Current Microbiology

, Volume 75, Issue 3, pp 296–304 | Cite as

A New Molecular Approach Based on the Secondary Structure of Ribosomal RNA for Phylogenetic Analysis of Mobilid Ciliates



We analyzed the secondary structure of the small subunit (SSU) rRNA genes of Mobilida (Ciliophora, Peritrichia) and found that the secondary structures of some regions within the SSU-rRNA gene are distinct between the families Trichodinidae and Urceolariidae. Therefore, some of these important regions including H10, H11, H17, H47, H29, H30, H37, E10-1, H45-H46, and V4 (E23-4, E23-7) could be used as the barcodes for classification of these two families. In contrast, V4 (E23-1, E23-2) belongs to a hypervariable region and is not a good barcode at the genus level because of its great inter-specific variation. Our results indicated that the comprehensive analysis of the secondary structure of SSU-rRNA genes is a reliable auxiliary approach for phylogenic study of mobilid ciliates. It was further found that the coevolution between hosts or habitats and the Mobilida ciliates was existent, because the host types and their habitats were critical ecological factors that influenced the evolution of Mobilida ciliates.



This present work was supported by grants from the National Natural Science Foundation of China (Nos. 31672280, 31471980) and the project of Chongqing Science and Technology Commission (No. cstc2010ca1010).


  1. 1.
    Chen XM, Li LQ, Hu XZ, Shao C, Al-Farraj SA, Al-Rasheid KAS (2013) A morphogenetic description of Thigmokeronopsis stoecki shao et al. 2008 (ciliophora, hypotricha) and a comparison with members of the family Pseudokeronopsidae. Acta Protozool 52:65–72Google Scholar
  2. 2.
    Chen ZG, Song WB (2000) Application of molecular markers to the studies on the systematics and classification of ciliated protozoa. J Ocean Univ Qingdao 30:237–243Google Scholar
  3. 3.
    De Rijk P, Wuyts J, De Wachter R (2003) RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics 19:299–300CrossRefPubMedGoogle Scholar
  4. 4.
    Gao F, Gao S, Wang P, Song WB (2014) Phylogenetic analyses of cyclidiids (Protista, Ciliophora, Scuticociliatia) based on multiple genes suggest their close relationship with thigmotrichids. Mol Phylogenet Evol 75:219–226CrossRefPubMedGoogle Scholar
  5. 5.
    Gong YC, Yu YH (2007) Progress in the taxonomy and phylogeny of trichodinids. Zool Res 28:217–224Google Scholar
  6. 6.
    Gong YC, Yu YH, Feng WS, Shen YF (2005) Phylogenetic relationships among Trichodinidae (Ciliophora: Peritricha) derived from the characteristic values of denticles. Acta Protozool 44:237–243Google Scholar
  7. 7.
    Gonzalez P, Labarère J (2000) Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains. Microbiology 146:209–221CrossRefPubMedGoogle Scholar
  8. 8.
    Holzer AS, Wootten R, Sommerville C (2007) The secondary structure of the unusually long 18S ribosomal RNA of the myxozoan Sphaerospora truttae and structural evolutionary trends in the Myxozoa. Int J Parasitol 37:1281–1295CrossRefPubMedGoogle Scholar
  9. 9.
    Hong SG, Jung HS (2004) Phylogenetic analysis of Ganoderma based on nearly complete mitochondrial small-subunit ribosomal DNA sequences. Mycologia 4:742–755CrossRefGoogle Scholar
  10. 10.
    Jiang Y, Tang SK, Xu LH, Imhoff JF, Liu ZH, Jiang CL (2006) Analysis for secondary structure of variable regions of 16S rRNA of the family Yaniaceae. Microbiology 33:176–182Google Scholar
  11. 11.
    Liu CY, Zhang WY (2007) An attempt to use rRNA secondary structure characters in fungal systematics. Mycosystema 26:22–31Google Scholar
  12. 12.
    Liu Y, Cui XL, Li WJ, Peng Q (2006) Application of RNA secondary structure in phylogenetic analysis of microbiology. Microbiology 33:147–150Google Scholar
  13. 13.
    Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, pp. 1–8Google Scholar
  14. 14.
    Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574CrossRefPubMedGoogle Scholar
  15. 15.
    Tang FH, Zhang Y, Zhao YJ (2017) Morphological and molecular identification of the new species, Trichodina pseudoheterodentata sp. n. (Ciliophora, Mobilida, Trichodinidae) from the channel catfish, Ictalurus punctatus, in Chongqing China. J Eukaryot Microbiol 64:45–55CrossRefPubMedGoogle Scholar
  16. 16.
    Tang FH, Zhao YJ (2010) Taxonomic study on trichodinids parasitic on gills of freshwater fish, Carassius auratus from chongqing, china, with the description of Trichodina brevicirra sp. nov. Acta Hydrobiol Sin 36:1009–1011CrossRefGoogle Scholar
  17. 17.
    Tang FH, Zhao YJ (2016) Molecular phylogenetic evidences on mobilida based on genetic distance and GC content of 18s rDNA using broad taxon sampling. Acta Hydrobiol Sin 40:358–369Google Scholar
  18. 18.
    Tang FH, Zhao YJ, Warren A (2013) Phylogenetic analyses of Trichodinids (Ciliophora, Oligohymenophorea) inferred from 18S rRNA gene sequence data. Curr Microbiol 66:306–313CrossRefPubMedGoogle Scholar
  19. 19.
    Wang P, Gao F, Huang J, Yi ZZ (2015) A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates. Zool Scr 44:574–585CrossRefGoogle Scholar
  20. 20.
    Wuyts J, De Rijk P, Van de Peer Y, de Wachter R (2001) Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res 24:5017–5028CrossRefGoogle Scholar
  21. 21.
    Xu KD, Song WB (1998) A morphological study on a new species of gill parasitic ciliate, Urceolaria cheni nov. spec. from the clam Scapharca subcrenata. J Fisheryences of China 5:13–17Google Scholar
  22. 22.
    Xu KD, Song WB (2000) Diagnostic methods for identification of the species within the genus Trichodina Ehrenberg, 1838 (Protozoa, Ciliophora). J Ocean Univ Qingdao 30:397–405Google Scholar
  23. 23.
    Zhan ZF, Xu KD, Dunthorn M (2013) Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships within the Mobilida (Ciliophora, Oligohymenophorea). Zool Scr 42:213–226CrossRefGoogle Scholar
  24. 24.
    Zhang Y, Zhao YJ, Wang Q, Tang FH (2015) New comparative analysis based on the secondary structure of SSU-rRNA gene reveals the evolutionary trend and the Family-Genus characters of Mobilida (Ciliophora, Peritrichia). Curr Microbiol 71:259–267CrossRefPubMedGoogle Scholar
  25. 25.
    Zhao Y, Yi ZZ, Gentekaki E, Song WB (2015) Utility of combining morphological characters, nuclear and mitochondrial genes: an attempt to resolve the conflicts of species identification for ciliated protists. Mol Phylogenet Evol 94:718–729CrossRefPubMedGoogle Scholar
  26. 26.
    Zuker M (2003) MFold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:1–10CrossRefGoogle Scholar

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© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.Chongqing Key Laboratory of Animal BiologyChongqing Normal UniversityChongqingPeople’s Republic of China

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