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Ahmed Shazib SU, Cote-L’Heureux A, Ahsan R, Muñoz-Gómez SA, Lee J, Katz LA, Shin MK. Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596006. [PMID: 38854132 PMCID: PMC11160781 DOI: 10.1101/2024.05.29.596006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genus Spirostomum are abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, some Spirostomum species are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25 Spirostomum species populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37 Spirostomum populations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships among Spirostomum species and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in the Spirostomum genus, three in S. minus, two in S. ambiguum, S. subtilis, and S. teres each. Overall, our fine sampling of closely related Spirostomum populations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genus Spirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.
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Affiliation(s)
- Shahed Uddin Ahmed Shazib
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
| | - Ragib Ahsan
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Sergio A. Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, South Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, South Korea
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
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New contributions to the phylogeny of the ciliate class Heterotrichea (Protista, Ciliophora): analyses at family-genus level and new evolutionary hypotheses. SCIENCE CHINA-LIFE SCIENCES 2020; 64:606-620. [PMID: 33068287 DOI: 10.1007/s11427-020-1817-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/06/2020] [Indexed: 01/15/2023]
Abstract
Heterotrichous ciliates play an important role in aquatic ecosystem energy flow processes and many are model organisms for research in cytology, regenerative biology, and toxicology. In the present study, we combine both morphological and molecular data to infer phylogenetic relationships at family-genus level and propose new evolutionary hypotheses for the class Heterotrichea. The main results include: (1) 96 new ribosomal DNA sequences from 36 populations, representing eight families and 13 genera, including three poorly annotated genera, Folliculinopsis, Ampullofolliculina and Linostomella; (2) the earliest-branching families are Spirostomidae in single-gene trees and Peritromidae in the concatenated tree, but the family Peritromidae probably represents the basal lineage based on its possession of many "primitive" morphological characters; (3) some findings in molecular trees are not supported by morphological evidence, such as the family Blepharismidae is one of the most recent branches and the relationship between Fabreidae and Folliculinidae is very close; (4) the systematic positions of Condylostomatidae, Climacostomidae, and Gruberiidae remain uncertain based either on morphological or molecular data; and (5) the monophyly of each genus included in the present study is supported by the molecular phylogenetic trees, except for Blepharisma in the SSU rDNA tree and Folliculina in the ITS1-5.8S-ITS2 tree.
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Hines HN, McCarthy PJ, Esteban GF. First Records of 'Flagship' Soil Ciliates in North America. Protist 2020; 171:125739. [PMID: 32535352 DOI: 10.1016/j.protis.2020.125739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 10/24/2022]
Abstract
'Flagship' ciliates were investigated from soil samples collected in Florida, USA. This was undertaken to determine if species thought to be restricted to a given world region could be uncovered from similar habitats in a novel location, e.g. another continent. Two species of Condylostomides were discovered, and recorded from the North American continent for the first time. Condylostomides etoschensis was known only from Africa, but was found to be thriving in a Florida study site. An 18S rDNA sequence for this species was determined for the first time. Also discovered from the same study site was the ciliate Condylostomides coeruleus, previously known only from Central and South America. These two 'flagship' ciliates were found in the same habitat, from a continent well outside of their previously recorded biogeographies. Molecular sequencing and microscopy investigations were conducted to form the baseline for future work within this genus. Soil ciliates can obtain large population numbers and form cysts and are therefore likely able to disperse globally. These new records provide additional evidence that large distances, even between continents, do not hinder microbes from thriving globally. The absence of these conspicuously-colored gold and blue ciliates from previous studies is likely due to undersampling, rather than to any physical barriers.
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Affiliation(s)
- Hunter N Hines
- Bournemouth University, Faculty of Science and Technology, Department of Life and Environmental Sciences, Poole, Dorset BH12 5BB, UK; Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL 34946, USA.
| | - Peter J McCarthy
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL 34946, USA
| | - Genoveva F Esteban
- Bournemouth University, Faculty of Science and Technology, Department of Life and Environmental Sciences, Poole, Dorset BH12 5BB, UK
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Chen X, Li J, Xu K. Multigene‐based phylogeny analyses of the controversial family Condylostomatidae (Ciliophora, Heterotrichea). ZOOL SCR 2019. [DOI: 10.1111/zsc.12383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xumiao Chen
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology (Qingdao) Qingdao China
- Center for Ocean Mega‐Science Chinese Academy of Sciences Qingdao 266071 China
| | - Ju Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Kuidong Xu
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology (Qingdao) Qingdao China
- University of Chinese Academy of Sciences Beijing China
- Center for Ocean Mega‐Science Chinese Academy of Sciences Qingdao 266071 China
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Campello-Nunes PH, Fernandes NM, Szokoli F, Petroni G, da Silva-Neto ID. Morphology and Phylogenetic Position of Gruberia lanceolata (Gruber 1884) (Ciliophora, Heterotrichea) from Rio de Janeiro, Brazil. J Eukaryot Microbiol 2018; 65:902-912. [PMID: 29779265 DOI: 10.1111/jeu.12636] [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: 08/29/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 11/29/2022]
Abstract
Ciliates of the genus Gruberia are poorly studied. Consequently, most species lack detailed morphological descriptions, and all gene sequences in GenBank are not classified at the species level. In this study, a detailed morphological description of a population of G. lanceolata from Brazil is presented, based on live and protargol-stained organisms. We also present the 18S rRNA gene sequence and the phylogenetic position of this species. The primary characteristics of G. lanceolata from the Maricá Lagoon are as follows: an elongate fusiform body 280-870 × 40-160 μm in size; rosy cortical granules; a peristome occupying approximately 1/3-1/2 of body length; an adoral zone comprising 115-330 membranelles; a paroral membrane in 35-50 fragments; and a moniliform macronucleus with 11-16 nodules. Based on our observations and data from pertinent literature, we suggest G. beninensis to be a junior synonym of G. lanceolata.
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Affiliation(s)
- Pedro H Campello-Nunes
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro - UFRJ, CEP: 21941-092 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Noemi M Fernandes
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro - UFRJ, CEP: 21941-092 Ilha do Fundão, Rio de Janeiro, Brazil
| | - Franziska Szokoli
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany.,Dipartimento di Biologia, Università di Pisa, via A. Volta 4-6, Pisa, 56126, Italy
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, via A. Volta 4-6, Pisa, 56126, Italy
| | - Inácio D da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro - UFRJ, CEP: 21941-092 Ilha do Fundão, Rio de Janeiro, Brazil
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Chen X, Shazib SUA, Kim JH, Kim MS, Shin MK. New contributions to Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of multiple populations and genes (Ciliophora, Heterotrichea, Gruberiidae). Eur J Protistol 2018; 65:16-30. [PMID: 29793141 DOI: 10.1016/j.ejop.2018.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 04/23/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
Abstract
Gruberia Kahl, 1932 is a species-poor genus comprising only seven named species. Most of these species have not been reinvestigated since the original reports. In the present work, we investigated the taxonomy and phylogeny of Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of morphology and multiple gene sequences from four South Korean populations. This species is mainly characterized by a well-developed peristome region, segmented paroral membrane, and moniliform macronucleus. Some morphological features were not stable among the four populations investigated, such as body shape and size, cell color, and the ratio of oral length to body length. However, our molecular analyses of four different genetic markers - three nuclear DNA markers (18S rDNA, ITS1-5.8S-ITS2 region, D1D2 of 28S rDNA) and one mitochondrial (mt) marker (CO1 gene) - indicated that all Korean populations examined were the same species. Based on our present findings and historic works, we propose that G. calkinsi, G. aculeata, and G. beninensis are junior synonyms of G. lanceolata.
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Affiliation(s)
- Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | | | - Ji Hye Kim
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea; Natural Science Research Institute, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Min Seok Kim
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea; Nakdong River Environment Research Center, Goryeong-gun, Gyeongbuk 40103, South Korea
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea.
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Chen X, Kim JH, Shazib SUA, Kwon CB, Shin MK. Morphology and molecular phylogeny of three heterotrichid species (Ciliophora, Heterotrichea), including a new species of Anigsteinia. Eur J Protistol 2017; 61:278-293. [DOI: 10.1016/j.ejop.2017.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/14/2017] [Accepted: 06/17/2017] [Indexed: 10/19/2022]
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Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Mol Phylogenet Evol 2016; 102:128-44. [DOI: 10.1016/j.ympev.2016.05.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022]
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Yan Y, Fan Y, Chen X, Li L, Warren A, Al-Farraj SA, Song W. Taxonomy and phylogeny of three heterotrich ciliates (Protozoa, Ciliophora), with description of a newBlepharismaspecies. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12369] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Yan
- School of Marine Sciences; Ningbo University; Ningbo 315211 China
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Yangbo Fan
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Xiangrui Chen
- School of Marine Sciences; Ningbo University; Ningbo 315211 China
| | - Lifang Li
- Marine College; Shandong University; Weihai 264209 China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | | | - Weibo Song
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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Fernandes NM, Paiva TDS, da Silva-Neto ID, Schlegel M, Schrago CG. Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data. Mol Phylogenet Evol 2015; 95:229-46. [PMID: 26549427 DOI: 10.1016/j.ympev.2015.10.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 11/25/2022]
Abstract
Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree.
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Affiliation(s)
- Noemi M Fernandes
- Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil.
| | - Thiago da Silva Paiva
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil; Laboratório de Biologia Molecular "Francisco Mauro Salzano", Instituto de Ciências Biológicas, Universidade Federal do Pará, Brazil
| | - Inácio D da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany
| | - Carlos G Schrago
- Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil.
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Fernandes NM, Dias RJP, Schrago CG, Silva-Neto ID. Redescription and Phylogenetic Position of Condylostoma arenarium
Spiegel, 1926 (Ciliophora, Heterotrichea) from Guanabara Bay, Brazil. J Eukaryot Microbiol 2015; 62:722-32. [DOI: 10.1111/jeu.12228] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 02/14/2015] [Accepted: 03/08/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Noemi M. Fernandes
- Laboratório de Biologia Evolutiva Teórica e Aplicada; Dept. de Genética; Inst. de Biologia, CCS; Universidade Federal do Rio de Janeiro; CEP: 21941-617 Ilha do Fundão Rio de Janeiro - RJ Brazil
| | - Roberto J. P. Dias
- Laboratório de Protozoologia; Dept. de Zoologia; ICB; Universidade Federal de Juiz de Fora; CEP: 36036-900 Juiz de Fora - MG Brazil
| | - Carlos G. Schrago
- Laboratório de Biologia Evolutiva Teórica e Aplicada; Dept. de Genética; Inst. de Biologia, CCS; Universidade Federal do Rio de Janeiro; CEP: 21941-617 Ilha do Fundão Rio de Janeiro - RJ Brazil
| | - Inácio D. Silva-Neto
- Laboratório de Protistologia; Dept. de Zoologia; Inst. de Biologia, CCS; Universidade Federal do Rio de Janeiro - UFRJ; CEP: 21941-590 Ilha do Fundão Rio de Janeiro - RJ Brazil
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Morphology and molecular phylogeny of three marine Condylostoma species from China, including two new ones (Ciliophora, Heterotrichea). Eur J Protistol 2015; 51:66-78. [DOI: 10.1016/j.ejop.2014.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 11/22/2022]
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13
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Fernandes NM, da Silva Neto ID, Schrago CG. Morphology and phylogenetic position of an unusual Stentor polymorphus (Ciliophora: Heterotrichea) without symbiotic algae. J Eukaryot Microbiol 2014; 61:305-12. [PMID: 24547923 DOI: 10.1111/jeu.12108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/07/2014] [Accepted: 01/07/2014] [Indexed: 11/27/2022]
Abstract
We investigated the live morphology, infraciliature, and small subunit rRNA gene sequences of an unusual population of Stentor polymorphus without symbiotic algae that was isolated from the southeastern region of Brazil. The morphological and molecular data confirmed the identity of this strain as S. polymorphus. The Brazilian S. polymorphus organism is 850-2,000 μm in length in vivo and has colorless cortical granules, a moniliform macronucleus with 6-12 nodules, somatic ciliature composed of 50-60 kineties, a single contractile vacuole located to the left of the cytostome, and a conspicuous oral pouch, and it does not build a lorica. Based on the phylogenetic analyses, the Brazilian S. polymorphus was located within a cluster consisting of four other S. polymorphus sequences, with high support values using both the Bayesian inference and maximum likelihood algorithms. Our study presents the first report of a S. polymorphus population without its symbionts under natural conditions. On the basis of our findings, we propose that the presence or absence of symbiotic algae should not be used as a taxonomic character for the identification of Stentor species.
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Affiliation(s)
- Noemi M Fernandes
- Departmento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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Phylogenetic relationships of the ciliate class Heterotrichea (Protista, Ciliophora, Postciliodesmatophora) inferred from multiple molecular markers and multifaceted analysis strategy. Mol Phylogenet Evol 2014; 78:118-35. [DOI: 10.1016/j.ympev.2014.05.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/07/2014] [Accepted: 05/09/2014] [Indexed: 01/31/2023]
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15
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Focusing on Genera to Improve Species Identification: Revised Systematics of the Ciliate Spirostomum. Protist 2014; 165:527-41. [DOI: 10.1016/j.protis.2014.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
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16
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Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S, Stock A, Kauff F, Stoeck T. Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Mol Biol Evol 2014; 31:993-1009. [PMID: 24473288 DOI: 10.1093/molbev/msu055] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.
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Affiliation(s)
- Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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Morphology and 18S rDNA gene sequence of Blepharisma sinuosum Sawaya, 1940 (Ciliophora: Heterotrichea) from Brazil. Eur J Protistol 2013; 49:623-33. [PMID: 23694684 DOI: 10.1016/j.ejop.2013.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 04/03/2013] [Accepted: 04/10/2013] [Indexed: 11/24/2022]
Abstract
The morphology and morphometric data of seven populations of Blepharisma sinuosum from southeastern Brazil were investigated. The description is based on live observations, protargol impregnation, and scanning electron microscopy. Blepharisma sinuosum measures 75-255μm in length and 25-93μm in width and has a spindle-shaped body, pink color, a single contractile vacuole located at the posterior end, 50 adoral membranelles, a conspicuous paroral, 17-35 somatic kineties, a moniliform macronucleus with 2-7 connected nodules, and 3-20 micronuclei. Morphological comparisons with similar species were performed and suggest that B. americanum is the junior synonym of B. sinuosum. The 18S rDNA gene sequence of B. sinuosum was obtained and compared with that of other Blepharisma species. The length and GC content of the obtained sequence is 1652bp and 47.03%, respectively, and has a very high structural similarity (99.9%) with the B. undulans sequence. The validity of the classification of Blepharisma species in morphonuclear subgenera is also discussed.
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Vďačný P, Orsi W, Bourland WA, Shimano S, Epstein SS, Foissner W. Morphological and molecular phylogeny of dileptid and tracheliid ciliates: resolution at the base of the class Litostomatea (Ciliophora, Rhynchostomatia). Eur J Protistol 2011; 47:295-313. [PMID: 21641780 PMCID: PMC3234341 DOI: 10.1016/j.ejop.2011.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/18/2011] [Accepted: 04/29/2011] [Indexed: 11/28/2022]
Abstract
Dileptid and tracheliid ciliates have been traditionally classified within the subclass Haptoria of the class Litostomatea. However, their phylogenetic position among haptorians has been controversial and indicated that they may play a key role in understanding litostomatean evolution. In order to reconstruct the evolutionary history of dileptids and tracheliids, and to unravel their affinity to other haptorians, we have used a cladistic approach based on morphological evidence and a phylogenetic approach based on 18S rRNA gene sequences, including eight new ones. The molecular trees demonstrate that dileptids and tracheliids represent a separate subclass, Rhynchostomatia, that is sister to the subclasses Haptoria and Trichostomatia. The Rhynchostomatia are characterized by a ventrally located oral opening at the base of a proboscis that carries a complex oral ciliature. We have recognized two orders within Rhynchostomatia. The new order Tracheliida is monotypic, while the order Dileptida comprises two families: the new, typically bimacronucleate family Dimacrocaryonidae and the multimacronucleate family Dileptidae. The Haptoria evolved from the last common ancestor of the Litostomatea by polarization of the body, the oral opening locating more or less apically and the oral ciliature simplifying. The Trichostomatia originated from a microaerophylic haptorian by further simplification of the oral ciliature, possibly due to an endosymbiotic lifestyle.
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Affiliation(s)
- Peter Vďačný
- Department of Zoology, Comenius University, Mlynská dolina B-1, SK 84215 Bratislava, Slovak Republic.
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Shimano S, Sanbe M, Kasahara Y. Linkage between light microscopic observations and molecular analysis by single-cell PCR for ciliates. Microbes Environ 2011; 23:356-9. [PMID: 21558732 DOI: 10.1264/jsme2.me08532] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The molecular analysis of ciliates for identification and phylogeny is usually conducted through PCR amplification and DNA sequencing, with DNA extracted from a large number of cells. Therefore, the analysis of ciliates is limited to only those species that can be cultured. We propose a single-cell PCR procedure to overcome the difficulty in the analysis of unculturable species. The procedure has been tested on 6 Stichotrichia strains and uncultured Levicoleps biwae cells, targeting 18S rRNA gene sequences, after carrying out microscopic observations and obtaining photographic records. This procedure enables the systematic analysis of unculturable ciliate strains in natural environments by linking the morphology and genotype of a single cell.
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Affiliation(s)
- Satoshi Shimano
- Environment Education Center, Miyagi University of Education, 149 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
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Small subunit ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 gene sequences of 21 strains of the parasitic scuticociliate Miamiensis avidus (Ciliophora, Scuticociliatia). Parasitol Res 2010; 108:1153-61. [PMID: 21113725 DOI: 10.1007/s00436-010-2157-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 11/07/2010] [Indexed: 10/18/2022]
Abstract
The scuticociliate Miamiensis avidus is a histophagous parasite that causes high mortality in cultured marine fishes. Small subunit ribosomal RNA (SSU rRNA) and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes were analyzed for 21 strains of M. avidus isolated from diseased olive flounder (Paralichthys olivaceus), ridged-eye flounder (Pleuronichthys cornutus), and spotted knifejaw (Oplegnathus fasciatus) in Korea and Japan (collected in 2003-2007). Analysis of SSU rRNA gene sequences (1,759 bp) indicates they are very conserved with less than 0.17% (3 nucleotides) differences suggesting that SSU rRNA are useful to identify M. avidus; however, the cox1 gene (900 bp) has higher variations with intraspecific divergences up to 5.67% (51 nucleotides). A distance tree of cox1 gene sequences based on a neighbor-joining analysis can separate 21 strains into five cox1 types (two heterogeneous clusters and three individual branches). The cox1-type matches with serotype of strains but do not reflect geographical origins, host species, or pathogenicity.
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Dunthorn M, Foissner W, Katz LA. Expanding character sampling for ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker. Protist 2010; 162:85-99. [PMID: 20708960 DOI: 10.1016/j.protis.2010.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 06/12/2010] [Indexed: 11/28/2022]
Abstract
Molecular systematics of ciliates, particularly at deep nodes, has largely focused on increasing taxon sampling using the nuclear small subunit rDNA (nSSU-rDNA) locus. These previous analyses have generally been congruent with morphologically-based classifications, although there is extensive non-monophyly at many levels. However, caution is needed in interpreting these results as nSSU-rDNA is just a single molecular marker. Here the mitochondrial small subunit rDNA (mtSSU-rDNA) is evaluated for deep ciliate nodes using the Colpodea as an example. Overall, well-supported nodes in the mtSSU-rDNA and concatenated topologies are well supported in the nSSU-rDNA topology; e.g., the non-monophyly of the Cyrtolophosidida. The two moderately- to well-supported incongruences between the loci are the placement of the Sorogenida andColpoda aspera.Our analyses of mtSSU-rDNA support the conclusion, originally derived from nSSU-rDNA, that the morphological characters used in taxonomic circumscriptions of the Colpodea represent a mixture of ancestral and derived states. This demonstration of the efficacy of the mtSSU-rDNA will enable phylogenetic reconstructions of deep nodes in the ciliate tree of life to move from a single-locus to a multi-locus approach.
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Andreoli I, Mangini L, Ferrantini F, Santangelo G, Verni F, Petroni G. Molecular phylogeny of unculturable Karyorelictea (Alveolata, Ciliophora). ZOOL SCR 2009. [DOI: 10.1111/j.1463-6409.2009.00395.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Miao M, Song W, Clamp JC, Al-Rasheid KAS, Al-Khedhairy AA, Al-Arifi S. Further consideration of the phylogeny of some "traditional" heterotrichs (Protista, Ciliophora) of uncertain affinities, based on new sequences of the small subunit rRNA gene. J Eukaryot Microbiol 2009; 56:244-50. [PMID: 19527351 DOI: 10.1111/j.1550-7408.2009.00391.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The systematic relationships and taxonomic positions of the traditional heterotrich genera Condylostentor, Climacostomum, Fabrea, Folliculina, Peritromus, and Condylostoma, as well as the licnophorid genus Licnophora, were re-examined using new data from sequences of the gene coding for small subunit ribosomal RNA. Trees constructed using distance-matrix, Bayesian inference, and maximum-parsimony methods all showed the following relationships: (1) the "traditional" heterotrichs consist of several paraphyletic groups, including the current classes Heterotrichea, Armophorea and part of the Spirotrichea; (2) the class Heterotrichea was confirmed as a monophyletic assemblage based on our analyses of 31 taxa, and the genus Peritromus was demonstrated to be a peripheral group; (3) the genus Licnophora occupied an isolated branch on one side of the deepest divergence in the subphylum Intramacronucleata and was closely affiliated with spirotrichs, armophoreans, and clevelandellids; (4) Condylostentor, a recently defined genus with several truly unique morphological features, is more closely related to Condylostoma than to Stentor; (5) Folliculina, Eufolliculina, and Maristentor always clustered together with high bootstrap support; and (6) Climacostomum occupied a paraphyletic position distant from Fabrea, showing a close relationship with Condylostomatidae and Chattonidiidae despite of modest support.
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Affiliation(s)
- Miao Miao
- Ocean University of China, Qingdao, China
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