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Wei Miao - One of the best experts on this subject based on the ideXlab platform.
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vorticella linnaeus 1767 ciliophora oligohymenophora Peritrichia is a grade not a clade redefinition of vorticella and the families vorticellidae and astylozoidae using molecular characters derived from the gene coding for small subunit ribosomal rna
Protist, 2012Co-Authors: Ping Sun, John C. Clamp, Yasushi Kusuoka, Wei MiaoAbstract:Recent phylogenetic analyses of the Peritrich genus Vorticella have suggested that it might be paraphyletic, with one Vorticella species - Vorticella microstoma grouping with the swimming Peritrichs Astylozoon and Opisthonecta in a distant clade. These results were based on very limited taxon sampling and thus could not be accepted as conclusive evidence for revising the generic classification. We tested paraphyly of the genus Vorticella by making a new analysis with a broad range of samples from three continents that yielded 52 new sequences of the gene coding for small subunit rRNA. Our results, together with the available sequences in Genbank, form a comprehensive set of data for the genus Vorticella. Analyses of these data showed that Vorticella microstoma morphotypes, Astylozoon, and Opisthonecta form a well-supported, monophyletic clade, that is distinct from and basal to the family Vorticellidae containing other species of Vorticella. Paraphyly of the genus Vorticella and family Vorticellidae was strongly confirmed by these results. Furthermore, the two clades of Vorticella identified by the SSU rRNA gene are so genetically diverse whereas the genetic distances within the one containing Vorticella microstoma morphotypes, Astylozoon, and Opisthonecta were so slight, which marked it as a separate family that must be defined by molecular characters in the absence of unifying morphological and morphogenetic characters. An emended characterization and status of the genus Vorticella, the families Vorticellidae and Astylozoidae are presented and discussed.
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Reevaluation of the phylogenetic relationship between mobilid and sessilid Peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences.
The Journal of eukaryotic microbiology, 2006Co-Authors: Yingchun Gong, Eduardo Villalobo, Fei-yun Zhu, Wei MiaoAbstract:Based on morphological characters, Peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on Peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within Peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the Peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of Peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the center of the adhesive disc, branched separately from its congeners, Trichodina nobilis and Trichodina heterodentata, trichodinids without such granules. This indicates that granules in the adhesive disc might be a phylogenetic character of high importance within the Family Trichodinidae.
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Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences.
The Journal of eukaryotic microbiology, 2004Co-Authors: Wei Miao, Wei-song Fen, Xi-yuan Zhang, Yunfen ShenAbstract:The phylogenetic relationships among Peritrichs remain unresolved. In this study, the complete small subunit rRNA (SSrRNA) gene sequences of seven species (Epistylis galea, Campanella umbellaria, Carchesium polypinum, Zoothamnium arbuscula, Vaginicola crystallina, Ophrydium versatile, and Opercularia microdiscum) were determined. Trees were constructed using distance-matrix, maximum-likelihood and maximum-parsimony methods, all of which strongly supported the monophyly of the subclass Peritrichia. Within the Peritrichs, 1) E. galea grouped with Opercularia microdiscum and Campanella umbellaria but not the other Epistylis species, which indicates that the genus Epistylis might not be monophyletic; 2) the topological position of Carchesium and Campanella suggested that Carchesium should be placed in the family Zoothamniidae, or be elevated to a higher taxonomic rank, and that Campanella should be independent of the family Epistylididae, and probably be given a new rank; and 3) Opisthonecta grouped strongly with Astylozoon, which suggested that Opisthonecta species were not the ancestors of the stalked Peritrichs.
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Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) with emphasis on the genus Epistylis, inferred from small subunit rRNA gene sequences
The Journal of eukaryotic microbiology, 2001Co-Authors: Wei Miao, Yunfen ShenAbstract:The Peritrichs have been recognized as a higher taxon of ciliates since 1968. However, the phylogenetic relationships among them are still unsettled, and their placement within the class Oligohymenophorea has only been supported by the analysis of the small subunit rRNA gene sequence of Opisthonecta henneguyi. DNA was isolated directly from field-sampled species for PCR, and was used to resolve relationships within the genus Epistylis and to confirm the stability of the placement of Peritrichs. Small subunit rRNA gene sequences of Epistylis plicatilis, Epistylis urceolata, Epistylis chysemydis, Epistylis hentscheli, Epistylis wenrichi, and Vorticella campanula were sequenced and analyzed using both distance-matrix and maximum-parsimony methods. In phylogenetic trees, the monophyly of both the genus Epistylis and the subclass Peritrichia was strongly supported, while V. campanula clustered with Vorticella microstoma. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the peristomial area, especially the. peristomial lip, might be the important phylogenetic character within the genus Epistylis.
Alan Warren - One of the best experts on this subject based on the ideXlab platform.
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morphology and molecular phylogeny of three epistylis species found in freshwater habitats in china including the description of e foissneri n sp ciliophora Peritrichia
European Journal of Protistology, 2021Co-Authors: Tengteng Zhang, Jun Hou, Alan WarrenAbstract:Abstract The Peritrich genus Epistylis is speciose, however many species lack complete morphological description based on modern criteria and/or molecular data. In the present study, one new species, i.e., E. foissneri n. sp., and two morphologically similar species, i.e., E. hentscheli Kahl, 1935 and E. vaginula Stokes, 1884, collected from freshwater habitats in China, were studied. Epistylis foissneri n. sp. is characterized by its extremely slender zooids encased in a gelatinous sheath, symmetrically dichotomously branched stalk, trochal band located at mid-body, contractile vacuole located on dorsal wall of infundibulum, infundibular polykinety 3 (P3) composed of three equal-length rows that terminate above infundibular polykinety 1 (P1), 105–110 silverlines between the peristome and the trochal band, and about 110 silverlines between the trochal band and the scopula. Epistylis hentscheli is characterized by its asymmetric pyriform zooids (average length ca. 160 μm in vivo), dichotomously branched stalk with transverse striations on the surface of the upper portion, P3 three-rowed and terminating slightly above P1, 60–75 silverlines between the peristome and the trochal band, and 55–90 silverlines between the trochal band and the scopula. Epistylis vaginula is characterized by its elongated body shape (about 100 μm in length in vivo), dichotomously branched and smooth stalk, P3 three-rowed and terminating above P1, 80–100 silverlines between the peristome and the trochal band, and 45–80 silverlines between the trochal band and the scopula. The small subunit ribosomal DNA gene (SSU rDNA) of these three species was sequenced and supported the validity of each. Phylogenetic analyses based on SSU rDNA sequence data revealed that all three morphospecies group with other congeners within the major clade of Epistylis.
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single cell genomic sequencing of three Peritrichs protista ciliophora reveals less biased stop codon usage and more prevalent programmed ribosomal frameshifting than in other ciliates
Frontiers in Marine Science, 2020Co-Authors: Xiao Chen, Chundi Wang, Zhuo Shen, Bo Pan, Alan WarrenAbstract:Peritrichs are one of the largest groups of ciliates with over 1,000 species described so far. However, their genomic features are largely unknown. By single-cell genomic sequencing, we acquired the genomic data of three sessilid Peritrichs (Cothurnia ceramicola, Vaginicola sp. and Zoothamnium sp.2). Using genomic data from another 53 ciliates including 14 Peritrichs, we reconstructed their evolutionary relationships and confirmed genome skimming as an efficient approach for expanding sampling. In addition, we profiled the stop codon usage and programmed ribosomal frameshifting (PRF) events in Peritrichs for the first time. Our analysis reveals no evidence of stop codon reassignment for Peritrichs, but they have prevalent +1 or -1 PRF events. These genomic features are distinguishable from other ciliates and our observations suggest a unique evolutionary strategy for Peritrichs.
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morphology and molecular analyses of four epibiotic Peritrichs on crustacean and polychaete hosts including descriptions of two new species ciliophora Peritrichia
European Journal of Protistology, 2020Co-Authors: Zhuo Shen, Alan Warren, Qianqian Zhang, Weibo SongAbstract:Four epibiotic sessilid Peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalisMobius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.
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systematic studies on ciliates alveolata ciliophora in china progress and achievements based on molecular information
European Journal of Protistology, 2017Co-Authors: Feng Gao, Alan Warren, Qianqian Zhang, Jie Huang, Yan Zhao, Weiwei Liu, Miao Miao, Hamed A Elserehy, Weibo SongAbstract:Due to complex morphological and convergent morphogenetic characters, the systematics of ciliates has long been ambiguous. Since 1990, the Laboratory of Protozoology, Ocean University of China, in collaboration with other research groups worldwide, has carried out a series of integrative investigations on ciliate systematics. To date, genomic DNA has been extracted from about 1700 ciliate strains, and phylogenetic analyses have been performed for two-thirds of orders. Main findings are: (1) Classifications of about 50 hypotrichous species have been resolved, although the monophylies of three hypotrichous orders remain unconfirmed; (2) Euplotia and two orders and all seven families within them are monophyletic assemblages; (3) Lynnella represents an order-level taxon, and is separated from two sister monophyletic subclasses Oligotrichia and Choreotrichia; (4) the Peritrich families Zoothamniidae and Vorticellidae are separated from each other, and Zoothamnium exhibits a high genetic diversity; (5) the scuticociliate order Philasterida is monophyletic and separated from loxocephalids, and the thigmotrichids is a suborder within Pleuronematida; (6) 14 classes were recovered including one new class Protocruziea, and Mesodiniea is basal to subphyla Intramacronucleata and Postciliodesmatophora; (7) mitochondrial cytochrome c oxidase subunit I heteroplasmy was reported in ciliates for the first time, and candidate barcoding genes for Frontonia species identification were identified.
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morphology of four new solitary sessile Peritrich ciliates from the yellow sea china with description of an unidentified species of paravorticella ciliophora Peritrichia
European Journal of Protistology, 2017Co-Authors: Saleh A Alfarraj, Alan WarrenAbstract:Abstract Sessile Peritrichs are a large assemblage of ciliates that have a wide distribution in soil, freshwater and marine waters. Here, we document four new and one unidentified species of solitary sessile Peritrichs from aquaculture ponds and coastal waters of the northern Yellow Sea, China. Based on their living morphology, infraciliature and silverline system, four of the five forms were identified as new members belonging to one of three genera, Vorticella , Pseudovorticella and Scyphidia, representing two families, Vorticellidae and Scyphidiidae. The other isolate was found to be an unidentified species of the poorly known genus Paravorticella . Vorticella chiangi sp. nov. is characterized by its inverted bell-shaped zooid, short row 3 in infundibular polykinety 3 and marine habitat. Pseudovorticella liangae sp. nov. posseses a thin, broad peristomial lip and a granular pellicle. Pseudovorticella haiboensis sp. nov. is differentiated from its congeners by having an elongated zooid that is covered by a layer of thin pellicular vesicles, and two rows of kineties in infundibular polykinety 3. Scyphidia perezuzae sp. nov. and Paravorticella sp. are stalkless ectoparasites or ectocommensals of aquatic animals. The former has a short, plump body, a narrow peristomial lip and a conspicuous, flattened, disc-shaped scopula for adhesion. Paravorticella sp. has an extremely elongated clavate body, a broad peristomial lip, and a narrow scopula.
Laura R. P. Utz - One of the best experts on this subject based on the ideXlab platform.
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host parasite relationship during epistylis sp ciliophora epistylididae infestation in farmed cichlid and pimelodid fish
Pesquisa Agropecuaria Brasileira, 2016Co-Authors: Santiago Benites De Padua, Laura R. P. Utz, Mauricio Laterca Martins, Gustavo Moraes Ramos Valladao, Fernando Jose Zara, Marcia Mayumi Ishikawa, Marco Antonio De Andrade BeloAbstract:The objective of this work was to describe the host‑ Epistylis sp. relationship during infestation on farmed fish. Five Nile tilapia ( Oreochromis niloticus ) and ten hybrid surubim catfish ( Pseudoplatystoma reticulatum x P. corruscans ), all diseased, were used for in vivo morphological analysis of sessile Peritrichs by contrast microscopy. Fragments of infected tissues were subjected to histological processing and scanning electron microscopy. Epistylis sp. caused hemorrhagic ulcer disease, and cichlids were more prone to develop infestations throughout the body surface due to the attachment of the colonies to the scales, which did not occur with pimelodids. Multifocal granulomatous dermatitis was observed, associated with the hydropic degeneration of the epithelium and to ulcerative areas of necrosis. Microscopic examination showed the presence of bacterial microflora associated to Epistylis sp. peduncles. Therefore, this species can be considered a portal of entry for opportunistic bacteria.
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Description of Epistylis riograndensis n.sp. (Ciliophora: Peritrichia) found in an
2016Co-Authors: Laura R. P. Utz, Eduarda Correa Freitas, Ana Carolina, Silva Rodrigues Farias, Gabriella Oliveira, De AraújoAbstract:Epistylis riograndensis n. sp., a freshwater Peritrich hosting symbiotic algae in its cytoplasm, was collected from an arti-ficial lake, in a Botanical garden in Southern Brazil. Its detailed morphology was investigated using live and silver-stained specimens. The colonial sessile E. riograndensis has elongate zooids measuring, on average, 162 μm in length and 45 μm in width. A single contractile vacuole located near the infundibulum and a C-shaped macronucleus located transversely in the adoral half of the cell were also observed. The oral infraciliature revealed in silver-stained specimens was typical of Peritrich ciliates. Three infundibular polykineties consisting of 3 rows of kinetosomes were observed. Molecular analy-ses of 18s rDNA placed E. riograndensis among other Epistylis species in the Order Vorticellida
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attachment of the Peritrich epibiont zoothamnium intermedium precht 1935 ciliophora Peritrichia to artificial substrates in a natural environment
Brazilian Journal of Biology, 2008Co-Authors: Laura R. P. UtzAbstract:Peritrich ciliates are commonly found as epibionts, colonizing living organisms, or attached to non-living substrates in freshwater, estuarine and marine environments. Several species of Peritrich epibionts are obligate, which means that they are able to only colonize other organisms, while others are facultative attaching to living or non-living substrates. The Peritrich Zoothamnium intermedium is commonly found as epibiont on the copepod species Acartia tonsa and Eurytemora affinis in Chesapeake Bay, USA. Previous studies demonstrated that Z. intermedium is not able to attach to non-living substrates in the laboratory; with free-swimming stages (telotrochs) dying when living substrates are not available for colonization. The present study investigated the ability of Z. intermdium to colonize artificial substrates in the field. Observations were carried out while the Peritrich ciliate was colonizing copepods in Rhode River, a tributary of Chesapeake Bay. Results demonstrated that four species of Zoothamnium were recovered from artificial substrates, but none of them was Z. intermedium. At the same time, Z. intermedium was colonizing adults and copepodites of E. affinis and A. tonsa during the whole study period. These results, in addition to laboratory observations, suggest that Z. intermedium is an obligate epibiont.
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growth of the Peritrich epibiont zoothamnium intermedium precht 1935 ciliophora Peritrichia estimated from laboratory experiments
Brazilian Journal of Biology, 2008Co-Authors: Laura R. P. UtzAbstract:Peritrich ciliates are commonly found colonizing living substrates. Although this a well known phenomenon, biological aspects of this relationship need to be studied in more detail. Assessment of growth rates in Peritrichs has been the subject of very few studies. Only species in the genera Carchesium Ehrenberg, 1830 and Vorticella Linnaeus, 1767 had their growth rates evaluated in the field and in the laboratory. In the present study, growth, colonization (colonies/host), and proliferation (zooids/colony) rates of the Peritrich epibiont Zoothamnium intermedium Precht, 1935 attached to the calanoid copepod Acartia tonsa Dana 1848 were evaluated in the laboratory in two food regimes: bacteria only, and algal based diet. Results showed that growth, colonization, and proliferation rates were similar for both diets. Maximum growth rates obtained for Z. intermedium was 0.85 and 0.83 per day, for bacteria and algae respectively. Maximum colonization rates were 0.5 per day for both diets, and the maximum proliferation rates were 0.44 and 0.42 per day for bacteria and algae respectively. These results demonstrate that Z. intermedium is able to grow at the same rate of other Peritrichs on bacterial and algal based diets.
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spatial and temporal patterns in the occurrence of Peritrich ciliates as epibionts on calanoid copepods in the chesapeake bay usa
Journal of Eukaryotic Microbiology, 2005Co-Authors: Laura R. P. Utz, Wayne D CoatsAbstract:We investigated temporal and spatial patterns of distribution in two Peritrich ciliates (i.e. Zoothamnium intermedium and Epistylis sp.) living as epibionts on calanoid copepods (i.e. Acartia tonsa and Eurytemora affinis) in Chesapeake Bay. Net tow samples collected along the main axis of the Bay were analyzed to estimate the occurrence of epibionts on copepods and to explore relationships among infestation prevalence, host abundance, and environmental variables. Zoothamnium intermedium and Epistylis sp. colonized populations of A. tonsa during spring and summer months, while only Z. intermedium colonized E. affinis during spring. Occurrence of epibionts on copepods showed high interannual variation, marked seasonality, and geographic heterogeneity. Extensive statistical analyses rejected simple scenarios of interactions between epibiosis, environmental variables, and host density, suggesting a more complex dynamics for the system. Analyses of epibiont colonies and zooids per host area (i.e. the sum of width and length of the body including antennae and swimming legs calculated assuming a cylindrical shape) were also performed. Overall, epibiont infestation prevalence (i.e. colonies/host area) and load (i.e. zooids/host area) were higher on copepodites than on adults for both host species, suggesting a preferential attachment to juveniles, or a higher predation pressure on adult stages. Infestation density and loads of both epibiont species were higher on the cephalothorax and abdomen of A. tonsa and E. affinis in comparison to the antennae and swimming legs, suggesting that ciliates can more easily colonize less active parts of the host.
Yingchun Gong - One of the best experts on this subject based on the ideXlab platform.
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Alpha-tubulin and small subunit rRNA phylogenies of Peritrichs are congruent and do not support the clustering of mobilids and sessilids (Ciliophora, Oligohymenophorea).
The Journal of eukaryotic microbiology, 2010Co-Authors: Yingchun Gong, Eduardo Villalobo, Zifeng Zhan, Weisong FengAbstract:Peritrich ciliates have been traditionally subdivided into two orders, Sessilida and Mobilida within the subclass Peritrichia. However, all the existing small subunit (SSU) rRNA phylogenetic trees showed that the sessilids and mobilids did not branch together. To shed some light on this disagreement, we tested whether or not the classic Peritrichia is a monophyletic group by assessing the reliability of the SSU rRNA phylogeny in terms of congruency with alpha-tubulin phylogeny. For this purpose, we obtained 10 partial alpha-tubulin sequences from Peritrichs and built phylogenetic trees based on alpha-tubulin nucleotide and amino acid data. A phylogenetic tree from the alpha-tubulin and SSU rRNA genes in combination was also constructed and compared with that from the SSU rRNA gene using a similar species sampling. Our results show that the mobilids and sessilids are consistently separated in all trees, which reinforces the idea that the Peritrichs do not constitute a monophyletic group. However, in all alpha-tubulin gene trees, the urceolariids and trichodiniids do not group together, suggested mobilids may not be a monophyletic group.
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reconsideration of phylogenetic relationships of the subclass Peritrichia ciliophora oligohymenophorea based on small subunit ribosomal rna gene sequences with the establishment of a new subclass mobilia kahl 1933
Journal of Eukaryotic Microbiology, 2009Co-Authors: Zifeng Zhan, Alan Warren, Yingchun GongAbstract:Based on its characteristic oral apparatus, the ciliate subclass Peritrichia has long been recognized as a monophyletic assemblage composed of the orders Mobilida and Sessilida. Following the application of molecular methods, the monophyly of Peritrichia has recently been questioned. We investigated the phylogenetic relationships of the Peritrichous ciliates based on four further complete small subunit ribosomal RNA sequences of mobilids, namely Urceolaria urechi, Trichodina meretricis, Trichodina sinonovaculae, and Trichodina ruditapicis. In all phylogenetic trees, the mobilids never clustered with the sessilids, but instead formed a monophyletic assemblage related to the peniculines. By contrast, the sessilids formed a sister clade with the hymenostomes at a terminal position within the Oligohymenophorea. We therefore formally separate the mobilids from the sessilids (Peritrichia sensu stricto) and establish a new subclass, Mobilia Kahl, 1933, which contains the order Mobilida Kahl, 1933. We argue that the oral apparatus in the mobilians and sessilid Peritrichs is a homoplasy, probably due to convergent evolution driven by their similar life-styles and feeding strategies. Morphologically, the mobilians are distinguished from all other oligohymenophoreans by the presence of the adhesive disc, this character being a synapomorphy for the Mobilia.
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Reevaluation of the phylogenetic relationship between mobilid and sessilid Peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences.
The Journal of eukaryotic microbiology, 2006Co-Authors: Yingchun Gong, Eduardo Villalobo, Fei-yun Zhu, Wei MiaoAbstract:Based on morphological characters, Peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on Peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within Peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the Peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of Peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the center of the adhesive disc, branched separately from its congeners, Trichodina nobilis and Trichodina heterodentata, trichodinids without such granules. This indicates that granules in the adhesive disc might be a phylogenetic character of high importance within the Family Trichodinidae.
Weibo Song - One of the best experts on this subject based on the ideXlab platform.
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Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl.
Molecular phylogenetics and evolution, 2021Co-Authors: Chundi Wang, Tengteng Zhang, Weibo Song, Saleh A. Al-farraj, Yunyi Gao, Yong Chi, Hamed A. El-serehy, Feng GaoAbstract:Abstract The class Oligohymenophorea is one of the most diverse assemblage of ciliated protists, which are particularly important in fundamental biological studies including understanding the evolutionary relationships among the lineages. Phylogenetic relationships within the class remain largely elusive, especially within the subclass Peniculia, which contains the long-standing problematic taxa Urocentrum and Paranassula. In the present study, we sequenced the genomes and/or transcriptomes of six non-culturable oligohymenophoreans using single-cell sequencing techniques. Phylogenomic analysis was performed based on expanded taxon sampling of 86 taxa, including 157 nuclear genes encoding 36,953 amino acids. The results indicate that: (1) urocentrids form an independent branch that is sister to the clade formed by Scuticociliatia and Hymenostomatia, which, together with the morphological data, supports the establishment of a new subclass, Urocentria n. subcl., within Oligohymenophorea; (2) phylogenomic analysis and ortholog comparison reveal a close relationship between Paranassula and peniculines, providing corroborative evidence for removing Paranassula from Nassulida and elevating it as an order, Paranassulida, within the subclass Peniculia; (3) based on the phylogenomic analyses and morphological data, we hypothesize that Peritrichia is the earliest diverging clade within Oligohymenophorea while Scuticociliatia and Hymenostomatia share the most common ancestor, followed successively by Urocentria and Peniculia. In addition, stop codon analyses indicate that oligohymenophoreans widely use UGA as the stop codon, while UAR are reassigned to glutamate (Peritrichs) or glutamine (others), supporting the evolutionary hypothesis.
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morphology and molecular analyses of four epibiotic Peritrichs on crustacean and polychaete hosts including descriptions of two new species ciliophora Peritrichia
European Journal of Protistology, 2020Co-Authors: Zhuo Shen, Alan Warren, Qianqian Zhang, Weibo SongAbstract:Four epibiotic sessilid Peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalisMobius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.
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systematic studies on ciliates alveolata ciliophora in china progress and achievements based on molecular information
European Journal of Protistology, 2017Co-Authors: Feng Gao, Alan Warren, Qianqian Zhang, Jie Huang, Yan Zhao, Weiwei Liu, Miao Miao, Hamed A Elserehy, Weibo SongAbstract:Due to complex morphological and convergent morphogenetic characters, the systematics of ciliates has long been ambiguous. Since 1990, the Laboratory of Protozoology, Ocean University of China, in collaboration with other research groups worldwide, has carried out a series of integrative investigations on ciliate systematics. To date, genomic DNA has been extracted from about 1700 ciliate strains, and phylogenetic analyses have been performed for two-thirds of orders. Main findings are: (1) Classifications of about 50 hypotrichous species have been resolved, although the monophylies of three hypotrichous orders remain unconfirmed; (2) Euplotia and two orders and all seven families within them are monophyletic assemblages; (3) Lynnella represents an order-level taxon, and is separated from two sister monophyletic subclasses Oligotrichia and Choreotrichia; (4) the Peritrich families Zoothamniidae and Vorticellidae are separated from each other, and Zoothamnium exhibits a high genetic diversity; (5) the scuticociliate order Philasterida is monophyletic and separated from loxocephalids, and the thigmotrichids is a suborder within Pleuronematida; (6) 14 classes were recovered including one new class Protocruziea, and Mesodiniea is basal to subphyla Intramacronucleata and Postciliodesmatophora; (7) mitochondrial cytochrome c oxidase subunit I heteroplasmy was reported in ciliates for the first time, and candidate barcoding genes for Frontonia species identification were identified.
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the all data based evolutionary hypothesis of ciliated protists with a revised classification of the phylum ciliophora eukaryota alveolata
Scientific Reports, 2016Co-Authors: Feng Gao, Alan Warren, Qianqian Zhang, Jun Gong, Ping Sun, Jie Huang, Miao Miao, Weibo SongAbstract: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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description of paratetrahymena parawassi n sp using morphological and molecular evidence and a phylogenetic analysis of paratetrahymena and other taxonomically ambiguous genera in the order loxocephalida ciliophora oligohymenophorea
Journal of Eukaryotic Microbiology, 2010Co-Authors: Qianqian Zhang, John C. Clamp, Xinpeng Fan, Khaled A S Alrasheid, Weibo SongAbstract:The marine scuticociliate Paratetrahymena parawassi n. sp. is described on the basis of morphology, especially infraciliature, and the sequence of its small subunit (SSU) rRNA gene to become the second known member of its genus. Paratetrahymena and other ciliates in the order Loxocephalida possess a mixture of morphological and morphogenetic features characteristic of the subclasses Hymenostomatia and Scuticociliatia. Accordingly, we used SSU rRNA sequences to analyze the phylogeny of Paratetrahymena and three other loxocephalid genera. Paratetrahymena and Cardiostomatella vermiformis formed a moderately well-supported clade that diverged at a deep level from all other scuticociliates, supporting separation of loxocephalids from other scuticociliates as a suprafamilial taxon. Sathrophilus holtae was a sister taxon to Paratetrahymena and Cardiostomatella in a poorly supported, unresolved relationship; nevertheless, association of all three genera into a single clade was supported by an approximately unbiased (AU) test. Any association of these genera singly or as a group with the Hymenostomatia was rejected decisively by AU tests and by a complete absence in the loxocephalids of the unique nucleotide identities that distinguish hymenostomes. Therefore, the morphological and morphogenetic similarities of loxocephalids to hymenostomes may be plesiomorphies, and the conflicting mix of scuticociliate and hymenostome characteristics seen in loxocephalids may result from differing rates of character evolution. Dexiotrichides pangi and Urocentrum, which is currently classified as a peniculid, formed a small clade that associated with hymenostomes and Peritrichs. Monophyly of the Loxocephalida with Dexiotrichides and/or Urocentrum included was not rejected by AU; however, inclusion of Urocentrum in the Peniculia was rejected by AU tests. A hypothesis is offered to explain the lack of resolution of loxocephalid ciliates and Urocentrum in phylogenetic trees, namely that their phylogenetic positions are influenced by a combination of heterogeneous data and long-branch attraction caused by poor representation of taxa in analyses. The well-known genus Cyclidium, a member of the order Pleuronematida, was revealed to be polyphyletic as a byproduct of our analyses of loxocephalids. In particular, Cyclidium porcatum appears to fall outside the clade containing typical members of the subclass Scuticociliatia and thus invites investigation as a possible member of the order Loxocephalida.
