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Song W, Zhang T, Dong J, Luo X, Bourland WA, Wang Y. Taxonomy and Molecular Phylogeny of Two New Urostylid Ciliates (Protozoa: Ciliophora) From Chinese Wetlands and Establishment of a New Genus. Front Microbiol 2021; 12:707954. [PMID: 34394057 PMCID: PMC8361796 DOI: 10.3389/fmicb.2021.707954] [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: 05/11/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022] Open
Abstract
Hypotrich ciliates with evolutionary novelties are continually being discovered, challenging the current taxonomic system and attracting increased attention. In the present work, two new urostylid ciliates, Heterobakuella bergeri gen. nov., sp. nov. and Anteholosticha perezuzae sp. nov., isolated from Chinese wetland samples, were identified based on morphology and 18S rRNA gene sequences. Heterobakuella gen. nov. is defined by three frontal cirri, single buccal cirrus, one parabuccal cirrus, midventral complex composed of cirral pairs and one cirral row, one left and two right marginal cirral rows, transverse and pretransverse cirri present, caudal and frontoterminal cirri absent. Heterobakuella can be easily distinguished from the morphologically most similar genus, Apobakuella, mainly by the single buccal cirrus (vs. one buccal cirral row) and one parabuccal cirrus (vs. several parabuccal cirral rows originated from different anlagen). Phylogenetic analyses show that H. bergeri branches within the clade formed by Bergeriella ovata, Monocoronella carnea, Anteholosticha gracilis, and Neourostylopsis spp., rather than the clade represented by Apobakuella. The other species, A. perezuzae, is mainly characterized by a distinctly slender body shape with an average length:width ratio about 7, distinctively shaped biconcave and greenish cortical granules, as well as one or two pretransverse cirri. Phylogenetic analyses indicate the genus Anteholosticha is non-monophyletic.
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Affiliation(s)
- Wenya Song
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Tengyue Zhang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jingyi Dong
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiaotian Luo
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - William A. Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, China
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2
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Jung JH, Omar A, Park MH, Nguyen TV, Jung YH, Yang HM, Min GS. Anteholosticha foissneri n. sp., a marine hypotrich ciliate (Ciliophora: Spirotrichea) from Vietnam: Morphology, morphogenesis, and molecular phylogeny. Eur J Protistol 2021; 78:125768. [PMID: 33549970 DOI: 10.1016/j.ejop.2021.125768] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 12/25/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
In a study of marine ciliate diversity, we collected an Anteholosticha monilata-like population from Vietnam. To identify this population, we analyzed its morphology, some morphogenetic stages, and molecular phylogeny. Based on these data, we conclude that the Vietnamese population is new to science. Anteholosticha foissneri n. sp. resembles Anteholosticha monilata-like species considering (1) the number and arrangement of macronuclear nodules and micronuclei; (2) the presence of cortical granules; and (3) the saline habitat. However, the new species can be easily distinguished from these species by the arrangement, color, and shape of the cortical granules. The divisional morphogenesis commences with the de novo proliferation of basal bodies as a single longitudinal patch left of the posteriormost midventral cirral pair. This character state has not been reported before in Anteholosticha (based on check of the available data) and probably reflects a distinct clade within the nuclear small subunit ribosomal RNA gene tree.
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Affiliation(s)
- Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung, 25457, South Korea.
| | - Atef Omar
- Natural Science Research Institute, Gangneung-Wonju National University, Gangneung, 25457, South Korea; Department of Zoology, Al Azhar University, Assiut, 71524, Egypt
| | - Mi-Hyun Park
- Natural Science Research Institute, Gangneung-Wonju National University, Gangneung, 25457, South Korea
| | - Tu Van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh city, Vietnam
| | - Yun-Hwan Jung
- International Center for Marine Biodiversity, National Marine Biodiversity Institute of Korea, Seocheon-gun, 33662, South Korea; Marine Bio-Resources Research Unit, Korea Institute of Ocean Science & Technology (KIOST), Busan Metropolitan City, 49111, South Korea
| | - Hee-Min Yang
- Department of Biological Sciences, Inha University, Incheon, 22212, South Korea
| | - Gi-Sik Min
- Department of Biological Sciences, Inha University, Incheon, 22212, South Korea
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3
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Morphology and molecular phylogeny of a new hypotrich ciliate, Anteholosticha songi nov. spec., and an American population of Holosticha pullaster (Müller, 1773) Foissner et al., 1991 (Ciliophora, Hypotrichia). Eur J Protistol 2020; 72:125646. [DOI: 10.1016/j.ejop.2019.125646] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 11/20/2022]
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4
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Moon JH, Kim JH, Quintela‐Alonso P, Jung J. Morphology, Morphogenesis, and Molecular Phylogeny of
Neobakuella aenigmatica
n. sp. (Ciliophora, Spirotrichea, Bakuellidae). J Eukaryot Microbiol 2019; 67:54-65. [DOI: 10.1111/jeu.12753] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/18/2019] [Accepted: 07/21/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Ji Hye Moon
- Department of Biology Gangneung‐Wonju National University Jukheon‐gil 7 Gangneung Gangwon‐do 25457 South Korea
| | - Ji Hye Kim
- Natural Science Research Institute Gangneung‐Wonju National University Gangneung 25457 South Korea
| | - Pablo Quintela‐Alonso
- Department of Genetics, Physiology and Microbiology Faculty of Biology Complutense University of Madrid Madrid 28040 Spain
| | - Jae‐Ho Jung
- Department of Biology Gangneung‐Wonju National University Jukheon‐gil 7 Gangneung Gangwon‐do 25457 South Korea
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Sheng Y, He M, Zhao F, Shao C, Miao M. Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti. Mol Phylogenet Evol 2018; 129:338-345. [DOI: 10.1016/j.ympev.2018.06.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/13/2018] [Indexed: 11/25/2022]
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6
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Zheng W, Wang C, Yan Y, Gao F, Doak TG, Song W. Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina. Genome Biol Evol 2018; 10:883-894. [PMID: 29608728 PMCID: PMC5863220 DOI: 10.1093/gbe/evy055] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2018] [Indexed: 02/04/2023] Open
Abstract
Ciliated protists are a large group of single-celled eukaryotes with separate germline and somatic nuclei in each cell. The somatic genome is developed from the zygotic nucleus through a series of chromosomal rearrangements, including fragmentation, DNA elimination, de novo telomere addition, and DNA amplification. This unique feature makes them perfect models for research in genome biology and evolution. However, genomic research of ciliates has been limited to a few species, owing to problems with DNA contamination and obstacles in cultivation. Here, we introduce a method combining telomere-primer PCR amplification and high-throughput sequencing, which can reduce DNA contamination and obtain genomic data efficiently. Based on this method, we report a draft somatic genome of a multimacronuclear ciliate, Uroleptopsis citrina. 1) The telomeric sequence in U. citrina is confirmed to be C4A4C4A4C4 by directly blunt-end cloning. 2) Genomic analysis of the resulting chromosomes shows a "one-gene one-chromosome" pattern, with a small number of multiple-gene chromosomes. 3) Amino acid usage is analyzed, and reassignment of stop codons is confirmed. 4) Chromosomal analysis shows an obvious asymmetrical GC skew and high bias between A and T in the subtelomeric regions of the sense-strand, with the detection of an 11-bp high AT motif region in the 3' subtelomeric region. 5) The subtelomeric sequence also has an obvious 40 nt strand oscillation of nucleotide ratio. 6) In the 5' subtelomeric region of the coding strand, the distribution of potential TATA-box regions is illustrated, which accumulate between 30 and 50 nt. This work provides a valuable reference for genomic research and furthers our understanding of the dynamic nature of unicellular eukaryotic genomes.
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Affiliation(s)
- Weibo Zheng
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - Chundi Wang
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Ying Yan
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Feng Gao
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington.,National Center for Genome Analysis Support, Indiana University, Bloomington
| | - Weibo Song
- Laboratory of Protozoology, 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
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Lyu Z, Li J, Zhu E, Shao C. Morphology and morphogenesis of a new soil urostylid ciliate, with the establishment of a new genus Caudiurostyla gen. nov. (Ciliophora, Hypotrichia). Eur J Protistol 2018; 66:166-176. [DOI: 10.1016/j.ejop.2018.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
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8
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Chen L, Wu W, El-Serehy HA, Hu X, Clamp JC. Morphology, morphogenesis, and phylogeny of an Anteholosticha intermedia (Ciliophora, Urostylida) population from the United States. Eur J Protistol 2018; 65:1-15. [DOI: 10.1016/j.ejop.2018.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 11/26/2022]
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Li F, Li Y, Luo D, Miao M, Shao C. Morphology, Morphogenesis, and Molecular Phylogeny of a New Soil Ciliate, Sterkiella multicirrata
sp. nov. (Ciliophora, Hypotrichia) from China. J Eukaryot Microbiol 2018; 65:627-636. [DOI: 10.1111/jeu.12508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/12/2018] [Accepted: 01/23/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Fengchao Li
- The Key Laboratory of Zoological Systematics and Application; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Yanbo Li
- The Key Laboratory of Zoological Systematics and Application; College of Life Sciences; Hebei University; Baoding 071002 China
- Handan Foreign Language School of Hebei Province; Handan 056002 China
| | - Dan Luo
- The Key Laboratory of Zoological Systematics and Application; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Miao Miao
- Savaid Medical School; University of Chinese Academy of Sciences; Beijing 100049 China
| | - Chen Shao
- The Key Laboratory of Biomedical Information Engineering; Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an 710049 China
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Lyu Z, Wang J, Huang J, Warren A, Shao C. Multigene-based phylogeny of Urostylida (Ciliophora, Hypotrichia), with establishment of a novel family. ZOOL SCR 2018. [DOI: 10.1111/zsc.12267] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhao Lyu
- The Key Laboratory of Biomedical Information Engineering; Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an China
| | - Jingyi Wang
- The Key Laboratory of Biomedical Information Engineering; Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; London UK
| | - Chen Shao
- The Key Laboratory of Biomedical Information Engineering; Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an China
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The diverse morphogenetic patterns in spirotrichs and philasterids: Researches based on five-year-projects supported by IRCN-BC and NSFC. Eur J Protistol 2017; 61:439-452. [DOI: 10.1016/j.ejop.2017.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 05/02/2017] [Accepted: 05/09/2017] [Indexed: 11/23/2022]
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12
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Morphology, morphogenesis and molecular phylogeny of a new soil ciliate Paragonostomoides xianicum n. sp. (Ciliophora, Hypotrichia, Gonostomatidae). Eur J Protistol 2017; 61:233-243. [DOI: 10.1016/j.ejop.2017.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 11/23/2022]
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13
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Lu X, Huang J, Shao C, Al-Farraj SA, Gao S. Morphology and Morphogenesis of a Novel Saline Soil Hypotrichous Ciliate, Gonostomum sinicum nov. spec. (Ciliophora, Hypotrichia, Gonostomatidae), Including a Report on the Small Subunit rDNA Sequence. J Eukaryot Microbiol 2017; 64:632-646. [PMID: 28166376 DOI: 10.1111/jeu.12398] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 11/29/2022]
Abstract
Morphology, cirral pattern, and morphogenesis of the new saline soil hypotrich, Gonostomum sinicum nov. spec. collected from Longfeng Wetland in Daqing, north China, were studied, using detailed live observations and protargol-stained specimens. The new species is characterized as follows: (i) a size in vivo of 100-125 × 30-40 μm, (ii) colorless cortical granules, 0.5 μm across, arranged in short rows, (iii) an adoral zone composed of 28-33 membranelles, (iv) three or four frontoventral rows, one of which extends onto the postoral area, (v) left and right marginal rows composed of 18-27 and 21-35, cirri, respectively, and (vi) usually two transverse cirri. Morphogenesis is as usual for the genus Gonostomum, i.e. the cirral primordia II-VI are primary primordia which split into two sets for proter and opisthe in division middle stages, except for anlage I which develops independently. However, the number of frontoventral transverse anlagen is either five or six not only in different individuals but even in proter and opisthe of the same divider. The phylogenetic analyses based on SSU rDNA sequences showed that the genus Gonostomum is nonmonophyletic, indicating that the patterns of cirri and dorsal kineties are homoplasious characters. The new species G. sinicum nov. spec. is perhaps closely related to Cotterillia bromelicola and two congeners.
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Affiliation(s)
- Xiaoteng Lu
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.,University of Innsbruck, Research Institute for Limnology, Mondseestr. 9, Mondsee, 5310, Austria.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chen Shao
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
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Chen L, Zhao X, Shao C, Miao M, Clamp JC. Morphology and phylogeny of two new ciliates, Sterkiella sinica sp. nov. and Rubrioxytricha tsinlingensis sp. nov. (Protozoa, Ciliophora, Hypotrichia) from north-west China. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1219426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lingyun Chen
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaolu Zhao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Chen Shao
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - John C. Clamp
- Department of Biology, North Carolina Central University, Durham, 1801 Fayetteville St., North Carolina 27707, USA
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