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Denis H. Lynn - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic Analysis of Nassula variabilis n. sp., Furgasonia blochmanni , and Pseudomicrothorax dubius Confirms a Nassophorean Clade
Protist, 2018Co-Authors: Denis H. Lynn, Martin Kolisko, William A BourlandAbstract:The class Nassophorea includes the microthoracids and nassulids, which share morphological similarities in their somatic kinetids and cytopharyngeal baskets. The monophyly of this clade has been challenged by small subunit rRNA gene sequences and multi-gene analyses that do not provide strong support. To provide a more robust test of the monophyly of the Nassophorea, phylogenomic analyses were based on 124 genes derived from the single-cell transcriptomes of the microthoracid Pseudomicrothorax dubius and the nassulid Furgasonia blochmanni. The nassulid Nassula sorex from the Culture Centre for Algae and Protozoa was also included, but this isolate was discovered to have been misidentified. We first redescribe, using light and scanning electron microscopical techniques, this "N. sorex" as a new species of Nassula, Nassula variabilis n. sp., characterized by its highly variable nassulid frange. We have sequenced the single-cell transcriptomes to obtain data for phylogenomic analyses. These gave robust support for the Nassophorea, which are sister to a clade of Colpodea species. If our topology truly represents the order of divergence of taxa, a cytopharyngeal basket with microtubular nematodesmata and with Y and Z microtubular ribbons was likely an ancestral feature, at least of the Phyllopharyngea, Colpodea, Nassophorea, and Oligohymenophorea.
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Redescription and phylogenetic analyses of Durchoniella spp. (Ciliophora, Astomatida) associated with the polychaete Cirriformia tentaculata (Montagu, 1808).
European journal of protistology, 2017Co-Authors: Anne-laure Sauvadet, Denis H. Lynn, Erwan Roussel, Sophie Le Panse, Estelle Bigeard, Joseph Schrével, Laure GuillouAbstract:Microscopic and phylogenetic analyses were performed on endocommensal astome ciliates retrieved from the middle intestine of a marine cirratulid polychaete, Cirriformia tentaculata, collected in the bay of Roscoff (English Channel, Northwest French coast) and on the Southwest English coast. Three morphotypes of the astome genus Durchoniella were identified, two corresponding to described species (the type species Durchoniella brasili (Leger and Duboscq, 1904) De Puytorac, 1954 and Durchoniella legeriduboscqui De Puytorac, 1954) while a third morphotype remains undescribed. Their small subunit (SSU) rRNA gene sequences showed at least 97.2% identity and phylogenetic analyses grouped them at the base of the subclass Scuticociliatia (Oligohymenophorea), as a sister lineage to all astomes from terrestrial oligochaete annelids. Ultrastructural examination by transmission electron microscopy and fluorescence in situ hybridization analyses revealed the presence of endocytoplasmic cocci and rod-shaped bacteria surrounded by a very thin membrane. These endocytoplasmic bacteria may play a role in the association between endocommensal astome ciliates and cirratulid polychaetes inhabiting in anoxic coastal sediments.
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Redescription and phylogenetic analyses of Durchoniella spp. (Ciliophora, Astomatida) associated with the polychaete Cirriformia tentaculata (Montagu, 1808)
European Journal of Protistology, 2017Co-Authors: Laure Sauvadet, Denis H. Lynn, Erwan Roussel, Sophie Le Panse, Estelle Bigeard, Joseph Schrével, Laure GuillouAbstract:Microscopic and phylogenetic analyses were performed on endocommensal astome ciliates retrieved from the middle intestine of a marine cirratulid polychaete, Cirriformia tentaculata, collected in the bay of Roscoff (English Channel, Northwest French coast) and on the Southwest English coast. Three morphotypes of the astome genus Durchoniella were identified, two corresponding to described species (the type species Durchoniella brasili (Léger and Duboscq, 1904) De Puytorac, 1954 and Durchoniella legeriduboscqui De Puytorac, 1954) while a third morphotype remains undescribed. Their small subunit (SSU) rRNA gene sequences showed at least 97.2% identity and phylogenetic analyses grouped them at the base of the subclass Scuticociliatia (Oligohymenophorea), as a sister lineage to all astomes from terrestrial oligochaete annelids. Ultrastructural examination by transmission electron microscopy and fluorescence in situ hybridization analyses revealed the presence of endocytoplasmic cocci and rod-shaped bacteria surrounded by a very thin membrane. These endocytoplasmic bacteria may play a role in the association between endocommensal astome ciliates and cirratulid polychaetes inhabiting in anoxic coastal sediments.
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Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic.
Molecular phylogenetics and evolution, 2016Co-Authors: Eleni Gentekaki, Martin Kolisko, Yingchun Gong, Denis H. LynnAbstract:The phylum Ciliophora is one of the most broadly studied protozoan lineages. The era of molecular investigation has brought forth a major ongoing debate: is the subclass Peritrichia Stein, 1859 monophyletic? Numerous analyses mostly using the small subunit (SSU) rRNA gene have failed to recover the Mobilida and Sessilida, the two peritrich orders, as sister clades. Here we have sequenced five peritrich species - three sessilids and two mobilids. We constructed a supermatrix of 158 genes and 44,696 characters for 24 ciliate species, and as outgroup taxa, nine species from the Apicomplexa and four from the Dinophyceae. Our analyses using both maximum likelihood and Bayesian methods recover a monophyletic class Oligohymenophorea and two robust clades within it. The first clade is a monophyletic Peritrichia with the orders Sessilida and Mobilida maximally supported as sister clades. The second Oligohymenophorean clade includes species of the subclasses Scuticociliatia and Hymenostomatia, which are sister clades. Our analyses resolve a long-standing debate in ciliate molecular phylogenetics and provide support for the classical view that the morphological features of the two peritrich orders Mobilida and Sessilida arose by descent from the same common ancestor and are not the result of convergence.
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comparative analysis of the mitochondrial cytochrome c oxidase subunit i coi gene in ciliates alveolata ciliophora and evaluation of its suitability as a biodiversity marker
Systematics and Biodiversity, 2010Co-Authors: Michaela C Struderkypke, Denis H. LynnAbstract:The mitochondrial cytochrome c oxidase subunit 1 (COI) gene of ciliates was first successfully sequenced in species of the genera Tetrahymena and Paramecium (Class Oligohymenophorea). The sequence of the COI gene is extremely divergent from other eukaryotes and includes an insert, which is over 300 nucleotides long. In this study, we designed a primer pair that successfully amplified the COI gene of ciliates from five different classes: Heterotrichea, Spirotrichea, Oligohymenophorea, Nassophorea and Colpodea. These classes represent the diversity of the phylum Ciliophora very well, since they are widely distributed on the ciliate small subunit rRNA tree. The amplified region is approximately 850 nucleotides long and corresponds to the general barcoding region; it also includes the insert region. In this study, 58 new COI sequences from over 38 species in 13 orders are analysed and compared, and distance trees are constructed. While the COI gene shows high divergence within ciliates, the insert region, whi...
Wei Miao - One of the best experts on this subject based on the ideXlab platform.
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Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics
Molecular phylogenetics and evolution, 2018Co-Authors: Chuanqi Jiang, Alan Warren, Jin-mei Feng, Jie Xiong, Guangying Wang, Wentao Yang, Zong-yi Sun, Wei MiaoAbstract:Peritrichia is a large and distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades the evolutionary relationships of this subclass have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions. In this study, we provide genomic-scale data from 12 typical representatives. We combine taxon- and gene-rich phylogenomic analyses, with up to 151 genes (43,956 amino acid residues) from 18 freshwater, brackish and marine isolates in order to assess the systematics and evolutionary history of the Peritrichia. The main findings were: (1) the subclass Peritrichia originates from the end of the Proterozoic to the Cambrian; (2) the monophyletic Peritrichia is sister to the Peniculia (represented by Paramecium) within the class Oligohymenophorea; (3) spasmin plays a significant role in peritrich evolution: we detected the spasmin gene in target ciliates and traced the molecular evolution of spasmin, a key spasmoneme component, together with phylogenetic relationships and morphology of the peritrichs. These findings provide evidence that spasmin is an important molecule to illustrate the phylogenetic position of Peritrichia within the class Oligohymenophorea, the monophyly of Peritrichia, and the diverse and rapid evolution of sessilid peritrichs.
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Phylogenomic analysis of Balantidium ctenopharyngodoni (Ciliophora, Litostomatea) based on single-cell transcriptome sequencing
Parasite (Paris France), 2017Co-Authors: Zong-yi Sun, Chuanqi Jiang, Jin-mei Feng, Wentao Yang, Wei MiaoAbstract:In this paper, we present transcriptome data for Balantidium ctenopharyngodoni Chen, 1955 collected from the hindgut of grass carp (Ctenopharyngodon idella ). We evaluated sequence quality and de novo assembled a preliminary transcriptome, including 43.3 megabits and 119,141 transcripts. Then we obtained a final transcriptome, including 17.7 megabits and 35,560 transcripts, by removing contaminative and redundant sequences. Phylogenomic analysis based on a supermatrix with 132 genes comprising 53,873 amino acid residues and phylogenetic analysis based on SSU rDNA of 27 species were carried out herein to reveal the evolutionary relationships among six ciliate groups: Colpodea, Oligohymenophorea, Litostomatea, Spirotrichea, Heterotrichea and Protocruziida. The topologies of both phylogenomic and phylogenetic trees are discussed in this paper. In addition, our results suggest that single-cell sequencing is a sound method of obtaining sufficient omics data for phylogenomic analysis, which is a good choice for uncultivable ciliates. The transcriptome data for Balantidium ctenopharyngodoni are the first omics data within the subclass Trichostomatia, and provide a good basis for ciliate phylogenomic analysis, as well as related omics analysis.
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Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea
Molecular phylogenetics and evolution, 2015Co-Authors: Jin-mei Feng, Alan Warren, Chuanqi Jiang, Miao Tian, Jun Cheng, Guang-long Liu, Jie Xiong, Wei MiaoAbstract:Scuticociliates and hymenostomes are two groups of the ciliate class Oligohymenophorea, a diverse clade that includes two model genera, Tetrahymena and Paramecium, which have been intensively studied due to their ease of culture and their amenability to a wide range of biochemical and genetic investigations. However, phylogenetic relationships among the subclasses of the Oligohymenophorea, and especially between the Scuticociliatia and Hymenostomatia, are not clearly resolved. Here, we investigate the phylogenetic relationship between the subclasses Scuticociliatia and Hymenostomatia based on omics data. The transcriptomes of five species, comprising four Oligohymenophoreans and one colpodean, were sequenced. A supermatrix was constructed for phylogenomic analyses based on 113 genes encoding 43,528 amino acid residues from 26 taxa, including ten representatives of the class Oligohymenophorea. Our phylogenomic analyses revealed that the monophyletic Scuticociliatia is sister to the monophyletic Hymenostomatia, which together form the terminal branch within the monophyletic class Oligohymenophorea. Competing hypotheses for this relationship were rejected by topological tests. Our results provide corroborative evidence for the close relationship between the subclasses Scuticociliatia and Hymenostomatia, justifying the possible use of the model hymenostome T. thermophila as an effective experimental system to study the molecular and cellular biology of the scuticociliates. (C) 2015 Elsevier Inc. All rights reserved.
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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.
Sergei I. Fokin - One of the best experts on this subject based on the ideXlab platform.
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New Paramecium (Ciliophora, Oligohymenophorea) congeners shape our view on its biodiversity
Organisms Diversity & Evolution, 2015Co-Authors: Sascha Krenek, Thomas U. Berendonk, Sergei I. FokinAbstract:Paramecium is one of the best known and most intensely studied ciliate genera. It currently comprises 18 morphospecies including the P. aurelia complex of 15 sibling species. Here, we describe the new morphospecies Paramecium buetschlii sp. nov. from a freshwater pool in Norway, featuring unusual combinations of morphological characters and a high genetic diversity relative to other congeners. Three further investigated Paramecium spp. from Germany, Hungary, and Brazil are treated as cryptic species, because they are difficult to discriminate from other members of the genus relying on morphological criteria only. However, DNA-based taxonomic markers (18S-rDNA and mitochondrial COI) clearly indicate they are separate species. Due to the lack of an appropriate systematic term within the International Code of Zoological Nomenclature for distinguishing cryptic from valid biological species, we propose the provisional status Eucandidatus as a component of the taxonomic name when describing new but cryptic eukaryotes. Based on our data, we postulate that even within Europe there is a higher biodiversity within this common ciliate group that is heavily used in the classroom. By uncovering potentially distinct species that have been classified under the same species names, our molecular analyses further suggest a higher current stock diversity in Paramecium than previously thought. We also would like to emphasize that under-sampling is another major issue in estimating protist diversity. Future large-scale studies based on extensive sampling not only in exotic and remote regions, but also in less frequently sampled areas, will therefore likely improve our understanding of species richness and diversity.
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Paramecium tredecaurelia: A unique non-polymorphic species of the p. aurelia spp. complex (Oligohymenophorea, Ciliophora)
Acta Protozoologica, 2013Co-Authors: Ewa Przyboś, Sebastian Tarcz, Marta Surmacz, Natalia Sawka, Sergei I. FokinAbstract:New stands of Paramecium tredecaurelia , a rare species of the P. aurelia spp. complex, were identified in Thailand and Madagascar on the basis of mating reactions and molecular markers (rDNA and mtDNA). Analysis of DNA fragments showed that all P. tredecaurelia strains, the recently recorded ones and the ones known previously from France, Mexico, and Israel, form a monophyletic and well-defined clade in the P. aurelia species trees. All of these strains, collected from different localities around the world, represent identical or nearly identical haplotypes in terms of all the studied DNA fragments. Given the huge distances between particular collection sites, such a low level of variability of the studied sequences may result from a slow rate of evolution in P. tredecaurelia .
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Frequency and biodiversity of symbionts in representatives of the main classes of Ciliophora.
European journal of protistology, 2012Co-Authors: Sergei I. FokinAbstract:Abstract Representatives of all classes of Ciliophora have been studied for the detection and investigation of both prokaryotic and eukaryotic (not algal) endo- (EnS) and ectosymbionts (EcS). Different methods including transmission electron microscopy (TEM) and fluorescence in situ hybridisation (FISH) have been used. Apparently, the capability of keeping symbionts varies among the different ciliate groups as it generally is the case in different protist taxa. Most of the prokaryotic EnSs detected belong to Alphaproteobacteria. Holospora or Holospora -like infectious bacteria of this group were found in representatives of Heterotrichea, Armophorea, Phyllopharyngea, Prostomatea and mainly of Oligohymenophorea. Bacteria associated with bacteriophages were found in species of Heterotrichea and Oligohymenophorea. This holds true also for bacteria with R-bodies. A quite rare type of EnS – motile bacteria – was found in ciliates of the same two classes as well, either in the cytoplasm (Heterotrichea) or in the macronucleus and its perinuclear space (Oligohymenophorea). EcSs are more common in Heterotrichea, Armophorea and Plagiopylea, but were never found in other groups. Among the eukaryotic EnSs of ciliates, very few representatives of Microsporidia and Trypanosomatidae were recorded. In conclusion, heterotrichs and Oligohymenophoreans are the most promising groups of Ciliophora for the investigation of symbiosis.
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apofrontonia dohrni sp n and the phylogenetic relationships within peniculia protista ciliophora Oligohymenophorea
Zoologica Scripta, 2006Co-Authors: Sergei I. Fokin, Ilaria Andreoli, Franco Verni, Giulio PetroniAbstract:Apofrontonia dohrni, a new peniculine ciliate, was discovered in a slightly brackish water sample from Mediterranean coastline puddle in Naples, Italy. Its morphology was studied in vivo, in silver- and Feulgen-stained preparations, as well as at the scanning electron microscope; 18S rRNA gene sequence was also determined. The species is characterized by a medium cell size (118 × 61 µm — fixed cell) and an oval-extended body, flattened dorsoventrally; a very long sausage-like macronucleus rolled up into almost a ring; a comparatively large compact micronucleus; relatively small number of vestibular kineties (4) and a peculiar structure of 3 peniculi, consisting of 5-6, 4-5 and 3 ciliary rows, respectively. The ciliate always has about 20 contractile vacuoles distributed beneath its entire body surface. Using these features, A. dohrni, definitely, can be easily discriminated from the two other species of the genus: Apofrontonia lametschwandtneri and Apofrontonia obtusa. The general re-analysis of morphological characters of Apofrontonia spp. allowed us to remove this genus from family Frontoniidae, where it was put in the first description (Foissner & Song 2002). We provisionally consider genus Apofrontonia as incertae sedis within the order Peniculida due to (i) the limited number of morphological characters joining Apofrontonia to already described Peniculida families and (ii) the absence of molecular data for most representatives of Peniculida families. Frontonia leucas 18S rRNA gene was also characterized to increase the balance among represented taxa. According to the present analysis, Apofrontonia so far appears more closely related to Paramecium than to Frontonia.
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Phylogenetic Relationships of the Genus Paramecium Inferred from Small Subunit rRNA Gene Sequences
Molecular phylogenetics and evolution, 2000Co-Authors: Michaela C. Strüder-kypke, Sergei I. Fokin, André-denis G. Wright, Denis H. LynnAbstract:Abstract The genus Paramecium includes species that are well known and very common in freshwater environments. Species of Paramecium are morphologically divided into two distinct groups: the “ bursaria ” subgroup (foot-shaped) and the “ aurelia ” subgroup (cigar-shaped). Their placement within the class Oligohymenophorea has been supported by the analysis of the small subunit rRNA gene sequence of P. tetraurelia. To confirm the stability of this placement and to resolve relationships within the genus, small subunit rRNA gene sequences of P. bursaria, P. calkinsi, P. duboscqui, P. jenningsi, P. nephridiatum, P. primaurelia, and P. polycaryum were determined and aligned. Trees constructed using distance-matrix, maximum-likelihood, and maximum-parsimony methods all depicted the genus as a monophyletic group, clustering with the other Oligohymenophorean taxa. Within the Paramecium clade, P. bursaria branches basal to the other species, although the remaining species of the morphologically defined “ bursaria ” subgroup do not group with P. bursaria, nor do they form a monophyletic subgroup. However, the species of the “ aurelia ” subgroup are closely related and strongly supported as a monophyletic group.
Yingchun Gong - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic.
Molecular phylogenetics and evolution, 2016Co-Authors: Eleni Gentekaki, Martin Kolisko, Yingchun Gong, Denis H. LynnAbstract:The phylum Ciliophora is one of the most broadly studied protozoan lineages. The era of molecular investigation has brought forth a major ongoing debate: is the subclass Peritrichia Stein, 1859 monophyletic? Numerous analyses mostly using the small subunit (SSU) rRNA gene have failed to recover the Mobilida and Sessilida, the two peritrich orders, as sister clades. Here we have sequenced five peritrich species - three sessilids and two mobilids. We constructed a supermatrix of 158 genes and 44,696 characters for 24 ciliate species, and as outgroup taxa, nine species from the Apicomplexa and four from the Dinophyceae. Our analyses using both maximum likelihood and Bayesian methods recover a monophyletic class Oligohymenophorea and two robust clades within it. The first clade is a monophyletic Peritrichia with the orders Sessilida and Mobilida maximally supported as sister clades. The second Oligohymenophorean clade includes species of the subclasses Scuticociliatia and Hymenostomatia, which are sister clades. Our analyses resolve a long-standing debate in ciliate molecular phylogenetics and provide support for the classical view that the morphological features of the two peritrich orders Mobilida and Sessilida arose by descent from the same common ancestor and are not the result of convergence.
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Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages.
Molecular phylogenetics and evolution, 2014Co-Authors: Eleni Gentekaki, Martin Kolisko, Yingchun Gong, Letizia Modeo, V. Boscaro, K.j. Bright, F. Dini, G. Di Giuseppe, C. Miceli, R.e. MolestinaAbstract:The Ciliophora is one of the most studied protist lineages because of its important ecological role in the microbial loop. While there is an abundance of molecular data for many ciliate groups, it is commonly limited to the 18S ribosomal RNA locus. There is a paucity of data when it comes to availability of protein-coding genes especially for taxa that do not belong to the class Oligohymenophorea. To address this gap, we have sequenced EST libraries for 11 ciliate species. A supermatrix was constructed for phylogenomic analysis based on 158 genes and 42,158 characters and included 16 ciliates, four dinoflagellates and nine apicomplexans. This is the first multigene-based analysis focusing on the phylum Ciliophora. Our analyses reveal two robust superclades within the Intramacronucleata; one composed of the classes Spirotrichea, Armophorea and Litostomatea (SAL) and another with Colpodea and Oligohymenophorea. Furthermore, we provide corroborative evidence for removing the ambiguous taxon Protocruzia from the class Spirotrichea and placing it as incertae sedis in the phylum Ciliophora. (C) 2014 Elsevier Inc. All rights reserved.
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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.
Alan Warren - One of the best experts on this subject based on the ideXlab platform.
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Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics
Molecular phylogenetics and evolution, 2018Co-Authors: Chuanqi Jiang, Alan Warren, Jin-mei Feng, Jie Xiong, Guangying Wang, Wentao Yang, Zong-yi Sun, Wei MiaoAbstract:Peritrichia is a large and distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades the evolutionary relationships of this subclass have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions. In this study, we provide genomic-scale data from 12 typical representatives. We combine taxon- and gene-rich phylogenomic analyses, with up to 151 genes (43,956 amino acid residues) from 18 freshwater, brackish and marine isolates in order to assess the systematics and evolutionary history of the Peritrichia. The main findings were: (1) the subclass Peritrichia originates from the end of the Proterozoic to the Cambrian; (2) the monophyletic Peritrichia is sister to the Peniculia (represented by Paramecium) within the class Oligohymenophorea; (3) spasmin plays a significant role in peritrich evolution: we detected the spasmin gene in target ciliates and traced the molecular evolution of spasmin, a key spasmoneme component, together with phylogenetic relationships and morphology of the peritrichs. These findings provide evidence that spasmin is an important molecule to illustrate the phylogenetic position of Peritrichia within the class Oligohymenophorea, the monophyly of Peritrichia, and the diverse and rapid evolution of sessilid peritrichs.
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high density cultivation of the marine ciliate uronema marinum ciliophora Oligohymenophorea in axenic medium
Acta Protozoologica, 2015Co-Authors: Weibo Zheng, Alan WarrenAbstract:Uronema marinum is a cosmopolitan marine ciliate. It is a facultative parasite and the main causative agent of outbreaks of scuticociliatosis in aquaculture fish. This study reports a method for the axenic cultivation of U. marinum in high densities in an artificial medium comprising proteose peptone, glucose and yeast extract powder as its basic components. The absence of bacteria in the cultures was confirmed by fluorescence microscopy of DAPI-stained samples and the failure to recover bacterial SSU-rDNA using standard PCR methods. Using this axenic medium, a maximum cell density of 420,000 ciliate cells/ml was achieved, which is significantly higher than in cultures using living bacteria as food or in other axenic media reported previously. This method for high-density axenic cultivation of U. marinum should facilitate future research on this economically important facultative fish parasite.
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Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea
Molecular phylogenetics and evolution, 2015Co-Authors: Jin-mei Feng, Alan Warren, Chuanqi Jiang, Miao Tian, Jun Cheng, Guang-long Liu, Jie Xiong, Wei MiaoAbstract:Scuticociliates and hymenostomes are two groups of the ciliate class Oligohymenophorea, a diverse clade that includes two model genera, Tetrahymena and Paramecium, which have been intensively studied due to their ease of culture and their amenability to a wide range of biochemical and genetic investigations. However, phylogenetic relationships among the subclasses of the Oligohymenophorea, and especially between the Scuticociliatia and Hymenostomatia, are not clearly resolved. Here, we investigate the phylogenetic relationship between the subclasses Scuticociliatia and Hymenostomatia based on omics data. The transcriptomes of five species, comprising four Oligohymenophoreans and one colpodean, were sequenced. A supermatrix was constructed for phylogenomic analyses based on 113 genes encoding 43,528 amino acid residues from 26 taxa, including ten representatives of the class Oligohymenophorea. Our phylogenomic analyses revealed that the monophyletic Scuticociliatia is sister to the monophyletic Hymenostomatia, which together form the terminal branch within the monophyletic class Oligohymenophorea. Competing hypotheses for this relationship were rejected by topological tests. Our results provide corroborative evidence for the close relationship between the subclasses Scuticociliatia and Hymenostomatia, justifying the possible use of the model hymenostome T. thermophila as an effective experimental system to study the molecular and cellular biology of the scuticociliates. (C) 2015 Elsevier Inc. All rights reserved.
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Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora).
Molecular phylogenetics and evolution, 2013Co-Authors: Qianqian Zhang, Alan Warren, Xinpeng Fan, Jun Gong, Weibo SongAbstract:The Nassophorea and Prostomatea are two of the key classes in understanding the morphological diversification and higher classification of the phylum Ciliophora. However, their phylogenetic relationships with other ciliate groups within the subphylum Intramacronucleata remain elusive. In this study, we investigated the small and large subunit (SSU and LSU) rRNA gene-based phylogeny of these groups with sequences of additional taxa including several key species. The results show that: (1) the class Nassophorea remains polyphyletic, with the microthoracids clustering with the Phyllopharyngea, whereas the nassulids represent a basal group of the CONthreeP superclade in the SSU tree; (2) the Prostomatea is not depicted as a monophyletic group in phylogenetic trees, and the monophyly of this class is marginally rejected by statistical tree topology tests; (3) the nassulid genus Parafurgasonia is more closely related to the family Colpodidiidae than to Furgasonia; (4) Paranassula, which was previously thought to be a nassulid, is phylogenetically related to the Oligohymenophorean peniculids in both the SSU and LSU trees; (5) the microthoracid genus Discotricha does not group with the other microthoracids in either SSU or LSU trees; (6) the family Plagiocampidae is closely related to the prostome parasite Cryptocaryon irritans and to the family Urotrichidae in the order Prorodontida; and (7) the family Placidae, represented by Placus salinus, is sister to the family Holophryidae in the order Prorodontida. Based on the present data, we consider the genus Discotricha to be an unclassified taxon within the CONthreeP. We also propose resurrecting the order Paranassulida and classifying it within the subclass Peniculia, class Oligohymenophorea. Primary and secondary structure signatures for higher taxa within Phyllopharyngea and Nassophorea are supplied.
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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.
