The widely reported but poorly studied ciliate family Folliculinidae (Protozoa, Ciliophora, Heterotrichea): a revision with notes on its taxonomy, morphology and phylogenetic relationships

Ye, Tingting; Jiang, Yunpeng; Chen, Shuchang; Xu, Yan; Li, Lifang; Shin, Mann Kyoon; Chen, Xiangrui

doi:10.1007/s42995-022-00152-z

Cited by 12 publications

(6 citation statements)

References 66 publications

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“…We still observed dozens of stop codons in coding regions in both species after removing false positives caused by contaminations and detection artifacts, so we believe that they have low-frequency readthrough of TGA codons. Furthermore, we found many occurrences of TAG in coding regions in Brachonella spiralis (100) and Protocruzia tuzeti (316), which were previously assumed to use the standard genetic code ( Ye et al 2022 ).…”

Section: Resultsmentioning

confidence: 88%

Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates

Chen

Geng

Zhang

et al. 2023

Molecular Biology and Evolution

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Bifunctional stop codons that have both translation and termination functions in the same species are important for understanding the evolution and function of genetic codes in living organisms. Considering the high frequency of bifunctional codons but limited number of available genomes in ciliates, we de novo sequenced seven representative ciliate genomes to explore the evolutionary history of stop codons. We further propose a stop codon reassignment quantification method (stopCR) that can identify bifunctional codons and measure their frequencies in various eukaryotic organisms. Using our newly developed method, we found two previously undescribed genetic codes, illustrating the prevalence of bifunctional stop codons in ciliates. Overall, evolutionary genomic analyses suggest that gain or loss of reassigned stop codons in ciliates is shaped by their living environment, the eukaryotic release factor 1 (eRF1) and suppressor tRNAs (tRNAs with a stop codon anticodon). This study provides novel clues about the functional diversity and evolutionary history of stop codons in eukaryotic organisms.

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Section: Resultsmentioning

confidence: 88%

Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates

Chen

Geng

Zhang

et al. 2023

Molecular Biology and Evolution

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“…Four sequences from the order Colpodida, namely Colpoda magna EU039896, Colpoda minima EU039897, Bresslaua vorax MN160328, and Bresslauides discoideus OM278536, were set as the outgroup taxa. All sequences were aligned using the GUIDANCE2 Server (http://guidance.tau.ac.il) with default parameters (Penn et al, 2010), and both ends were manually trimmed in BioEdit 7.0.5.3 (Hall, 1999), following Ye et al (2022). Maximum likelihood (ML) analysis with 1000 bootstrap replicates was performed on the CIPRES Science Gateway server using RAxML-HPC2 on XSEDE v8.2.12 (Stamatakis, 2014) with the GTRGAMMA model.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

New contributions to the taxonomy and phylogeny of the ciliate genus Pleuronema (Ciliophora, Scuticociliatia), with descriptions of two new species collected from the subtropical coastal wetlands in China

Wu,

Liu,

et al. 2023

Front. Mar. Sci.

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Ciliates of the genus Pleuronema are a speciose and ubiquitous group. Recent studies suggest that there may be a sizable amount of undiscovered species diversity. In the present study, two new Pleuronema species have been isolated from the subtropical coastal waters of China and characterized using morphological and taxonomical methods: Pleuronema pulchra n. sp. is characterized by a body size of 75–90 × 25–40 µm in vivo, 32–48 somatic kineties, four to seven preoral kineties, somatic kinety 1 composed of about 80 kinetids, and membranelle 2a with a single-rowed mid-portion and hook-like posterior portion. Pleuronema warreni n. sp. is defined by a body size of 55–80 × 25–45 µm in vivo, 35–42 somatic kineties, three to six preoral kineties, somatic kinety 1 with approximately 75 kinetids, and a mid-portion of membranelle 2a that is single-rowed and extremely long (occupying > 75% length of M2a). The phylogenetic analysis of the small subunit ribosomal RNA genes of Pleuronema members, including those of the two novel species, shows that the genus Pleuronema is a polyphyletic group. Both new species form a cluster with Pleuronema binucleatum KT033424, P. elegans KF840518, and “P. coronatum” JX310014 (identification to be verified). Additionally, we provide an illustrated key for 20 “coronatum-type” Pleuronema species, including the two new ones.

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“…Ciliated protists, a diverse group of single-celled organisms, are vital components of various aquatic and terrestrial environments where they are important contributors to nutrient cycling and energy transfer (Hu et al 2019;Lu et al 2023;Lynn 2008;Wang et al 2022;Ye et al 2021a;Zhang et al 2022a). Members of the class Heterotrichea Stein 1859, a primitive group of ciliates characterized by their large cell size, somatic dikinetids associated with postciliodesmata, and a welldeveloped oral apparatus composed of an adoral zone of membranelles and a paroral membrane, have been widely used as model organisms in numerous biological disciplines including regeneration, ecology, nuclear function, and symbiotic relationships (Ahsan et al 2022;Chi et al 2021;Fernandes et al 2016;Hao et al 2022;Shazib et al 2014;Yan et al 2019;Ye et al 2022).…”

Section: Introductionmentioning

confidence: 99%

Exploring the biogeography, morphology, and phylogeny of the condylostomatid ciliates (Alveolata, Ciliophora, Heterotrichea), with establishment of four new Condylostoma species and a revision including redescriptions of five species found in China

Chi,

Wei,

Tang

et al. 2024

Mar Life Sci Technol

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Species of the ciliate class Heterotrichea Stein, 1859 are a cosmopolitan group of unicellular eukaryotic microorganisms, many of which have been widely used as models in various fields of research such as regenerative biology, functional ecology, environmental toxicology, and symbiotic behavior. However, species identification in the heterotrich family Condylostomatidae, especially the most species-rich and type genus Condylostoma Bory de Saint-Vincent, 1824, remains challenging due to incomplete original descriptions, few reliable distinguishing characters, and overlapping features between different species. This study presents an updated revision of Condylostoma and its related genus Condylostomides da Silva Neto, 1994 based on descriptions of five species, including nine populations collected from China, using both morphological and molecular methods. The main findings are as follows: (1) 43 nominal species and about 130 populations are reviewed, resulting in the recognition of 30 valid species of Condylostoma and eight valid species of Condylostomides; (2) keys, synonyms, biogeographic distributions and amended/improved diagnoses of all valid species are provided; (3) based on the available data, four new Condylostoma species (C. marinum sp. nov., C. petzi sp. nov., C. villeneuvei sp. nov., and C. microstomum sp. nov.), one new combination (Condylostomides minimus (Dragesco, 1954) comb. nov. & nom. corr.), and two corrected names (Condylostoma ancestrale Villeneuve-Brachon, 1940 nom. corr. and Condylostomides nigrus (Dragesco, 1960) nom. corr.) are suggested; (4) cryptic species are detected and proposed for the first time to form the Condylostoma curvum species complex; (5) three highly confusing Condylostoma species, C. kris, C. spatiosum, and C. minutum, are redefined for the first time based on modern taxonomic methods; (6) a ‘flagship’ species, Condylostomides coeruleus, is recorded for the first time from the continent of Asia, substantially expanding its biogeography; (7) ciliature adjacent to the distal end of the paroral membrane within the family Condylostomatidae is uniformly defined as frontal membranelles and is classified into three patterns according to the arrangement of kinetosomes, which serve as important key features.

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The widely reported but poorly studied ciliate family Folliculinidae (Protozoa, Ciliophora, Heterotrichea): a revision with notes on its taxonomy, morphology and phylogenetic relationships

Cited by 12 publications

References 66 publications

Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates

Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates

New contributions to the taxonomy and phylogeny of the ciliate genus Pleuronema (Ciliophora, Scuticociliatia), with descriptions of two new species collected from the subtropical coastal wetlands in China

Exploring the biogeography, morphology, and phylogeny of the condylostomatid ciliates (Alveolata, Ciliophora, Heterotrichea), with establishment of four new Condylostoma species and a revision including redescriptions of five species found in China

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