life Sciences South China Normal University Guangzhou 510631 China
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16
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Richardson E, Dacks JB. Distribution of Membrane Trafficking System Components Across Ciliate Diversity Highlights Heterogenous Organelle-Associated Machinery. Traffic 2022; 23:208-220. [PMID: 35128766 DOI: 10.1111/tra.12834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
Abstract
The ciliate phylum is a group of protists noted for their unusual membrane trafficking system and apparent environmental ubiquity; as highly successful microbial predators, they are found in all manner of environments and the ability for specific species to adapt to extremely challenging conditions makes them valued as bioindicators. Ciliates have also been used for many years as cell biological models due to their large cell size and ease of culturing, and for many fundamental cell structures, particularly membrane-bound organelles, ciliates were some of the earliest organisms in which these were observed via microscopy. In this study, we carried out a comparative genomic survey of selected membrane trafficking proteins in a pan-ciliate transcriptome and genome dataset. We observed considerable loss of membrane trafficking system (MTS) proteins that would indicate a loss of machinery that is generally conserved across eukaryotic diversity, even after controlling for potentially incomplete genome representation. In particular, the DSL1 complex was missing in all surveyed ciliates. This protein complex has been shown as involved in peroxisome biogenesis in some model systems, and a paucity of DSL1 components has been indicative of degenerate peroxisome. However, Tetrahymena thermophila (formerly Tetrahymena pyroformis) was one of the original models for visualising peroxisomes. Conversely, the AP3 complex essential for mucocyst maturation in T. thermophila, is poorly conserved despite the presence of secretory lysosome-related organelles across ciliate diversity. We discuss potential resolutions for these apparent paradoxes in the context of the heterogenous distribution of MTS machinery across the diversity of ciliates.
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Affiliation(s)
- Elisabeth Richardson
- University of Alberta School of Public Health, Edmonton, Alberta, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Joel B Dacks
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Department of Life Sciences, The Natural History Museum, London, UK
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17
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Campello-Nunes PH, Silva-Neto ID, Sales MH, Soares CA, Paiva TS, Fernandes NM. Morphological and phylogenetic investigations shed light on evolutionary relationships of the enigmatic genus Copemetopus (Ciliophora, Alveolata), with the proposal of Copemetopus verae sp. nov. Eur J Protistol 2022; 83:125878. [DOI: 10.1016/j.ejop.2022.125878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/06/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
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18
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Zhou W, Wang R, Zhao W, Zou H, Li W, Wu S, Li M, Wang G. A new species of Trichodina lishuiensis n. sp. (Ciliophora: Trichodinidae) in urinary bladder of Odorrana schmackeri (Amphibia: Ranidae) from Zhejiang, China. Acta Trop 2021; 221:106015. [PMID: 34146536 DOI: 10.1016/j.actatropica.2021.106015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Endoparasitic trichodinids are rather rare ciliates. In this study we describe a new species named Trichodina lishuiensis from the bladder of Odorrana schmackeri collected in Zhejiang, China, with the prevalence of 20% (9/45). We identified T. lishuiensis as a new species by morphological comparison and molecular analysis. The ciliates were observed using the dry-silver and protargol staining methods, as well as SEM (scanning electron microscopy). Trichodina lishuiensis is a small species (cell diameter 31.8-43.9 μm), with incompact denticles connection, medium-wide blades and thick rays. We also sequenced a 1712 bp-long fragment of the small subunit ribosomal RNA gene (SSU rRNA). Phylogenetic analyses showed that the new species clustered with Trichodina unionis. The route of transmission of Trichodina species in the urinary bladder remains a mystery. We hypothesize that the transmisison takes place during the amplexus, with eggs and sperm discharged from the cloaca, and that trichodinids 'accompany' the amphibian through its whole life cycle, but further studies are needed to test this hypothesis.
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Affiliation(s)
- Weitian Zhou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runqiu Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, China
| | - Weishan Zhao
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Wenxiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Shangong Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.
| | - Guitang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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19
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Rajter Ľ, Dunthorn M. Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.69602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.
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20
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Wang Z, Wu T, Lu B, Chi Y, Zhang X, Al-Farraj SA, Song W, Warren A, Li L, Wang C. Integrative Studies on a New Ciliate Campanella sinica n. sp. (Protista, Ciliophora, Peritrichia) Based on the Morphological and Molecular Data, With Notes on the Phylogeny and Systematics of the Family Epistylididae. Front Microbiol 2021; 12:718757. [PMID: 34394066 PMCID: PMC8363228 DOI: 10.3389/fmicb.2021.718757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
During an investigation on freshwater peritrichs, a new colonial sessilid ciliate, Campanella sinica n. sp., was isolated from aquatic plants in an artificial freshwater pond in Qingdao, China. Specimen observations of this species were performed both in vivo and using silver staining. C. sinica n. sp. is characterized by the appearance of the mature colony, which is up to 2 cm high and contains more than 1,000 zooids, the asymmetric horn-shaped zooids, strongly everted and multi-layered peristomial lip, the slightly convex peristomial disc, and the well-developed haplokinety and polykinety, which make more than four circuits of the peristome before descending into the infundibulum. The small subunit ribosomal DNA (SSU rDNA), 5.8s rDNA and its flank internal transcribed spacers (ITS1-5.8s rDNA-ITS2), and large subunit ribosomal DNA (LSU rDNA) are sequenced and used for phylogenetic analyses which reveal that the family Epistylididae Kahl, 1933 is non-monophyletic whereas the genus Campanella is monophyletic and nests within the basal clade of the sessilids. The integrative results support the assertion that the genus Campanella represents a separate lineage from other epistylidids, suggesting a further revision of the family Epistylididae is needed. We revise Campanella including the transfer into this genus of a taxon formerly assigned to Epistylis, which we raise to species rank, i.e., Campanella ovata (Nenninger, 1948) n. grad. & n. comb. (original combination Epistylis purneri f. ovata Nenninger, 1948). In addition, we provide a key to the identification of the species of Campanella.
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Affiliation(s)
- Zhe Wang
- Marine College, Shandong University, Weihai, China
- Key Laboratory of Mariculture, Ministry of Education, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Tong Wu
- Key Laboratory of Mariculture, Ministry of Education, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Borong Lu
- Key Laboratory of Mariculture, Ministry of Education, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yong Chi
- Key Laboratory of Mariculture, Ministry of Education, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xue Zhang
- Key Laboratory of Mariculture, Ministry of Education, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Saleh A. Al-Farraj
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Weibo Song
- Marine College, Shandong University, Weihai, China
- Key Laboratory of Mariculture, Ministry of Education, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Lifang Li
- Marine College, Shandong University, Weihai, China
| | - Chundi Wang
- Marine College, Shandong University, Weihai, China
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21
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Rataj M, Vd'ačný P. Cryptic host-driven speciation of mobilid ciliates epibiotic on freshwater planarians. Mol Phylogenet Evol 2021; 161:107174. [PMID: 33831547 DOI: 10.1016/j.ympev.2021.107174] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 01/18/2023]
Abstract
Mobilids are among the most taxonomically diverse but morphologically uniform groups of epibiotic ciliates. They attach to their hosts by means of an adhesive disc as harmless commensals such as Urceolaria, or as parasites causing significant economic loss such as some Trichodina species. We investigated the diversity, species boundaries, and phylogenetic relationships of mobilids associated with freshwater planarians, using 114 new sequences of two mitochondrial (16S rRNA gene and cytochrome c oxidase gene) and five nuclear (18S rRNA gene, ITS1-5.8S-ITS2 region, D1/D2 domains of 28S rRNA gene) markers. Although the morphological disparity of the isolated trichodinids and urceolariids was low, Bayesian coalescent analyses revealed the existence of five distinct evolutionary lineages/species given the seven molecular markers. The occurrence of mobilids perfectly correlated with their planarian hosts: Trichodina steinii and two Urceolaria mitra-like taxa were associated exclusively with the planarian Dugesia gonocephala, Trichodina polycelis sp. n. with the planarian Polycelis felina, and Trichodina schmidtea sp. n. with the planarian Schmidtea polychroa. Host organisms thus very likely constitute sharply isolated niches that might permit speciation of their epibiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different hosts.
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Affiliation(s)
- Matej Rataj
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Peter Vd'ačný
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic.
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22
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Fernandes NM, Campello-Nunes PH, Paiva TS, Soares CAG, Silva-Neto ID. Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing. MICROBIAL ECOLOGY 2021; 81:630-643. [PMID: 33025060 DOI: 10.1007/s00248-020-01612-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/22/2020] [Indexed: 05/20/2023]
Abstract
Rainforest aquatic ecosystems include complex habitats with scarce information on their unicellular eukaryote diversity and community structure. We have investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest, based on the hypervariable V4 region of the 18S-rDNA obtained by high-throughput DNA sequencing. Our analyses detected 409 ciliate taxonomic units (OTUs), mostly attributed to the classes Oligohymenophorea and Spirotrichea. A total of 11 classes, 12 subclasses, 112 genera, and 144 species were reported. We found the following: (a) the ciliate communities are more diverse in freshwater- than in Atlantic Forest-associated brackish environments; (b) the ciliate communities are composed by a small amount of highly abundant OTUs, but a high number of low-abundant or rare OTUs; (c) nearly one-third of the ciliate OTUs share less than 97% sequence identity to reference sequences and (d) phylogenetic inference supports the hypothesis that the V4 region of the Ciliophora 18S-rDNA is a suitable marker for accurate evolutionary inferences at class level. Our results showed that a considerable fraction of the HTS-detected diversity of ciliates from Brazilian Atlantic Forest is not represented in the currently available molecular databases.
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Affiliation(s)
- Noemi M Fernandes
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil.
| | - Pedro H Campello-Nunes
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
| | - Thiago S Paiva
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
| | - Carlos A G Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
| | - Inácio D Silva-Neto
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
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Wang C, Gao Y, Lu B, Chi Y, Zhang T, El-Serehy HA, Al-Farraj SA, Li L, Song W, Gao F. Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl. Mol Phylogenet Evol 2021; 159:107112. [PMID: 33609708 DOI: 10.1016/j.ympev.2021.107112] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
The class Oligohymenophorea is one of the most diverse assemblage of ciliated protists, which are particularly important in fundamental biological studies including understanding the evolutionary relationships among the lineages. Phylogenetic relationships within the class remain largely elusive, especially within the subclass Peniculia, which contains the long-standing problematic taxa Urocentrum and Paranassula. In the present study, we sequenced the genomes and/or transcriptomes of six non-culturable oligohymenophoreans using single-cell sequencing techniques. Phylogenomic analysis was performed based on expanded taxon sampling of 85 taxa, including 157 nuclear genes encoding 36,953 amino acids. The results indicate that: (1) urocentrids form an independent branch that is sister to the clade formed by Scuticociliatia and Hymenostomatia, which, together with the morphological data, supports the establishment of a new subclass, Urocentria n. subcl., within Oligohymenophorea; (2) phylogenomic analysis and ortholog comparison reveal a close relationship between Paranassula and peniculines, providing corroborative evidence for removing Paranassula from Nassulida and elevating it as an order, Paranassulida, within the subclass Peniculia; (3) based on the phylogenomic analyses and morphological data, we hypothesize that Peritrichia is the earliest diverging clade within Oligohymenophorea while Scuticociliatia and Hymenostomatia share the most common ancestor, followed successively by Urocentria and Peniculia. In addition, stop codon analyses indicate that oligohymenophoreans widely use UGA as the stop codon, while UAR are reassigned to glutamate (peritrichs) or glutamine (others), supporting the evolutionary hypothesis.
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Affiliation(s)
- Chundi Wang
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China; Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Yunyi Gao
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Borong Lu
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Yong Chi
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Tengteng Zhang
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China; Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Liao W, Campello-Nunes PH, Gammuto L, Abreu Viana T, de Oliveira Marchesini R, da Silva Paiva T, da Silva-Neto ID, Modeo L, Petroni G. Incorporating mitogenome sequencing into integrative taxonomy: The multidisciplinary redescription of the ciliate Thuricola similis (Peritrichia, Vaginicolidae) provides new insights into the evolutionary relationships among Oligohymenophorea subclasses. Mol Phylogenet Evol 2021; 158:107089. [PMID: 33545277 DOI: 10.1016/j.ympev.2021.107089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/13/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
The evolutionary relationships among Oligohymenophorea subclasses are under debate as the phylogenomic analysis using a large dataset of nuclear coding genes is significantly different to the 18S rDNA phylogeny, and it is unfortunately not stable within and across different published studies. In addition to nuclear genes, the faster-evolving mitochondrial genes have also shown the ability to solve phylogenetic problems in many ciliated taxa. However, due to the paucity of mitochondrial data, the corresponding work is scarce, let alone the phylogenomic analysis based on mitochondrial gene dataset. In this work, we presented the characterization on Thuricola similis Bock, 1963, a loricate peritrich (Oligohymenophorea), incorporating mitogenome sequencing into integrative taxonomy. As the first mitogenome for the subclass Peritrichia, it is linear, 38,802 bp long, and contains two rRNAs, 12 tRNAs, and 43 open reading frames (ORFs). As a peculiarity, it includes a central repeated region composed of tandemly repeated A-T rich units working as a bi-transcriptional start. Moreover, taking this opportunity, the phylogenomic analyses based on a set of mitochondrial genes were also performed, revealing that T. similis, as a representative of Peritrichia subclass, branches basally to other three Oligohymenophorea subclasses, namely Hymenostomatia, Peniculia, and Scuticociliatia. Evolutionary relationships among those Oligohymenophorea subclasses were discussed, also in the light of recent phylogenomic reconstructions based on a set of nuclear genes. Besides, as a little-known species, T. similis was also redescribed and neotypified based on data from two populations collected from wastewater treatment plants (WWTPs) in Brazil and Italy, by means of integrative methods (i.e., living observation, silver staining methods, scanning and transmission electron microscopy, and 18S rDNA phylogeny). After emended diagnosis, it is characterized by: (1) the sewage habitat; (2) the lorica with a single valve and small undulations; (3) the 7-22 µm-long inner stalk; and (4) the presence of only a single postciliary microtubule on the left side of the aciliferous row in the haplokinety. Among Vaginicolidae family, our 18S rRNA gene-based phylogenetic analysis revealed that Thuricola and Cothurnia are monophyletic genera, and Vaginicola could be a polyphyletic genus.
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Affiliation(s)
- Wanying Liao
- Department of Biology, University of Pisa, Via A. Volta 4/6, 56126 Pisa, Italy
| | - Pedro Henrique Campello-Nunes
- Laboratório de Protistologia, Instituto de Biologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, CEP: 21941-902 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Leandro Gammuto
- Department of Biology, University of Pisa, Via A. Volta 4/6, 56126 Pisa, Italy
| | - Tiago Abreu Viana
- Laboratório de Protistologia, Instituto de Biologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, CEP: 21941-902 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Roberto de Oliveira Marchesini
- Laboratório de Protistologia, Instituto de Biologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, CEP: 21941-902 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Thiago da Silva Paiva
- Laboratório de Protistologia, Instituto de Biologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, CEP: 21941-902 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Inácio Domingos da Silva-Neto
- Laboratório de Protistologia, Instituto de Biologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, CEP: 21941-902 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Letizia Modeo
- Department of Biology, University of Pisa, Via A. Volta 4/6, 56126 Pisa, Italy; CISUP, Centro per l'Integrazione della Strumentazione Scientifica dell'Università di Pisa, Lungarno Pacinotti 43, 56126 Pisa, Italy.
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via A. Volta 4/6, 56126 Pisa, Italy; CISUP, Centro per l'Integrazione della Strumentazione Scientifica dell'Università di Pisa, Lungarno Pacinotti 43, 56126 Pisa, Italy.
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Zhang T, Vďačný P. Re-discovery and novel contributions to morphology and multigene phylogeny of Myxophyllum steenstrupi (Ciliophora: Pleuronematida), an obligate symbiont of terrestrial pulmonates. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Abstract
Myxophyllum steenstrupi is a symbiotic ciliate living in the body slime and mantle cavity of terrestrial pulmonates (Gastropoda: Pulmonata). In the present study, M. steenstrupi was re-discovered after almost 30 years and characterized using an integrative morpho-molecular approach for the first time. Myxophyllum is distinguished by a broadly ovate, about 140 × 115 μm-sized body, a nuclear apparatus typically composed of seven macronuclear nodules and a single micronucleus, a central contractile vacuole, a shallow oral cavity situated in the posterior body region and dense somatic ciliature with extensive thigmotactic field. According to the present phylogenetic analyses of two mitochondrial and five nuclear markers, M. steenstrupi is classified in the predominantly free-living order Pleuronematida (Oligohymenophorea: Scuticociliatia). This order also encompasses other taxa isolated from molluscs and traditionally classified along with Myxophyllum in the order Thigmotrichida. The proper classifications of Myxophyllum was hampered by the dramatic remodelling of its oral apparatus (reduction of the paroral membrane and adoral organelles, formation of vestibular kineties), a transformation that was likely induced by its firm association with terrestrial gastropods. The present study also documents that various ciliate lineages independently became commensals or parasites of various aquatic and terrestrial molluscs.
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Affiliation(s)
- Tengyue Zhang
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Peter Vďačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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26
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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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27
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Rotterová J, Salomaki E, Pánek T, Bourland W, Žihala D, Táborský P, Edgcomb VP, Beinart RA, Kolísko M, Čepička I. Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis. Curr Biol 2020; 30:2037-2050.e6. [PMID: 32330419 DOI: 10.1016/j.cub.2020.03.064] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/10/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet adaptations to low-oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrion-related organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate anaerobes (APM ciliates) within the Spirotrichea, Armophorea, and Litostomatea (SAL) group. To deepen our understanding of the evolution of anaerobiosis in ciliates, we predicted the mitochondrial metabolism of cultured representatives from all three classes in the APM clade by using transcriptomic and metagenomic data and performed phylogenomic analyses to assess their evolutionary relationships. The predicted mitochondrial metabolism of representatives from the APM ciliates reveals functional adaptations of metabolic pathways that were present in their last common ancestor and likely led to the successful colonization and diversification of the group in various anoxic environments. Furthermore, we discuss the possible relationship of Parablepharismea to the uncultured deep-sea class Cariacotrichea on the basis of single-gene analyses. Like most anaerobic ciliates, all studied species of the APM clade host symbionts, which we propose to be a significant accelerating factor in the transitions to an obligately anaerobic lifestyle. Our results provide an insight into the evolutionary mechanisms of early transitions to anaerobiosis and shed light on fine-scale adaptations in MROs over a relatively short evolutionary time frame.
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Affiliation(s)
- Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic.
| | - Eric Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Petr Táborský
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic; Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
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Agatha S, Utz LRP, Zufall RA, Warren A. Symposium on Ciliates in Memory of Denis Lynn. Eur J Protistol 2020; 78:125694. [PMID: 33500175 DOI: 10.1016/j.ejop.2020.125694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
Denis Lynn (1947-2018) was an outstanding protistologist, applying multiple techniques and data sources and thus pioneering an integrative approach in order to investigate ciliate biology. For example, he recognized the importance of the ultrastructure for inferring ciliate phylogeny, based on which he developed his widely accepted classification scheme for the phylum Ciliophora. In this paper, recent findings regarding the evolution and systematics of both peritrichs and the mainly marine planktonic oligotrichean spirotrichs are discussed and compared with the concepts and hypotheses formulated by Denis Lynn. Additionally, the state of knowledge concerning the diversity of ciliates in bromeliad phytotelmata and amitosis in ciliates is reviewed.
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Affiliation(s)
- Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria.
| | - Laura R P Utz
- School of Health and Life Sciences, PUCRS, Porto Alegre, Brazil
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK.
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29
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Documentation of a new hypotrich species in the family Amphisiellidae, Lamtostyla gui n. sp. (Protista, Ciliophora) using a multidisciplinary approach. Sci Rep 2020; 10:3763. [PMID: 32111909 PMCID: PMC7048753 DOI: 10.1038/s41598-020-60327-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 02/11/2020] [Indexed: 01/04/2023] Open
Abstract
An integrated approach considering both morphologic and molecular data is now required to improve biodiversity estimations and provide more robust systematics interpretations in hypotrichs, a highly differentiated group of ciliates. In present study, we document a new hypotrich species, Lamtostyla gui n. sp., collected from Chongming wetland, Shanghai, China, based on investigations using living observation, protargol staining, scanning and transmission electron microscopy, and gene sequencing. The new species is mainly recognized by having a short amphisiellid median cirral row composed of four cirri, three frontoventral cirri, three dorsal kinetids, four to eight macronuclear nodules, and small colorless cortical granules distributed as rosettes around dorsal bristles. Transmission electron microscope observation finds the associated microtubules of cirri and pharyngeal discs of L. gui are distinct from those in other hypotrichs. Morphogenesis of this species indicates that parental adoral membranelles retained intact or partial renewed is a potential feature to separate Lamtostyla granulifera-group and Lamtostyla lamottei-group. Phylogenetic analysis based on small subunit ribosomal RNA (rRNA) gene shows that this molecular marker is not useful to resolve phylogenetic relationships of the genus Lamtostyla, as well as many other hypotrichous taxa. We additionally characterize the internal transcribed spacers (ITS) region and the almost complete large subunit rRNA, which will be essential for future studies aimed at solving phylogenetic problems of Lamtostyla, or even the family Amphisiellidae. As a final remark, the critical screening of GenBank using ITS genes of our organism allows us to recognize a large amount of hypotrichous sequences have been misclassified as fungi. This observation suggests that hypotrichs could be frequently found in fungi-rich environment and overlooked by fungal specialists.
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30
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Cedrola F, Senra MVX, Rossi MF, Fregulia P, D’Agosto M, Dias RJP. Trichostomatid Ciliates (Alveolata, Ciliophora, Trichostomatia) Systematics and Diversity: Past, Present, and Future. Front Microbiol 2020; 10:2967. [PMID: 32010077 PMCID: PMC6974537 DOI: 10.3389/fmicb.2019.02967] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/09/2019] [Indexed: 01/14/2023] Open
Abstract
The gastrointestinal tracts of most herbivorous mammals are colonized by symbiotic ciliates of the subclass Trichostomatia, which form a well-supported monophyletic group, currently composed by ∼1,000 species, 129 genera, and 21 families, distributed into three orders, Entodiniomorphida, Macropodiniida, and Vestibuliferida. In recent years, trichostomatid ciliates have been playing a part in many relevant functional studies, such as those focusing in host feeding efficiency optimization and those investigating their role in the gastrointestinal methanogenesis, as many trichostomatids are known to establish endosymbiotic associations with methanogenic Archaea. However, the systematics of trichostomatids presents many inconsistencies. Here, we stress the importance of more taxonomic works, to improve classification schemes of this group of organisms, preparing the ground to proper development of such relevant applied works. We will present a historical review of the systematics of the subclass Trichostomatia highlighting taxonomic problems and inconsistencies. Further on, we will discuss possible solutions to these issues and propose future directions to leverage our comprehension about taxonomy and evolution of these symbiotic microeukaryotes.
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Affiliation(s)
- Franciane Cedrola
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Marcus Vinicius Xavier Senra
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
- Instituto de Recursos Naturais Renováveis, Universidade Federal de Itajubá, Itajubá, Brazil
| | - Mariana Fonseca Rossi
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Priscila Fregulia
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Marta D’Agosto
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
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31
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Morphology and molecular analyses of four epibiotic peritrichs on crustacean and polychaete hosts, including descriptions of two new species (Ciliophora, Peritrichia). Eur J Protistol 2020; 73:125670. [PMID: 31968298 DOI: 10.1016/j.ejop.2019.125670] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/11/2019] [Accepted: 12/28/2019] [Indexed: 12/20/2022]
Abstract
Four epibiotic sessilid peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalisMöbius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.
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Pan B, Chen X, Hou L, Zhang Q, Qu Z, Warren A, Miao M. Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage. Front Microbiol 2019; 10:2819. [PMID: 31921016 PMCID: PMC6920121 DOI: 10.3389/fmicb.2019.02819] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/20/2019] [Indexed: 11/13/2022] Open
Abstract
Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the "Nassophorea-Synhymenia-Phyllopharyngea" assemblage.
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Affiliation(s)
- Bo Pan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, United States
| | - Lina Hou
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhishuai Qu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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Dong J, Li L, Fan X, Ma H, Warren A. Two Urosoma species (Ciliophora, Hypotrichia): A multidisciplinary approach provides new insights into their ultrastructure and systematics. Eur J Protistol 2019; 72:125661. [PMID: 31841799 DOI: 10.1016/j.ejop.2019.125661] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/18/2019] [Accepted: 11/27/2019] [Indexed: 11/29/2022]
Abstract
The general morphology and ultrastructure of two soil hypotrichous ciliates, Urosoma emarginata and U. salmastra, were investigated using light microscopy, scanning electron microscopy and transmission electron microscopy. Phylogenetic analyses, based on the newly sequenced small subunit ribosomal (SSU) rRNA genes, were conducted on three U. emarginata populations and one U. salmastra population. Our findings support for the validity of Perilemmaphora Berger, 2008, a rankless taxon comprising spirotrich ciliates having a perilemma. The cortical granules of both species are extrusomes representing a new type of mucocyst in U. emarginata and possibly a new type of pigmentocyst in U. salmastra. Additionally, the lithosomes were revealed as subglobose structures composed of a low electron-dense, homogeneous inner part and an electron-dense outer part. The ultrastructural features of the cortical granules, together with ontogenetic and molecular phylogenetic data, suggest that the genus Urosoma might need to be divided. It is posited that ultrastructural features of hypotrichous ciliates in general may have important taxonomic value warranting further investigation.
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Affiliation(s)
- Jingyi Dong
- Institute of Evolution and Marine Biodiversity and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lifang Li
- Marine College, Shandong University, Weihai 264209, China
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai 200241, China.
| | - Honggang Ma
- Institute of Evolution and Marine Biodiversity and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
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Lasek-Nesselquist E, Johnson MD. A Phylogenomic Approach to Clarifying the Relationship of Mesodinium within the Ciliophora: A Case Study in the Complexity of Mixed-Species Transcriptome Analyses. Genome Biol Evol 2019; 11:3218-3232. [PMID: 31665294 PMCID: PMC6859813 DOI: 10.1093/gbe/evz233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2019] [Indexed: 11/25/2022] Open
Abstract
Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium-M. rubrum, M. major, and M. chamaeleon-being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination-particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate-requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
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Affiliation(s)
| | - Matthew D Johnson
- Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts
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Zhou T, Wang Z, Yang H, Gu Z. Morphological and molecular identification of epibiontic sessilid Epistylis semiciculus n. sp. (ciliophora, Peritrichia) from Procambarus clarkia (Crustacea, Decapoda) in China. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2019; 10:289-298. [PMID: 31737486 PMCID: PMC6849154 DOI: 10.1016/j.ijppaw.2019.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/21/2019] [Accepted: 09/21/2019] [Indexed: 11/24/2022]
Abstract
Data on sessilinasis from Procambarus clarkia are limited. This study investigates sessilid diversity in Hubei Province, China in 2016. Procambarus clarkia pereopods were covered by two sessilid morphotypes in April and May, and the gills were adhered by one of these two morphotypes (morphotype I) in January. Identifying the two morphotypes according to their morphological characters through live observations and protargol-stained method is difficult. Both morphotypes show almost identical morphological characteristics: zooids present vase-shaped, the length-to-width ratio is 2:1, the semicircle-shaped peristomial disk is evidently above the peristomial lip, single contractile vacuole is located below the peristomial lip, and the oral infraciliature shows identical arrangement which can be distinguished from other Epistylis. However, the morphometric data of the two morphotypes are significant different: body size of morphotype I is 78.9–103.8 × 32.1–54.6 μm, whereas that of morphotypes II is 136.7–171.5 × 60.9–88.0 μm. To further identify the two morphotypes, molecular regions including small subunit ribosomal DNA (SSU rDNA) sequences, large subunit ribosomal DNA (LSU rDNA) sequences, and ITS1-5.8S-ITS2 sequences were used. Results supported that the two morphotypes are single species of genus Epistylis rather than distinct species based in their distinct size ranges and temporal presence events. We assigned it the name E. semiciculus n. sp. with respect to the semicircular peristomial disk. Overall, these findings emphasized the importance of using molecular data to solve the identification confusion caused by ontogenetic processes. This study is the first morphological and molecular characterization of a sessilid isolated from P. clarkia under aquaculture conditions. The first identification of epibiontic sessilid from Procambarus clarkia. Different attachment sites of sessilids in spring and winter. Two morphotypes of a new Epistylis with significant different morphometric data. Species descriptions include morphological (vivo and stained) and molecular data. Present Epistylis distinguished by body shape, contractile vacuole and infraciliature.
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Affiliation(s)
- Tong Zhou
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, PR China
| | - Zhe Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, PR China
| | - Hao Yang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, PR China
| | - Zemao Gu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, PR China
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Chen X, Jiang Y, Gao F, Zheng W, Krock TJ, Stover NA, Lu C, Katz LA, Song W. Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors. Mol Ecol Resour 2019; 19:1292-1308. [PMID: 30985983 PMCID: PMC6764898 DOI: 10.1111/1755-0998.13023] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022]
Abstract
As a model organism for studies of cell and environmental biology, the free-living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), "gene-sized" chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high-quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete "gene-sized" nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5'-TA-3' is conserved at nearly all internally-eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature-resistance to the evolved loss of temperature stress-sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online at Euplotes vannus Genome Database (http://evan.ciliate.org), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.
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Affiliation(s)
- Xiao Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China
| | - Weibo Zheng
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Timothy J. Krock
- Department of Computer Science and Information Systems, Bradley University, Peoria, IL 61625, USA
| | - Naomi A. Stover
- Department of Biology, Bradley University, Peoria, IL 61625, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
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Wang C, Yan Y, Chen X, Al‐Farraj SA, El‐Serehy HA, Gao F. Further analyses on the evolutionary “key‐protist”
Halteria
(Protista, Ciliophora) based on transcriptomic data. ZOOL SCR 2019. [DOI: 10.1111/zsc.12380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chundi Wang
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
- Department of Genetics and Development Columbia University Medical Center New York NY USA
| | - Saleh A. Al‐Farraj
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Hamed A. El‐Serehy
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
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38
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Zhang T, Fan X, Gao F, Al-Farraj SA, El-Serehy HA, Song W. Further analyses on the phylogeny of the subclass Scuticociliatia (Protozoa, Ciliophora) based on both nuclear and mitochondrial data. Mol Phylogenet Evol 2019; 139:106565. [PMID: 31326515 DOI: 10.1016/j.ympev.2019.106565] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 11/24/2022]
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.
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Affiliation(s)
- Tengteng Zhang
- 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
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai 200241 China
| | - Feng Gao
- 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.
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Weibo Song
- 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.
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Chen K, Wang G, Xiong J, Jiang C, Miao W. Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila. J Eukaryot Microbiol 2019; 66:954-965. [PMID: 31188517 DOI: 10.1111/jeu.12746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/05/2019] [Accepted: 05/30/2019] [Indexed: 01/05/2023]
Abstract
Ciliates are unicellular eukaryotes with separate germline and somatic genomes and diverse life cycles, which make them a unique model to improve our understanding of population genetics through the detection of genetic variations. However, traditional sequencing methods cannot be directly applied to ciliates because the majority are uncultivated. Single-cell whole-genome sequencing (WGS) is a powerful tool for studying genetic variation in microbes, but no studies have been performed in ciliates. We compared the use of single-cell WGS and bulk DNA WGS to detect genetic variation, specifically single nucleotide polymorphisms (SNPs), in the model ciliate Tetrahymena thermophila. Our analyses showed that (i) single-cell WGS has excellent performance regarding mapping rate and genome coverage but lower sequencing uniformity compared with bulk DNA WGS due to amplification bias (which was reproducible); (ii) false-positive SNP sites detected by single-cell WGS tend to occur in genomic regions with particularly high sequencing depth and high rate of C:G to T:A base changes; (iii) SNPs detected in three or more cells should be reliable (an detection efficiency of 83.4-97.4% was obtained for combined data from three cells). This analytical method could be adapted to measure genetic variation in other ciliates and broaden research into ciliate population genetics.
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Affiliation(s)
- Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chuanqi Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,CAS Center for Excellence in Animal Evolution and Genetics, Kunming, 650223, China
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Vďačný P, Foissner W. A huge diversity of metopids (Ciliophora, Armophorea) in soil from the Murray River floodplain, Australia. III. Morphology, ontogenesis and conjugation of Metopus boletus nov. spec., with implications for the phylogeny of the SAL supercluster. Eur J Protistol 2019; 69:117-137. [DOI: 10.1016/j.ejop.2019.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 02/02/2023]
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Fernandes NM, Schrago CG. A multigene timescale and diversification dynamics of Ciliophora evolution. Mol Phylogenet Evol 2019; 139:106521. [PMID: 31152779 DOI: 10.1016/j.ympev.2019.106521] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 11/25/2022]
Abstract
Ciliophora is one of the most diverse lineages of unicellular eukaryotes. Nevertheless, a robust timescale including all main lineages and employing properly identified ciliate fossils as primary calibrations is lacking. Here, we inferred a time-calibrated multigene phylogeny of Ciliophora evolution, and we used this timetree to investigate the rates and patterns of lineage diversification through time. We implemented a two-step analytical approach that favored both gene and taxon sampling, reducing the uncertainty of time estimates and yielding narrower credibility intervals on the ribosomal-derived chronogram. We estimate the origin of Ciliophora at 1143 Ma, which is substantially younger than previously proposed ages, and the huge diversity explosion occurred during the Paleozoic. Among the current groups recognized as classes, Spirotrichea diverged earlier, its origin was dated at ca. 850 Ma, and Protocruziea was the younger class, with crown age estimated at 56 Ma. Macroevolutionary analysis detected a significant rate shift in diversification dynamics in the spirotrichean clade Hypotrichia + Oligotrichia + Choreotrichia, which had accelerated speciation rate ca. 570 Ma, during the Ediacaran-Cambrian transition. For all crown lineages investigated, speciation rates declined through time, whereas extinction rates remained low and relatively constant throughout the evolutionary history of ciliates.
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Affiliation(s)
- Noemi Mendes Fernandes
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil.
| | - Carlos G Schrago
- Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil
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42
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Monographic treatment of Paraholosticha muscicola (Ciliophora, Keronopsidae), including morphological and molecular biological characterization of a brackish water population from Korea. Eur J Protistol 2019; 68:48-67. [DOI: 10.1016/j.ejop.2018.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022]
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43
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Jiang CQ, Wang GY, Xiong J, Yang WT, Sun ZY, Feng JM, Warren A, Miao W. Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics. Mol Phylogenet Evol 2019; 132:25-35. [DOI: 10.1016/j.ympev.2018.11.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 10/29/2018] [Accepted: 11/24/2018] [Indexed: 11/30/2022]
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44
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Vd’ačný P, Foissner W. Re-analysis of the 18S rRNA gene phylogeny of the ciliate class Colpodea. Eur J Protistol 2019; 67:89-105. [DOI: 10.1016/j.ejop.2018.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/20/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
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Boscaro V, Syberg-Olsen MJ, Irwin NAT, del Campo J, Keeling PJ. What Can Environmental Sequences Tell Us About the Distribution of Low-Rank Taxa? The Case of Euplotes
(Ciliophora, Spirotrichea), Including a Description of Euplotes enigma
sp. nov. J Eukaryot Microbiol 2018; 66:281-293. [DOI: 10.1111/jeu.12669] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Vittorio Boscaro
- Department of Botany; University of British Columbia; 3529-6270 University Boulevard Vancouver British Columbia V6T1Z4 Canada
| | - Mitchell J. Syberg-Olsen
- Department of Botany; University of British Columbia; 3529-6270 University Boulevard Vancouver British Columbia V6T1Z4 Canada
| | - Nicholas A. T. Irwin
- Department of Botany; University of British Columbia; 3529-6270 University Boulevard Vancouver British Columbia V6T1Z4 Canada
| | - Javier del Campo
- Department of Botany; University of British Columbia; 3529-6270 University Boulevard Vancouver British Columbia V6T1Z4 Canada
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar - CSIC; Passeig Marítim de la Barceloneta, 37-49 08003 Barcelona Catalonia Spain
| | - Patrick J. Keeling
- Department of Botany; University of British Columbia; 3529-6270 University Boulevard Vancouver British Columbia V6T1Z4 Canada
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Boscaro V, Santoferrara LF, Zhang Q, Gentekaki E, Syberg-Olsen MJ, Del Campo J, Keeling PJ. EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates. Environ Microbiol 2018; 20:2218-2230. [PMID: 29727060 DOI: 10.1111/1462-2920.14264] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Abstract
High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11 500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Luciana F Santoferrara
- Department of Marine Sciences, University of Connecticut, Stamford, CT, USA.,Department of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, USA
| | - Qianqian Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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Vďačný P. Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial-Placental Split. Mol Biol Evol 2018; 35:1757-1769. [PMID: 29659942 PMCID: PMC5995207 DOI: 10.1093/molbev/msy071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Trichostome ciliates are among the most conspicuous protists in the gastrointestinal tract of a large variety of vertebrates. However, little is still known about phylogeny of the trichostome/vertebrate symbiotic systems, evolutionary correlations between trichostome extrinsic traits, and character-dependent diversification of trichostomes. These issues were investigated here, using the relaxed molecular clock technique along with stochastic mapping of character evolution, and binary-state speciation and extinction models. Clock analyses revealed that trichostomes colonized the vertebrate gastrointestinal tract ∼135 Ma, that is, near the paleontological minimum for the split of therian mammals into marsupials and placentals. According to stochastic mapping, the last common ancestor of trichostomes most likely invaded the hindgut of a mammal. Although multiple shifts to fish/amphibian or avian hosts and to the foregut compartments took place during the trichostome phylogeny, only transition to the foregut was recognized as a key innovation responsible for the explosive radiation of ophryoscolecid trichostomes after the Cretaceous/Tertiary boundary, when ungulates began their diversification. Since crown radiations of main trichostome lineages follow those of their mammalian hosts and are in agreement with their historic dispersal routes, the present time-calibrated phylogeny might help to elucidate controversies in the geological and molecular timing of the split between marsupials and placental mammals.
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Affiliation(s)
- Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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48
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Abdelkhalek NK, El-Adl MA, Salama MF, Elmishmishy B, Ali MO, El-Ashram A, Hamed MF, Al-Araby MA. Molecular identification of Trichodina compacta Van As and Basson, 1989 (Ciliophora: Peritrichia) from cultured Oreochromis niloticus in Egypt and its impact on immune responses and tissue pathology. Parasitol Res 2018; 117:1907-1914. [PMID: 29717369 DOI: 10.1007/s00436-018-5883-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/16/2018] [Indexed: 11/28/2022]
Abstract
Trichodinids are peritrichous ciliated protozoa that affect both wild and cultured fishes. Several Trichodina species have low host specificity and are morphologically distinct, facilitating their identification based primarily on the presence of adhesive discs and the number of attached denticles. A trichodinid species named Trichodina compacta was first reported by Van As and Basson (1989) (Protozoa: Ciliophora: Peritrichia). However, in trichodinid infestations, morphological characteristics are insufficient for identifying the infesting species. Therefore, molecular and phylogenetic analyses are considered to be promising and useful tools for identifying the infesting species. This study aimed to achieve the molecular identification of a trichodinid infestation in Nile tilapia and to construct the phylogenetic relationships between the identified species and other peritrichous parasites. Moreover, we also aimed to study the pathological and immunological impacts of trichodinids on fry tissue to improve our understanding of the immune responses of teleost fish to trichodinae parasitic infestations and develop a better control method. Here, we used molecular techniques to identify the isolated trichodina species as T. compacta and demonstrated that Trichodina infestation in Nile tilapia is associated with remarkable immunogenic and inflammatory responses (increased il-1β expression and decreased il-8 and tgf-β expression). These findings improve our understanding of the responses of teleost fish to trichodinid parasite infestation and will be helpful for the development of novel control strategies that reverse the inflammatory and immunogenic alterations that occur in infested fish.
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Affiliation(s)
- Nevien K Abdelkhalek
- Internal Medicine, Infectious and Fish Diseases Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.
| | - Mohamed A El-Adl
- Department of Biochemistry, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Mohamed F Salama
- Department of Biochemistry, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Bassem Elmishmishy
- Parasitology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Mayar O Ali
- Animal Husbandry and Genetics Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Ahmed El-Ashram
- Fish Health and Fish Diseases Department, Faculty of Fish Resources, Suez University, Suez, Egypt
| | - Mohamed F Hamed
- Pathology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Moustafa A Al-Araby
- Parasitology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
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Lynn DH, Kolisko M, Bourland W. Phylogenomic Analysis of Nassula variabilis n. sp., Furgasonia blochmanni, and Pseudomicrothorax dubius Confirms a Nassophorean Clade. Protist 2018; 169:180-189. [DOI: 10.1016/j.protis.2018.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 10/18/2022]
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50
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Chen X, Wang Y, Sheng Y, Warren A, Gao S. GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes. Mol Ecol Resour 2018; 18:700-713. [DOI: 10.1111/1755-0998.12750] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/25/2017] [Accepted: 12/26/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Xiao Chen
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yurui Wang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yalan Sheng
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; London UK
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
- College of Marine Life Sciences; Ocean University of China; Qingdao China
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