Published November 3, 2023
| Version v1
Journal article
Restricted
A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
Authors/Creators
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology* and Key Laboratory of Aquaculture Disease Control* Ministry of Agriculture* Institute of Hydrobiology* Chinese Academy of Sciences* Wuhan 430072* China
- 2. State Key Laboratory of Freshwater Ecology and Biotechnology* and Key Laboratory of Aquaculture Disease Control* Ministry of Agriculture* Institute of Hydrobiology* Chinese Academy of Sciences* Wuhan 430072* China & College of Advanced Agricultural Sciences* University of Chinese Academy of Sciences* Beijing 100049* China
- 3. Departamento de Microbiología y Parasitología* Facultad de Farmacia* Universidad Complutense de Madrid* Plaza Ramón y Cajal s/n* Madrid 28040* Spain
Description
Li, Ming, Hu, Guangran, Zhao, Weishan, Zou, Hong, Li, Wenxiang, Wu, Shangong, Wang, Guitang, Ponce-Gordo, Francisco (2024): A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes. Zoological Journal of the Linnean Society 201 (2): 269-289, DOI: 10.1093/zoolinnean/zlad150, URL: http://dx.doi.org/10.1093/zoolinnean/zlad150
Files
Linked records
Additional details
References
- Adl SM* Simpson AGB* Lane CE et al. The revised classification of eukaryotes. The Journal of Eukaryotic Microbiology 2012;59:429-93.
- Adl SM* Bass D* Lane CE et al. Revisions to the classification* nomenclature* and diversity of eukaryotes. Journal of Eukaryotic Microbiology 2019;66:4-119.
- Affa'a F-M. A propos des criteres de separation des genres d'Opalines: Protoopalina Metcalf*1918*Cepedea Metcalf*1920et Opalina(Purkinje et Valentin* 1835). Archiv fur Protistenkunde 1992;141:304-14.
- Affa'a F-M* Lynn D. A review of the classification and distribution of five opalinids from Africa and North America. Canadian Journal of Zoology 1994;72:665-74.
- Akaike H. A new look at the statistical model identification. IEEE Transactions on Automatic Control 1974;19:716-23.
- Allen MB* Armstrong HA. Arabia-Eurasia collision and the forcing of mid-Cenozoic global cooling. Palaeogeography, Palaeoclimatology, Palaeoecology 2008;265:52-8.
- Alvarez I* Wendel JF. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 2003;29:417-34.
- Ankerbrand MJ* Keller A* Wolf M et al. ITS2 Database V: twice as much. Molecular Biology and Evolution 2015;32:3030-2.
- Arisue N* Hashimoto T* Yoshikawa H et al. Phylogenetic position of Blastocystis hominis and of Stramenopiles inferred from multiple molecular sequence data. The Journal of Eukaryotic Microbiology 2002;49:42-53.
- Atkins MS* Teske AP* Anderson OR.A survey of flagellate diversity at four deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular approaches. The Journal of Eukaryotic Microbiology 2000;47:400-11.
- Benson G. Tandem repeats finder: a program to analyse DNA sequences. Nucleic Acids Research 1999;27:573-80.
- Bezzenberger E. Uber Infusorien aus asiatischen Anuren. Archiv fur Protistenkunde 1904;3:138-74.
- Canone JJ* Subramanian S* Schnare N et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal* intron* and other RNAs. BMC Bioinformatics 2002;3:2.
- Cavalier-Smith T* Chao EE. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). Journal of Molecular Evolution 2006;62:388-420.
- Chandra AK* Choudhury A. A new opalinid Hegneriella mukundai sp.n. from an Old World hylid Kaloula pulchra taprobanica Parker from India. Acta Protozoologica 1980;19:51-4.
- Collins AG. Evaluating multiple alternative hypotheses for the origin of Bilateria:an analysis of the 18S rRNA molecular evidence.Proceedings of the National Academy of Sciences of the United States of America 1998;95:15458-63.
- Corliss JO. The opalinid infusorians: flagellates or ciliates? Journal of Eukaryotic Microbiology 1955;2:107-14.
- Corliss JO. Flagellates* opalinids and the search for the most primitive ciliate and its progenitor. Ceylon Journal of Science (Biological Sciences) 1979;13:65-78.
- Corliss JO* Balamuth W. Consideration of the opalinids as a new superclass in the subphylum Sarcomastigophora. Journal of Protozoology 1963;10:26-7.
- Delvinquier BLJ* Patterson DJ. The Opalines. In: Kreier JP* Baker JR (eds.)* Parasitic Protozoa (2nd edn). San Diego:Academic Press* 1993* 247-325.
- Delvinquier BLJ* Markus MB* Passmore NI. Opalinidae in African Anura. II. Genera Protozelleriella n.g. and Zelleriella. Systematic Parasitology 1991;19:159-85.
- Delvinquier BLJ* Markus MB* Passmore NI. Opalinidae in African Anura. III. Genus Cepedea. Systematic Parasitology 1993;24:53-80.
- Earl PR. Hegneriella dobelli gen.n.* sp.n.* (Opalinidae) from Bufo valliceps and some remarks on the systematic position of the Opalinidae. Acta Protozoologica 1971;9:41-8.
- Earl PR. Hegneriella cheni sp.n. and Opalina wessenbergi sp.n. (Protozoa). Acta Protozoologica 1972;10:267-8.
- Earl PR. Suppressions and other taxonomic changes in the protozoan subphylum Opalinida. Publicaciones Biologicas del Instituto de Investigaciones Cientificas 1973;1:25-32.
- Earl PR. Notes on the taxonomy of the opalinids (Protozoa)* including remarks on continental drift. Transactions of the American Microscopical Society 1979;98:549-57.
- Evans DS* Harris B* Short R. The incidence of parasites found in frogs in Mercer* Summers* and Wyoming Counties* West Virginia. Proceedings of the West Virginia Academy of Science 1977;49:23-4.
- Fan H* Chu J-Y.A brief review of short tandem repeat mutation.Genomics, Proteomics & Bioinformatics 2007;5:7-14.
- Gao S* Song W* Ma H et al. Phylogeny of six genera of the subclass Haptoria (Ciliophora* Litostomatea) inferred from sequences of the gene coding for small subunit ribosomal RNA. The Journal of Eukaryotic Microbiology 2008;55:562-6.
- Gruber AR* Lorenz R* Bernhart SH et al. The Vienna RNA Websuite. Nucleic Acids Research 2008;36:W70-4.
- Grzebyk D* Sako Y* Berland B. Phylogenetic analysis of nine species of Prorocentrum (Dinophyceae) inferred from 18S ribosomal DNA sequences*morphologicalcomparisonsanddescriptionof Prorocentrum panamensis sp. nov. Journal of Phycology 1998;34:1055-68.
- Hancock JM* Dover GA. Molecular coevolution among cryptically simple expansion segments in eukaryotic 26S/28S rRNAs. Molecular Biology and Evolution 1998;5:377-92.
- Hara Y. Study on the general morphology and neuromotor system of Protoopalina axonucleata lata Metcalf parasitic on the Tonosama frog. Shokubutsu oyobi Dobutsu [Botany and Zoology] 1934;2:2015-22.
- Harries PJ. Dynamics of survival following the Cenomanian-Turonian (Upper Cretaceous) mass extinction event. Cretaceous Research 1993;14:563-83.
- Honigberg BM* Balamuth W* Bovee EC et al. A revised classification of the phylum Protozoa. The Journal of Protozoology 1964;11:7-20.
- Kalvari I* Nawrocki EP* Ontiveros-Palacios N et al. Rfam14: expanded coverage of metagenomics* viral and microRNA families. Nucleic Acids Research 2020;49:D192-200.
- Keller A* Schleicher T* Schultz J et al. 58S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 2009;430:50-7.
- Kostka M. Opalinata. In: Archibald JM* Simpson AGB* Slamovits CH (eds.)* Handbook of the Protists (2nd edn). Cham: Springer International* 2017* 543-65.
- Kostka M* Hampl V* Cepicka I et al. Phylogenetic position of Protoopalina intestinalis based on SSU rRNA gene sequence.Molecular Phylogenetics and Evolution 2004;33:220-4.
- Kostka M* Cepicka I* Hampl V et al. Phylogenetic position of Karotomorpha and paraphyly of Proteromonadidae. Molecular Phylogenetics and Evolution 2007;43:1167-70.
- Krenek S* Berendonk TU* Fokin SI. New Paramecium (Ciliophora* Oligohymenophorea) congeners shape our view on its biodiversity. Organisms Diversity & Evolution 2015;15:215-33.
- Kumar S* Stecher G* Li M et al. MEGA X: Molecular Evolutionary Genetic Analysis across computing platforms. Molecular Biology and Evolution 2018;35:1547-9.
- Kumar S* Suleski M* Craig JM et al. TimeTree 5: an expanded resource for species divergence times. Molecular Biology and Evolution 2022;39:msac174.
- Larkin MA* Blackshields G* Brown NP et al. Clustal W and Clustal X version 20. Bioinformatics 2007;23:2947-8.
- Lee JC* Gutell RR. A comparison of the crystal structures of eukaryotic and bacterial SSU ribosomal RNAs reveals common structural features in the hypervariable regions. PLoS One 2012;7:e38203.
- Leipe DD* Tong SM* Goggin CL et al. 16S-like rDNA sequences from Developayella elegans* Labyrinthuloides haliotidis* and Proteromonas lacertae confirm that the stramenopiles are a primarily heterotrophic group. European Journal of Protistology 1996;32:449-58.
- Levine ND* Corliss JO* Cox FE et al. A newly revised classification of the protozoa. The Journal of Protozoology 1980;27:37-58.
- Li C* Jin X* Li M et al. Light and transmission electron microscopy of Cepedea longa (Opalinidae) from Fejervarya limnocharis. Parasite 2017a;24:6.
- Li M* Li C* Grim JN et al. Supplemental description of Nyctotheroides pyriformis n. comb. (=Macrocytopharynxa pyriformis (Nie* 1932) Li et al. 2002) from frog hosts with consideration of the validity of the genus Macrocytopharynxa (Armophorea* Clevelandellida). European Journal of Protistology 2017b;58:152-63.
- Li M* Ponce-Gordo F* Grim JN et al. Morphological redescription of Opalina undulata Nie 1932 from Fejervarya limnocharis with molecular phylogenetic study of Opalinids (Heterokonta* Opalinea). The Journal of Eukaryotic Microbiology 2018;65:783-91.
- Li W* Wang C* Huang F et al. Redescription of Protoopalina pingi Nie* 1935 inhabiting the recta of Hylarana guentheri and Pelophylax nigromaculatus in China. Parasite 2014;21:46.
- Mandal M* Banerjee PS* Kumar S et al. Development of loop-mediated isothermal amplification (LAMP) for detection of Babesia gibsoni infection in dogs. Veterinary Parasitology 2015;209:50-5.
- Medlin LK* Elwood HJ* Stickel S et al. The characterization of enzymatically amplified 16S-like rRNA coding regions. Gene 1988;71:491-9.
- Metcalf MM. Opalina and the origin of the ciliate Infusoria. Journal of the Washington Academy of Sciences 1918;8:427-31.
- Metcalf MM. The classification of the Opalinidae.Science 1920;52:135-6.
- Metcalf MM. The opalinid ciliate infusorians. Bulletin of the US National Museum 1923;120:1-484.
- Metcalf MM. Further studies on the opalinid ciliate infusorians and their hosts. Proceedings of the United States National Museum 1940;87:465-634.
- Mignot JP. Patterning in opalinids. I. Implications of new morphological and ultrastructural findings on the genesis of kinetics. European Journal of Protistology 1994;30:196-210.
- Mignot JP* Brugerolle G. Etude ultrastructurale de differents types de kystes d'Opalines. The Journal of Protozoology 1974;21:649-58.
- Mohr JL. M.M. Metcalf and the significance of opalinid distribution. Journal of Protozoology 1959;6:13.
- Moreira D* von der Heyden S* Bass D et al. Global eukaryote phylogeny: combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria* Retaria and Excavata. Molecular Phylogenetics and Evolution 2007;44:255-66.
- Moriya M* Nakayama T* Inouye I. Ultrastructure and 18S rDNA sequence analysis of Wobblia lunata gen. et sp. nov.* a new heterotrophic flagellate (Stramenopiles* incertae sedis). Protist 2000;151:41-55.
- Nei M* Kumar S. Molecular Evolution and Phylogenetics. New York: Oxford University Press* 2000.
- Nie D. Intestinal ciliates of amphibian of Nanking. Contributions from the Biological Laboratory of the Science Society of China (zoological series) 1935;11:47-95.
- Nikbakht H* Xia X* Hickey D. The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium. Genome 2014;57:507-11.
- Nishi A* Ishida KI* Endoh H. Reevaluation of the evolutionary position of opalinids based on 18S rDNA* and α- and β-tubulin gene phylogenies. Journal of Molecular Evolution 2005;60:695-705.
- Noel C* Dufernez F* Gerbod D et al. Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity* identification of species* and zoonosis.Journal of Clinical Microbiology 2005;43:348-55.
- Ogedengbe ME* Ogedengbe JD* Whale JC et al. Molecular phylogenetic analysis of tissue coccidian (Sarcocystidae; Apicomplexa) based on nuclear 18s rDNA and mitochondrial COI sequences confirms the paraphyly of the genus Hammondia. Parasitology Open 2016;2:e2.
- Okamura T* Kondo R. Suigetsumonas clinomigrationis gen. et sp. nov.* a novel facultative anaerobic nanoflagellate isolated from the Meromictic Lake Suigetsu* Japan. Protist 2015;166:409-21.
- Parker MS* Balasubramaniam A* Parker SL. The expansion segments of human 28S rRNA match microRNAs much above 18S rRNA or core segments. MicroRNA 2018;7:128-37.
- Patterson DJ. The fine structure of Opalina ranarum (Family Opalinidae): opalinid phylogeny and classification. Protistologica 1985;21:413-28.
- Patterson DJ. Stramenopiles* chromophytes from a protistan perspective. In:GreenJC* LeadbeaterBSC* DiverWL (eds.)* The Chromophyte Algae, Problems and Perspectives. Oxford: Clarendon Press* 1989* 357-79.
- Ponce-Gordo F* Li M* Hu G et al. On the taxonomy and phylogeny of opalinids (Stramenopiles* Opalinata) inferred from the analysis of complete nuclear ribosomal DNA (rDNA) genes - alignments and phylogenetic trees. Mendeley Data, v1 2023. https://doi. org/10.17632/jpkrj85dxm.1
- Ramesh M* Woolford JL Jr. Eukaryote-specific rRNA expansion segments function in ribosome biogenesis. RNA 2016;22:1153-62.
- Richard G-F* Kerrest A* Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiology and Molecular Biology Reviews : MMBR 2008;72:686-727.
- Rijk PD* Wuyts J* Wachter RD. Rna Viz 2: an improved representation of RNA secondary structure. Bioinformatics 2003;19:299-300.
- Ronquist F* Teslenko M* van der Mark P et al. MrBayes 32: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 2012;61:539-42.
- Sandon H. The species problem in the opalinids (Protozoa* Opalinata)* with special reference to Protoopalina. Transactions of the American Microscopical Society 1976;95:357-66.
- Schwarz G. Estimating the dimension of a model. Annals of Statistics 1978;6:461-4.
- Scotese CR. PALEOMAP PaleoAtlas for GPlates and the PaleoData Plotter Program, PALEOMAP Project. 2016. http://www.earthbyte.org/ paleomap-paleoatlas-for-gplates/ (20 June 2023* date last accessed).
- Seibel PN* Muller T* Dandekar T et al. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Research Notes 2008;1:91.
- Skovgaard A* Massana R* Saiz E. Parasitic species of the genus Blastodinium (Blastodiniphyceae) are peridinioid dinoflagellates. Journal of Phycology 2007;43:553-60.
- Tamura K* Battisluzzi FU* Billing-Ross P et al. Estimating divergence times in large molecular phylogenies. Proceedings of the National Academy of Sciences of the United States of America 2012;109:19333-8.
- Tamura K* Tao Q* Kumar S. Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates. Molecular Biology and Evolution 2018;35:1770-82.
- Tao Q* Tamura K* Mello B et al. Reliable confidence intervals for RelTime estimates of evolutionary divergence times. Molecular Biology and Evolution 2020;37:280-90.
- Tennant JP* Mannion PD* Upchurch P. Sea level regulated tetrapod diversity dynamics through the Jurassic/Cretaceous interval. Nature Communications 2016;7:12737.
- Tennant JP* Mannion PD* Upchurch P et al. Biotic and environmental dynamics through the Late Jurassic-Early Cretaceous transition: evidence for protracted faunal and ecological turnover.Biological Reviews of the Cambridge Philosophical Society 2017;92:776-814.
- Thompson JD* Higgins DG* Gibson TJ.CLUSTALW: improving the sensitivity of progressive multiple sequence alignment though sequence weighting* position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994;22:4673-80.
- Torres RA* Ganal M* Hemleben V.GC balance in the Internal Transcribed Spacers ITS1 and ITS2 of nuclear ribosomal RNA genes. Journal of Molecular Evolution 1990;30:170-81.
- Vrsansky P. Mass mutations of insects at the Jurassic/Cretaceous boundary? Geologica Carphatica 2005;56:473-81.
- Wang RQ* Zhao WS* Hu GR et al. Redescription of Opalina triangulata (Heterokonta* Opalinea) from Fejervarya limnocharis based on morphologicalandmoleculardata.EuropeanJournalofProtistology2019;71:125639.
- Yoon HS* Andersen RA* Boo SM et al. Stramenopiles. In: Schaechter M (ed.)* Encyclopedia of Microbiology. Oxford: Elsevier* 2009* 721-31.
- Yoshikawa H* Morimoto K* Wu Z et al. Problems in speciation in the genus Blastocystis. Trends in Parasitology 2004;20:251-5.
- Zachos J* Pagani M* Sloan L et al. Trends* rhythms* and aberrations in global climate 65 Ma to present. Science 2001;292:686-93.
- Zhao W* Hu G* Ponce-Gordo F et al. Morphological description of Opalina obtrigonoidea Metcalf* 1923 (Heterokonta* Opalinea) from Duttaphrynus melanostictus and evaluation of the ITS region as a suitable genetic marker for inter-species identification in Opalina. Parasitology International 2020;76:102103.
- Zou H* Li C* Wang RQ et al. The morphology of Protoopalina limnocharis Nie* 1932 from Fejervarya limnocharis. Acta Hydrobiologica Sinica 2018;42:364-8.