Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora)

References

• Agatha S, Laval-Peuto M, Simon P. 2013. The tintinnid lorica, in: Dolan JR, Montagnes DJS, Agatha S, Coats DW, Stoecker DK (Eds.), The biology and ecology of tintinnid ciliates. Models for marine plankton. John Wiley, Chichester, pp. 17–41.
   Google Scholar
• Barth D, Krenek S, Fokin SI, Berendonk TU. 2006. Intraspecific genetic variation in Paramecium revealed by mitochondrial cytochrome c oxidase I sequences. J Eukaryot Microbiol. 53:20–25.
   PubMed Web of Science ®Google Scholar
• Blaxter M. 2003. Molecular systematics: counting angels with DNA. Nature. 421:122–124.
   PubMed Web of Science ®Google Scholar
• Chantangsi C, Lynn DH, Brandl MT, Cole JC, Hetrick N, Ikonomi P. 2007. Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena. Int J Syst Evol Microbiol. 57:2412–2425.
   PubMed Web of Science ®Google Scholar
• Chantangsi C, Lynn DH. 2008. Phylogenetic relationships within the genus Tetrahymena inferred from the cytochrome c oxidase subunit 1 and the small subunit ribosomal RNA genes. Mol Phylogenet Evol. 49:979–987.
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 27:1164–1165.
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9:772.
   PubMed Web of Science ®Google Scholar
• Foissner W. 1991. Basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa. Eur J Protistol. 27:313–330.
   PubMed Web of Science ®Google Scholar
• Foissner W, Agatha S, Berger H. 2002. Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha region and the Namib desert. Part I: text and line drawings. Denisia. 5:1–1063.
   Google Scholar
• Foissner W, Chao A, Katz LA. 2008. Diversity and geographic distribution of ciliates (Protista: Ciliophora). Biodivers Conserv. 17:345–363.
   Web of Science ®Google Scholar
• Gao F, Huang J, Zhao Y, Li L, Liu W, Miao M, Zhang Q, Li J, Yi Z, El-Serehy HA, et al. 2017. Systematic studies on ciliates (Alveolata, Ciliophora) in China: progress and achievements based on molecular information. Eur J Protistol. 61:409–423.
   PubMed Web of Science ®Google Scholar
• Gentekaki E, Lynn DH. 2009. High-level genetic diversity but no population structure inferred from nuclear and mitochondrial markers of the peritrichous ciliate Carchesium polypinum in the Grand River Basin (North America). Appl Environ Microbiol. 75:3187–3195.
   PubMed Web of Science ®Google Scholar
• Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307–321.
   PubMed Web of Science ®Google Scholar
• Hall T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95–98.
   Google Scholar
• Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. 1998. Multiple sequence alignment with Clustal X. Trends Biochem Sci. 23:403–405.
   PubMed Web of Science ®Google Scholar
• Jung J-H, Park K-M, Min G-S. 2012. Morphology, morphogenesis, and molecular phylogeny of a new brackish water ciliate, Pseudourostyla cristatoides n. sp., from Songjiho lagoon on the coast of East Sea, South Korea. Zootaxa. 3334:42–54.
   Google Scholar
• Jung J-H, Park K-M, Min G-S. 2014. Morphology and molecular phylogeny of Pseudouroleptus jejuensis nov. spec., a new soil ciliate (Ciliophora, Spirotrichea) from South Korea. Acta Protozool. 53:195–206.
   Web of Science ®Google Scholar
• Jung SJ, Im EY, Strüder-Kypke MC, Kitamura SI, Woo PTK. 2011. Small subunit ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 gene sequences of 21 strains of the parasitic scuticociliate Miamiensis avidus (Ciliophora, Scuticociliatia). Parasitol Res. 108:1153–1161.
   PubMed Web of Science ®Google Scholar
• Kher CP, Doerder FP, Cooper J, Ikonomi P, Achilles-Day U, Küpper FC, Lynn DH. 2011. Barcoding Tetrahymena: discriminating species and identifying unknowns using the cytochrome c oxidase subunit I (cox-1) barcode. Protist. 162:2–13.
   PubMed Web of Science ®Google Scholar
• Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111–120.
   PubMed Web of Science ®Google Scholar
• Kim SY, Yang EJ, Gong J, Choi JK. 2010. Redescription of Favella ehrenbergii (Claparede and Lachmann, 1858) Jorgensen, 1924 (Ciliophora: Choreotrichia), with phylogenetic analyses based on small subunit rRNA gene sequences. J Eukaryot Microbiol. 57:460–467.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33:1870–1874.
   PubMed Web of Science ®Google Scholar
• Lefebure T, Douady CJ, Gouy M, Gibert J. 2006. Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Mol Phylogenet Evol. 40:435–447.
   PubMed Web of Science ®Google Scholar
• Logares R, Rengefors K, Kremp A, Shalchian-Tabrizi K, Boltovskoy A, Tengs T, Shurtleff A, Klaveness D. 2007. Phenotypically different microalgal morphospecies with identical ribosomal DNA: a case of rapid adaptive evolution? Microb Ecol. 53:549–561.
   PubMed Web of Science ®Google Scholar
• Lynn DH, Strüder-Kypke MC. 2006. Species of Tetrahymena identical by small subunit rRNA gene sequences are discriminated by mitochondrial cytochrome c oxidase I gene sequences. J Eukaryot Microbiol. 53:385–387.
   PubMed Web of Science ®Google Scholar
• Lynn DH. 2008. The ciliated protozoa: characterization, classification, and guide to the literature. New York: Springer.
   Google Scholar
• Markmann M, Tautz D. 2005. Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Phil Trans R Soc B. 360:1917–1924.
   Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61:539–542.
   PubMed Web of Science ®Google Scholar
• Santoferrara LF, McManus GB, Alder VA. 2013. Utility of genetic markers and morphology for species discrimination within the order Tintinnida (Ciliophora, Spirotrichea). Protist. 164:24–36.
   PubMed Web of Science ®Google Scholar
• Song W, Li J, Liu W, Al-Rasheid KAS, Hu X, Lin X. 2014. Taxonomy and molecular phylogeny of four Strombidium species, including description of S. pseudostylifer sp. nov. (Ciliophora, Oligotrichia). Syst Biodivers. 13:76–92.
   Web of Science ®Google Scholar
• Stoeck T, Przybos E, Dunthorn M. 2014. The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates. Mol Ecol Resour. 14:458–468.
   PubMed Web of Science ®Google Scholar
• Strüder-Kypke MC, Lynn DH. 2010. 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. Syst Biodivers. 8:131–148.
   Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
   PubMed Web of Science ®Google Scholar
• Tarcz S, Potekhin A, Rautian M, Przyboś E. 2012. Variation in ribosomal and mitochondrial DNA sequences demonstrates the existence of intraspecific groups in Paramecium multimicronucleatum (Ciliophora, Oligohymenophorea). Mol Phylogenet Evol. 63:500–509.
   PubMed Web of Science ®Google Scholar
• Tarcz S, Przyboś E, Surmacz M. 2013. An assessment of haplotype variation in ribosomal and mitochondrial DNA fragments suggests incomplete lineage sorting in some species of the Paramecium aurelia complex (Ciliophora, Protozoa). Mol Phylogenet Evol. 67:255–265.
   PubMed Web of Science ®Google Scholar
• Tarcz S, Rautian M, Potekhin A, Sawka N, Beliavskaya A, Kiselev A, Nekrasova I, Przyboś E. 2014. Paramecium putrinum (Ciliophora, Protozoa): the first insight into the variation of two DNA fragments – molecular support for the existence of cryptic species. Mol Phylogenet Evol. 73:140–145.
   PubMed Web of Science ®Google Scholar
• Xia X. 2013. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol. 30:1720–1728.
   PubMed Web of Science ®Google Scholar
• Xu D, Sun P, Shin MK, Kim YO. 2012. Species boundaries in tintinnid ciliates: A case study ? morphometric variability, molecular characterization, and temporal distribution of Helicostomella species (Ciliophora, Tintinnina). J Eukaryot Microbiol. 59:351–358.
   PubMed Web of Science ®Google Scholar
• Yi Z, Chen Z, Warren A, Roberts D, Al-Rasheid K, Miao M, Gao S, Shao C, Song W. 2008. Molecular phylogeny of Pseudokeronopsis (Protozoa, Ciliophora, Urostylida), with reconsideration of three closely related species at inter- and intra-specific levels inferred from the small subunit ribosomal RNA gene and the ITS1-5.8 S-ITS2 region sequences. J Zool. 275:268.
   Web of Science ®Google Scholar
• Zhao Y, Gentekaki E, Yi Z, Lin X. 2013. Genetic differentiation of the mitochondrial cytochrome oxidase c subunit I gene in genus Paramecium (Protista, Ciliophora). PLoS ONE. 8:e77044.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Yi Z, Gentekaki E, Zhan A, Al-Farraj SA, Song W. 2016. Utility of combining morphological characters, nuclear and mitochondrial genes: an attempt to resolve the conflicts of species identification for ciliated protists. Mol Phylogenet Evol. 94:718–729.
   PubMed Web of Science ®Google Scholar