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Morphology, molecular phylogeny, and taxonomy of trichodinids (Ciliophora, Mobilida) from Calanoid copepods. Parasitol Res 2020; 119:2597-2608. [DOI: 10.1007/s00436-020-06741-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/31/2020] [Indexed: 01/19/2023]
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Abdelkhalek NK, El-Adl MA, Salama MF, Elmishmishy B, Ali MO, El-Ashram A, Hamed MF, Al-Araby MA. Molecular identification of Trichodina compacta Van As and Basson, 1989 (Ciliophora: Peritrichia) from cultured Oreochromis niloticus in Egypt and its impact on immune responses and tissue pathology. Parasitol Res 2018; 117:1907-1914. [PMID: 29717369 DOI: 10.1007/s00436-018-5883-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/16/2018] [Indexed: 11/28/2022]
Abstract
Trichodinids are peritrichous ciliated protozoa that affect both wild and cultured fishes. Several Trichodina species have low host specificity and are morphologically distinct, facilitating their identification based primarily on the presence of adhesive discs and the number of attached denticles. A trichodinid species named Trichodina compacta was first reported by Van As and Basson (1989) (Protozoa: Ciliophora: Peritrichia). However, in trichodinid infestations, morphological characteristics are insufficient for identifying the infesting species. Therefore, molecular and phylogenetic analyses are considered to be promising and useful tools for identifying the infesting species. This study aimed to achieve the molecular identification of a trichodinid infestation in Nile tilapia and to construct the phylogenetic relationships between the identified species and other peritrichous parasites. Moreover, we also aimed to study the pathological and immunological impacts of trichodinids on fry tissue to improve our understanding of the immune responses of teleost fish to trichodinae parasitic infestations and develop a better control method. Here, we used molecular techniques to identify the isolated trichodina species as T. compacta and demonstrated that Trichodina infestation in Nile tilapia is associated with remarkable immunogenic and inflammatory responses (increased il-1β expression and decreased il-8 and tgf-β expression). These findings improve our understanding of the responses of teleost fish to trichodinid parasite infestation and will be helpful for the development of novel control strategies that reverse the inflammatory and immunogenic alterations that occur in infested fish.
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Affiliation(s)
- Nevien K Abdelkhalek
- Internal Medicine, Infectious and Fish Diseases Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.
| | - Mohamed A El-Adl
- Department of Biochemistry, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Mohamed F Salama
- Department of Biochemistry, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Bassem Elmishmishy
- Parasitology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Mayar O Ali
- Animal Husbandry and Genetics Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Ahmed El-Ashram
- Fish Health and Fish Diseases Department, Faculty of Fish Resources, Suez University, Suez, Egypt
| | - Mohamed F Hamed
- Pathology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Moustafa A Al-Araby
- Parasitology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
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Gao F, Warren A, Zhang Q, Gong J, Miao M, Sun P, Xu D, Huang J, Yi Z, Song W. The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata). Sci Rep 2016; 6:24874. [PMID: 27126745 PMCID: PMC4850378 DOI: 10.1038/srep24874] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/05/2016] [Indexed: 11/17/2022] Open
Abstract
The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous genera Askenasia, CyclotrichiumParaspathidium and Plagiocampa show close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported, and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded as incertae sedis within Spirotrichea.
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Affiliation(s)
- Feng Gao
- Institute of Evolution &Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Jun Gong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Miao Miao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Weibo Song
- Institute of Evolution &Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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Findeisen P, Mühlhausen S, Dempewolf S, Hertzog J, Zietlow A, Carlomagno T, Kollmar M. Six subgroups and extensive recent duplications characterize the evolution of the eukaryotic tubulin protein family. Genome Biol Evol 2014; 6:2274-88. [PMID: 25169981 PMCID: PMC4202323 DOI: 10.1093/gbe/evu187] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Tubulins belong to the most abundant proteins in eukaryotes providing the backbone for many cellular substructures like the mitotic and meiotic spindles, the intracellular cytoskeletal network, and the axonemes of cilia and flagella. Homologs have even been reported for archaea and bacteria. However, a taxonomically broad and whole-genome-based analysis of the tubulin protein family has never been performed, and thus, the number of subfamilies, their taxonomic distribution, and the exact grouping of the supposed archaeal and bacterial homologs are unknown. Here, we present the analysis of 3,524 tubulins from 504 species. The tubulins formed six major subfamilies, α to ζ. Species of all major kingdoms of the eukaryotes encode members of these subfamilies implying that they must have already been present in the last common eukaryotic ancestor. The proposed archaeal homologs grouped together with the bacterial TubZ proteins as sister clade to the FtsZ proteins indicating that tubulins are unique to eukaryotes. Most species contained α- and/or β-tubulin gene duplicates resulting from recent branch- and species-specific duplication events. This shows that tubulins cannot be used for constructing species phylogenies without resolving their ortholog–paralog relationships. The many gene duplicates and also the independent loss of the δ-, ε-, or ζ-tubulins, which have been shown to be part of the triplet microtubules in basal bodies, suggest that tubulins can functionally substitute each other.
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Affiliation(s)
- Peggy Findeisen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Silke Dempewolf
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jonny Hertzog
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander Zietlow
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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Tang FH, Zhao YJ, Warren A. Phylogenetic analyses of Trichodinids (Ciliophora, Oligohymenophora) inferred from 18S rRNA gene sequence data. Curr Microbiol 2012. [PMID: 23196703 PMCID: PMC3557388 DOI: 10.1007/s00284-012-0274-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Partial 18S rRNA gene sequences of the three trichodinids, namely Trichodina modesta Lom, 1970, Trichodina paraheterodentata Tang and Zhao 2012. and Trichodinella epizootica (Raabe 1950) Šrámek-Hušek, 1953, were acquired and used to construct phylogenetic trees. The results revealed that Trichodinella epizootica clustered with Trichodinella sp.; Trichodina paraheterodentata Tang and Zhao 2012 was sister to the clade composed of Trichodina heterodentata Duncan, 1977 and Trichodinanobilis Chen, 1963; Trichodina modesta Lom, 1970 clustered with Trichodina reticulata Hirschman and Partsch, 1955. The branching order of species within the Mobilia clade was closely correlated with GC content. Furthermore, blade morphology was also found to be the primary morphological character in determining the phylogenetic relationships among members of the genus Trichodina. The present findings suggest that the genus Trichodina is paraphyletic when species of Trichodinella are included in the analyses.
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Affiliation(s)
- Fa-Hui Tang
- The Key Laboratory of Animal Biology of Chongqing, Chongqing Normal University, Chongqing, 400047 People’s Republic of China
| | - Yuan-Jun Zhao
- The Key Laboratory of Animal Biology of Chongqing, Chongqing Normal University, Chongqing, 400047 People’s Republic of China
| | - Alan Warren
- Department of Zoology, Natural History Museum, Cromwell Road, London, SW7 5BD UK
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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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