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Do EH, Kwon HI, Yeo JH, Quintela-Alonso P, Jung JH. Morphology and molecular phylogeny of Euplotes baugilensis n. sp. (Ciliophora, Spirotrichea), with an illustrated key to Euplotes species with reduced cirri. Eur J Protistol 2024; 95:126110. [PMID: 39180835 DOI: 10.1016/j.ejop.2024.126110] [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: 05/22/2024] [Revised: 07/19/2024] [Accepted: 07/19/2024] [Indexed: 08/27/2024]
Abstract
Euplotes baugilensis n. sp. was discovered in a temporary puddle that formed after rainfall on a mountain footpath near Gangneung-Wonju National University in Gangneung, South Korea. After isolation, a pure culture was established, and the new species was examined using live observation, silver-impregnation (protargol and 'wet' silver nitrate), scanning electron microscopy, and the analysis of the 18S rRNA gene sequence. Morphologically, E. baugilensis n. sp. is characterized by small body size (on average 49 × 31 µm in vivo), 9 ordinary fronto-ventral cirri (cirrotype-9) with one reduced cirrus V/2 (composed of four non-ciliated basal bodies), 5 transverse cirri, 7 or 8 dorsolateral kineties, 6 dorsal prominent ridges, and a dargyrome (silverline system) of double type. In this study, we have used a combination of morphological and molecular techniques to characterize E. baugilensis n. sp. and determine its phylogenetic position within the genus Euplotes. Molecular analysis using 18S rRNA gene sequences indicated that E. baugilensis n. sp. is most closely related to E. curdsi (with a sequence identity of 96.8 %).
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Affiliation(s)
- Eun-Hye Do
- Department of Biology, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea; Department of Convergence Medical Science, Pusan National University, Yangsan, Gyeongsangnam-do, Republic of Korea
| | - Hye-In Kwon
- Department of Biology, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Jeong Hyeon Yeo
- Department of Biology, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Pablo Quintela-Alonso
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain.
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea.
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2
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Serra V, Gammuto L, Nitla V, Castelli M, Lanzoni O, Sassera D, Bandi C, Sandeep BV, Verni F, Modeo L, Petroni G. Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont "Candidatus Pinguicoccus supinus" sp. nov. Sci Rep 2020; 10:20311. [PMID: 33219271 PMCID: PMC7679464 DOI: 10.1038/s41598-020-76348-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/30/2020] [Indexed: 01/30/2023] Open
Abstract
Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as "holobionts". We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.
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Affiliation(s)
- Valentina Serra
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Leandro Gammuto
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Venkatamahesh Nitla
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Michele Castelli
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Olivia Lanzoni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Claudio Bandi
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
| | | | - Franco Verni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Letizia Modeo
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
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Valbonesi A, Di Giuseppe G, Vallesi A, Luporini P. Two new species of Euplotes with cirrotype-9, Euplotes foissneri sp. nov. and Euplotes warreni sp. nov. (Ciliophora, Spirotrichea, Euplotida), from the coasts of Patagonia: implications from their distant, early and late branching in the Euplotes phylogenetic tree. Int J Syst Evol Microbiol 2020; 71. [PMID: 33201796 DOI: 10.1099/ijsem.0.004568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two new Euplotes species have been isolated from cold shallow sandy sediments of the extreme Southern Chilean coasts: Euplotes foissneri sp. nov., from a low-salinity site at Puerto Natales on the Pacific coast, and Euplotes warreni sp. nov., from a marine site at Punta Arenas on the Atlantic coast. Euplotes foissneri has a medium body size (53×36 µm in vivo), a dorsal surface marked by six prominent ridges, a double dargyrome, six dorsal and two ventrolateral kineties, a buccal field extending to about 3/4 of the body length, an adoral zone composed of 28-32 membranelles, and nine fronto-ventral, five transverse and two or three caudal cirri. The bulky, hook-, horseshoe- or 3-shaped macronucleus is associated with one sub-spherical micronucleus. The central body region hosts taxonomically unidentified endosymbiotic eubacteria. Euplotes warreni has a small body size (39×27 µm in vivo), a smooth dorsal surface marked by three deep grooves, a double dargyrome, four dorsal and two ventrolateral kineties, a buccal field extending to about 2/3 of the body length, an adoral zone composed of 23-25 adoral membranelles, and nine fronto-ventral, five transverse and three caudal cirri. The macronucleus is hook- or C-shaped and associated with one spherical micronucleus. Endosymbiotic bacteria belonging to the genus Francisella reside preferentially in the anterior cell region. Both species lack the fronto-ventral cirrus numbered 'V/2', whereby their cirrotype-9 conforms to the so-called 'pattern I', which is the basic distinctive trait of the genus Euplotopsis Borror and Hill, 1995. Phylogenetic analyses of small subunit rRNA gene sequences, however, classify E. warreni into its own early branching clade and E. foissneri into a late branching clade. This indicates a polyphyletic nature and taxonomic inconsistency of the genus Euplotopsis, which was erected to include Euplotes species with cirrotype-9 pattern I.
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Affiliation(s)
- Alessandro Valbonesi
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Bioscience and Veterinary Medicine, University of Camerino, Italy
| | | | - Adriana Vallesi
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Bioscience and Veterinary Medicine, University of Camerino, Italy
| | - Pierangelo Luporini
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Bioscience and Veterinary Medicine, University of Camerino, Italy
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4
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Méndez-Sánchez D, Mayén-Estrada R, Hu X. Euplotes octocarinatus Carter, 1972 (Ciliophora, Spirotrichea, Euplotidae): Considerations on its morphology, phylogeny, and biogeography. Eur J Protistol 2020; 74:125667. [DOI: 10.1016/j.ejop.2019.125667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 11/28/2022]
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A barotolerant ciliate isolated from the abyssal deep sea of the North Atlantic: Euplotes dominicanus sp. n. (Ciliophora, Euplotia). Eur J Protistol 2020; 73:125664. [PMID: 31978632 DOI: 10.1016/j.ejop.2019.125664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 11/22/2022]
Abstract
A new Euplotes species, isolated from abyssal depths (>4000 m) of the North Atlantic Ocean, was described based on morphology, ciliary pattern and molecular data. Euplotes dominicanus sp. n. is characterized by a small body size (29-40 × 17-27 μm in vivo), 18-22 adoral membranelles, 10 frontoventral, five transverse and two left marginal cirri and one caudal cirrus, five or six dorsolateral kineties with 7-9 dikinetids in mid-dorsolateral kinety (DK3), and dorsal silverline system of the double-eurystomus type. Phylogenetic analyses inferred from 18S rRNA sequences show that Euplotes dominicanus sp. n. is most closely related to E. curdsi, with a sequence similarity of 97.6 %. Euplotes dominicanus sp. n. was able to survive hydrostatic pressures up to 500 bar indicating its barotolerance. Metabarcoding data demonstrate the presence of E. dominicanus sp. n. in sediments of several deep-sea basins.
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Lian C, Zhang T, Al-Rasheid KA, Yu Y, Jiang J, Huang J. Morphology and SSU rDNA-based phylogeny of two Euplotes species from China: E. wuhanensis sp. n. and E. muscicola Kahl, 1932 (Ciliophora, Euplotida). Eur J Protistol 2019; 67:1-14. [DOI: 10.1016/j.ejop.2018.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 11/25/2022]
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7
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Zhao Y, Yi Z, Warren A, Song W. Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora). Proc Biol Sci 2019; 285:rspb.2017.2159. [PMID: 29367393 DOI: 10.1098/rspb.2017.2159] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/03/2018] [Indexed: 11/12/2022] Open
Abstract
Recent advances in high-throughput sequencing and metabarcoding technologies are revolutionizing our understanding of the diversity and ecology of microbial eukaryotes (protists). The interpretation of protist diversity and the elucidation of their ecosystem function are, however, impeded by problems with species delimitation, especially as it applies to molecular taxonomy. Here, using the ciliate Euplotes as an example, we describe approaches for species delimitation based on integrative taxonomy by using evolutionary and ecological perspectives and selecting the most appropriate metabarcoding gene markers as proxies for species units. Our analyses show that: Euplotes (sensu lato) comprises six distinct clades, mainly as result of ecological speciation; the validity of the genera Euplotes (sensu stricto), Euplotoides, Euplotopsis and Moneuplotes are not supported; the vannus-type group, which includes species without distinct morphological differences, seems to be undergoing incipient speciation and contains cryptic species; the hypervariable V4 region of the small subunit rDNA and D1-D2 region of the large subunit rDNA are the promising candidates for general species delimitation in Euplotes.
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Affiliation(s)
- Yan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China .,Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, People's Republic of China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, People's Republic of China
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Yan Y, Fan Y, Luo X, El-Serehy HA, Bourland W, Chen X. New contribution to the species-rich genus Euplotes: Morphology, ontogeny and systematic position of two species (Ciliophora; Euplotia). Eur J Protistol 2018; 64:20-39. [PMID: 29621653 DOI: 10.1016/j.ejop.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 10/17/2022]
Abstract
The morphology, ontogeny and phylogeny of two Euplotes species, E. estuarinus sp. nov. and a population of E. platystoma Dragesco and Dragesco-Kernéis, 1986, both collected from tropical brackish waters in south China, were investigated based on living morphology, ciliary pattern and molecular data. Euplotes estuarinus sp. nov. is small (about 60 × 40 μm in vivo), has a dargyrome of the double-eurystomus type, and the transverse cirri are arranged in two groups, with two left and three right ones. The original description of the poorly known species, E. platystoma, is brief, and the species was never investigated using live observation and molecular methods Hence, we provided a detailed redescription. Some stages of their morphogenesis were observed which proceed in the same pattern as in their congeners. The new species E. estuarinus sp. nov. clusters with E. curdsi, differing only by 1 bp in their SSU rRNA gene sequences, which is likely due to the recent speciation event and the limited resolution of the SSU rRNA gene at species level in this group as the two species are clearly morphologically distinct.
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Affiliation(s)
- Ying Yan
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yangbo Fan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; School of Civil and Environment Engineering, Harbin Institute of Technology, Shenzhen 518000, China
| | - Xiaotian Luo
- Department of Biological Sciences, Boise State University, Boise 83725, USA
| | - Hamed A El-Serehy
- Department of Zoology, King Saud University, Riyadh 11451, Saudi Arabia
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise 83725, USA
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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Syberg-Olsen MJ, Irwin NAT, Vannini C, Erra F, Di Giuseppe G, Boscaro V, Keeling PJ. Biogeography and Character Evolution of the Ciliate Genus Euplotes (Spirotrichea, Euplotia), with Description of Euplotes curdsi sp. nov. PLoS One 2016; 11:e0165442. [PMID: 27828996 PMCID: PMC5102374 DOI: 10.1371/journal.pone.0165442] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 10/06/2016] [Indexed: 01/08/2023] Open
Abstract
Ciliates comprise a diverse and ecologically important phylum of unicellular protists. One of the most specious and best-defined genera is Euplotes, which constitutes more than 70 morphospecies, many of which have never been molecularly tested. The increasing number of described Euplotes taxa emphasizes the importance for detailed characterizations of new ones, requiring standardized morphological observations, sequencing of molecular markers and careful comparison with previous literature. Here we describe Euplotes curdsi sp. nov., distinguishable by the combination of the following features: 45–65 μm length, oval or elongated shape with both ends rounded, narrow peristome with 25–34 adoral membranelles, conspicuous paroral membrane, double-eurystomus dorsal argyrome type, 6–7 dorsolateral kineties and 10 frontoventral cirri. Three populations of the novel species have been found in brackish and marine samples in the Mediterranean and the White Sea. We provide the SSU rRNA gene sequences of these populations, and an updated phylogeny of the genus Euplotes. Using the molecular phylogenetic tree, we inferred aspects of the biogeographical history of the genus and the evolution of its most important taxonomic characters in order to provide a frame for future descriptions. Ultimately, these data reveal recurrent trends of freshwater invasion and highlight the dynamic, yet convergent, morphological evolution of Euplotes.
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Affiliation(s)
- Mitchell J. Syberg-Olsen
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas A. T. Irwin
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Fabrizio Erra
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | | | - Vittorio Boscaro
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| | - Patrick J. Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Fotedar R, Stoeck T, Filker S, Fell JW, Agatha S, Al Marri M, Jiang J. Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar. J Eukaryot Microbiol 2016; 63:578-90. [PMID: 26864150 DOI: 10.1111/jeu.12305] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 11/30/2022]
Abstract
The morphology, ontogenesis, and phylogenetic relationships of a halophile euplotid ciliates, Euplotes qatarensis nov. spec., isolated from the Khor Al-Adaid Lagoon in Qatar were investigated based on live observation as well as protargol- and silver nitrate-impregnated methods. The new species is characterised by a combination of features: the halophile habitat, a cell size of 50-65 × 33-40 μm, seven dorsal ridges, 10 commonly sized frontoventral cirri, two widely spaced marginal cirri, 10 dorsolateral kineties, and a double silverline pattern. The morphogenesis is similar to that of its congeners: (i) the oral primordium develops hypoapokinetally and the parental oral apparatus is retained; (ii) the frontoventral-transverse field of five streaks gives rise to the frontal, ventral, and transverse cirri, but not to the cirri I/1 and the marginal cirri; (iii) the dorsal somatic ciliature develops by intrakinetal proliferation of basal bodies in two anlagen per kinety that are just anterior and posterior to the future division furrow; (iv) the caudal cirri are formed by the two rightmost dorsolateral kineties. The SSU rDNA sequence of E. qatarensis branches with full support in the Euplotopsis elegans-Euplotes nobilii-Euplotopsis raikovi clade. The closest related publicly available SSU rDNA sequence is the one of E. nobilii, with which E. qatarensis has 93.4% sequence similarity. Euplotes parawoodruffi Song & Bradbury, 1997 is transferred to the genus Euplotoides based on the absence of frontoventral cirrus VI/3.
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Affiliation(s)
- Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, 7634 Doha, Qatar
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, D-67633, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Ecology, University of Kaiserslautern, D-67633, Kaiserslautern, Germany
| | - Jack W Fell
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, 33149, USA
| | - Sabine Agatha
- Department of Ecology and Evolution, University of Salzburg, Hellbrunnerstrasse 34, A-5020, Salzburg, Austria
| | - Masoud Al Marri
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Environment, 7634 Doha, Qatar
| | - Jiamei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 201306, Shanghai, China
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Di Giuseppe G, Erra F, Paolo Frontini F, Dini F, Vallesi A, Luporini P. Improved description of the bipolar ciliate, Euplotes petzi, and definition of its basal position in the Euplotes phylogenetic tree. Eur J Protistol 2014; 50:402-11. [DOI: 10.1016/j.ejop.2014.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 03/28/2014] [Accepted: 05/06/2014] [Indexed: 11/29/2022]
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12
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Dai R, Xu K, He Y. Morphological, Physiological, and Molecular Evidences Suggest that Euplotes parawoodruffi
is a Junior Synonym of Euplotes woodruffi
(Ciliophora, Euplotida). J Eukaryot Microbiol 2012. [DOI: 10.1111/jeu.12007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Renhai Dai
- Department of Marine Organism Taxonomy & Phylogeny; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
- Graduate University of Chinese Academy of Sciences; Beijing 100049 China
| | - Kuidong Xu
- Department of Marine Organism Taxonomy & Phylogeny; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Yingying He
- Department of Marine Organism Taxonomy & Phylogeny; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
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13
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Assessing whether alpha-tubulin sequences are suitable for phylogenetic reconstruction of Ciliophora with insights into its evolution in euplotids. PLoS One 2012; 7:e40635. [PMID: 22808216 PMCID: PMC3393704 DOI: 10.1371/journal.pone.0040635] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/11/2012] [Indexed: 11/19/2022] Open
Abstract
The current understanding of ciliate phylogeny is mainly based on analyses of a single gene, the small subunit ribosomal RNA (SSU-rDNA). However, phylogenetic trees based on single gene sequence are not reliable estimators of species trees, and SSU-rDNA genealogies are not useful for resolution of some branches within Ciliophora. Since congruence between multiple loci is the best tool to determine evolutionary history, we assessed the usefulness of alpha-tubulin gene, a protein-coding gene that is frequently sequenced, for ciliate phylogeny. Here, we generate alpha-tubulin gene sequences of 12 genera and 30 species within the order Euplotida, one of the most frequently encountered ciliate clades with numerous apparently cosmopolitan species, as well as four genera within its putative sister order Discocephalida. Analyses of the resulting data reveal that: 1) the alpha-tubulin gene is suitable phylogenetic marker for euplotids at the family level, since both nucleotide and amino acid phylogenies recover all monophyletic euplotid families as defined by both morphological criteria and SSU-rDNA trees; however, alpha-tubulin gene is not a good marker for defining species, order and subclass; 2) for seven out of nine euplotid species for which paralogs are detected, gene duplication appears recent as paralogs are monophyletic; 3) the order Euplotida is non-monophyletic, and the family Uronychiidae with sequences from four genera, is non-monophyletic; and 4) there is more genetic diversity within the family Euplotidae than is evident from dargyrome (geometrical pattern of dorsal “silverline system” in ciliates) patterns, habit and SSU-rDNA phylogeny, which indicates the urgent need for taxonomic revision in this area.
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Vannini C, Ferrantini F, Ristori A, Verni F, Petroni G. Betaproteobacterial symbionts of the ciliate Euplotes: origin and tangled evolutionary path of an obligate microbial association. Environ Microbiol 2012; 14:2553-63. [PMID: 22533449 DOI: 10.1111/j.1462-2920.2012.02760.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Polynucleobacter-Euplotes association is an obligatory symbiotic system between a monophyletic group of ciliate species belonging to the genus Euplotes and bacteria of the species Polynucleobacter necessarius (Betaproteobacteria). Both organisms are unable to survive independently. Several studies revealed the existence of free-living populations of Polynucleobacter bacteria which are phylogenetically closely related to the endosymbiotic ones, but never share associations with Euplotes in the natural environment. Hence, following the most parsimonious explanation on the origin of the association, this symbiosis should represent a synapomorphic character for the hosts' clade. Nevertheless, phylogenetic analyses performed on an increased number of strains here presented suggest that Euplotes species, during their evolution, recruited Polynucleobacter bacteria as symbionts more than once. Moreover, in three cases, we observed different bacteria as obligate symbionts. These symbionts are the first characterized representatives of a phylogenetic lineage branching in a basal position with respect to the genus Polynucleobacter. The hypothesis that the original obligate symbionts belonged to this newly discovered clade and that, only subsequently, in most cases they have been replaced by Polynucleobacter bacteria recruited from the environment is proposed and discussed. The evolutionary path of this association seems anyway to have been more complex than so far supposed.
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15
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Jiang J, Zhang Q, Warren A, Al-Rasheid KA, Song W. Morphology and SSU rRNA gene-based phylogeny of two marine Euplotes species, E. orientalis spec. nov. and E. raikovi (Ciliophora, Euplotida). Eur J Protistol 2010; 46:121-32. [DOI: 10.1016/j.ejop.2009.11.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Revised: 11/27/2009] [Accepted: 11/30/2009] [Indexed: 10/19/2022]
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Park MH, Kim SJ, Min GS. First Record of Two Euplotes Ciliates (Ciliophora: Spirotrichea: Euplotida) from Korea. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2010. [DOI: 10.5635/kjsz.2010.26.1.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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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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LYNN DENISH, SIMPSON ALASTAIRGB. From the Editors: Describing New Taxa of Unicellular Protists. J Eukaryot Microbiol 2009; 56:403-5. [DOI: 10.1111/j.1550-7408.2009.00440.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yi Z, Song W, Clamp JC, Chen Z, Gao S, Zhang Q. Reconsideration of systematic relationships within the order Euplotida (Protista, Ciliophora) using new sequences of the gene coding for small-subunit rRNA and testing the use of combined data sets to construct phylogenies of the Diophrys-complex. Mol Phylogenet Evol 2009; 50:599-607. [DOI: 10.1016/j.ympev.2008.12.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 11/27/2008] [Accepted: 12/04/2008] [Indexed: 10/21/2022]
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Miao M, Song W, Chen Z, Al-Rasheid KAS, Shao C, Jiang J, Guo W. A Unique Euplotid Ciliate, Gastrocirrhus (Protozoa, Ciliophora): Assessment of Its Phylogenetic Position Inferred from the Small Subunit rRNA Gene Sequence. J Eukaryot Microbiol 2007; 54:371-8. [PMID: 17669163 DOI: 10.1111/j.1550-7408.2007.00271.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The morphologically unique genus Gastrocirrhus has been considered a distinct but systematically uncertain euplotid due to the absence of both morphogenetic and molecular information. Based on the small subunit rRNA gene sequence, the phylogenetic position of Gastrocirrhus monilifer Ozaki & Yagui, 1942 was re-addressed using multiple algorithms (neighbor-joining, maximum parsimony, least-squares, and Bayesian inference methods). Results indicate that: (1) all phylogenetic trees using different methods are nearly identical in topology, placing G. monilifer closest to Euplotidium arenarium; (2) Gastrocirrhus and Euplotidium form a monophyletic group, namely the family Gastrocirrhidae, and appear to be intermediate taxa bridging the evolution of the Diophrys-Uronychia and Euplotes-complexes (i.e. Euplotes, Certesia, and Aspidisca); (3) the order Euplotida is a paraphyletic group composed of three deeply diverged clades (Euplotes-Certesia-Aspidisca-Gastrocirrhus-Euplotidium; Uronychia-Diophrys; and Prodiscocephalus); (4) together with Prodiscocephalus, the Diophrys-Uronychia complex forms a group at the suborder level and is placed at the root of the order Euplotida, and (5) results from molecular analyses conspicuously challenge the conclusions deduced from morphological as well as morphogenetical investigations-the characteristics traditionally used to define the euplotid taxa at the generic level and/or above may not be uniformly reliable.
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Affiliation(s)
- Miao Miao
- Laboratory of Protozoology, KLM, Ocean University of China, Qingdao 266003, China
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