Open Access
Research Article
Issue
Parasite
Volume 24, 2017
Article Number 43
Number of page(s) 10
DOI https://doi.org/10.1051/parasite/2017043
Published online 14 November 2017
  1. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouel A, Lepere G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Betermier M, Weissenbach J, Scarpelli C, Schachter V, Sperling L, Meyer E, Cohen J, Wincker P. 2006. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature, 444(7116), 171-178. [CrossRef] [PubMed] [Google Scholar]
  2. Chen CL. 1955. The protozoan parasites from four species of Chinese pond fishes: Ctenopharyngodon idellus, Mylopharyngodon aethiops, Aristichthys nobilis and Hypophthalmichthys molitrix, I. The protozoan parasites of Ctenopharyngodon idellus. Acta Hydrobiologica Sinica, 2, 123-164. [Google Scholar]
  3. Chen X, Zhao X, Liu X, Warren A, Zhao F, Miao M. 2015. Phylogenomics of non-model ciliates based on transcriptomic analyses. Protein Cell, 6(5), 373-85. [CrossRef] [PubMed] [Google Scholar]
  4. Claparède E, J Lachmann. 1858. Études sur les infusoires et les rhizopodes. Mémoires de l'Institut Genevois, 5, 1-260. [Google Scholar]
  5. Comas I, Moya A, González-Candelas F. 2007. From Phylogenetics to Phylogenomics. The evolutionary relationships of insect endosymbiotic γ-Proteobacteria as a test case. Systematic Biology, 56(1), 1-16. [CrossRef] [EDP Sciences] [PubMed] [Google Scholar]
  6. Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, Kumar U, Saier M, Wang YF, Cai H, Gu JY, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. 2011. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biology, 12(10), 1-26. [CrossRef] [Google Scholar]
  7. Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC. 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters, 8(5), 783-786. [CrossRef] [PubMed] [Google Scholar]
  8. Davidson NM, Oshlack A. 2014. Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. Genome Biology, 410, 1-14. [Google Scholar]
  9. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. [CrossRef] [PubMed] [Google Scholar]
  10. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Jr., Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. 2006. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology, 4(9), 1620-1642. [CrossRef] [Google Scholar]
  11. Feng JM, Jiang CQ, Warren A, Tian M, Cheng J, Liu GL, Xiong J, Miao W. 2015. Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea. Molecular Phylogenetics and Evolution, 90, 104-111. [CrossRef] [PubMed] [Google Scholar]
  12. Gentekaki E, Kolisko M, Boscaro V, Bright KJ, Dini F, Di Giuseppe G, Gong Y, Miceli C, Modeo L, Molestina RE, Petroni G, Pucciarelli S, Roger AJ, Strom SL, Lynn DH. 2014. 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, 78, 36-42. [CrossRef] [PubMed] [Google Scholar]
  13. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7), 644-652. [CrossRef] [PubMed] [Google Scholar]
  14. Hammerschmidt B, Schlegel M, Lynn DH, Leipe DD, Sogin ML, Raikov IB. 1996. Insights into the evolution of nuclear dualism in the ciliates revealed by phylogenetic analysis of rRNA sequences. Journal of Eukaryotic Microbiology, 43, 225-230. [CrossRef] [Google Scholar]
  15. Hirotugu Akaike M, Ieee. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control, Ac-19(6), 716-722. [Google Scholar]
  16. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9), 1236-40. [CrossRef] [PubMed] [Google Scholar]
  17. Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics, 25(17), 2286-2288. [CrossRef] [PubMed] [Google Scholar]
  18. Leache AD, Chavez AS, Jones LN, Grummer JA, Gottscho AD, Linkem CW. 2015. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biology and Evolution, 7(3), 706-719. [CrossRef] [PubMed] [Google Scholar]
  19. Li L, Thorsten S, Kyoon SM, Al-Rasheid Khaled AS, Al-Khedhairy Bdulaziz A, Song W. 2010. Protocruzia, a highly ambiguous ciliate (Protozoa; Ciliophora): very likely an ancestral form for Heterotrichea, Colpodea or Spirotrichea? With reevaluation of its evolutionary position based on multigene analyses. Science China Life Sciences, 53(1), 131-8. [CrossRef] [PubMed] [Google Scholar]
  20. Li M, Li D, Wang J, Zhang J, Gu Z, Gong X. 2007. Light and scanning electron microscopic study of Balantidium ctenopharyngodoni Chen, 1955 (Class: Litostomatea) from China. Parasitology Research, 101(1), 185-192. [CrossRef] [PubMed] [Google Scholar]
  21. Li M, Li W, Zhang L, Wang C. 2013. Balantidium honghuensis n. sp. (Ciliophora: Trichostomatidae) from the rectum of Rana nigromaculata and R. limnocharis from Honghu Lake, China. Korean Journal of Parasitology, 51(4), 427-431. [CrossRef] [Google Scholar]
  22. Li M, Wang C, Grim JN, Wang J, Gong X. 2014. Ultrastructural study of Balantidium ctenopharyngodoni Chen, 1955 (Class: Litostomatea) from China with an emphasis on its vestibulum. Acta Parasitologica, 59(3), 413-419. [PubMed] [Google Scholar]
  23. Lynn D, Sogin ML. 1988. Assessment of phylogenetic relationships among ciliated protists using partial ribosomal RNA sequences derived from reverse transcripts. BioSystems, 21, 249-254. [CrossRef] [PubMed] [Google Scholar]
  24. Marton S, Banyai K, Forro B, Lengyel G, Szekely C, Varga A, Molnar K. 2016. Molecular genetic investigations on Balantidium ctenopharyngodoni Chen, 1955, a parasite of the grass carp (Ctenopharyngodon idella). Acta Veterinaria Hungarica, 64(2), 213-221. [CrossRef] [PubMed] [Google Scholar]
  25. Mccormack JE, Faircloth BC. 2013. Next-generation phylogenetics takes root. Molecular Ecology, 22, 19-21. [CrossRef] [PubMed] [Google Scholar]
  26. Miao W, Fen W, Yu Y, XiyuanZhang, Shen Y. 2004. Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) Inferred from small subunit rRNA gene sequences. Journal of Eukaryotic Microbiology, 51(2), 180-186. [CrossRef] [Google Scholar]
  27. Miao W, Yu Y, Shen Y. 2001. Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) with emphasis on the genus Epistylis, inferred −from small subunit rrna gene sequences. Journal of Eukaryotic Microbiology, 48(5), 583-587. [CrossRef] [Google Scholar]
  28. Molnar K, Reinhardt M. 1978. Intestinal lesions in grass carp Ctenopharyngodon idella (Valenciennce) infected with Balantidium ctenopharyngodonis Chen. Journal of Fish Diseases, 1 (151-156). [CrossRef] [Google Scholar]
  29. Negrisolo E, Kuhl H, Forcato C, Vitulo N, Reinhardt R, Patarnello T, Bargelloni L. 2010. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species. Molecular Biology and Evolution, 27(12), 2757-2774. [CrossRef] [PubMed] [Google Scholar]
  30. Philippe H, Delsuc F, Brinkmann H, Lartillot N. 2005. Phylogenomics. Annual Review of Ecology, Evolution, and Systematics, 36(1), 541-562. [CrossRef] [Google Scholar]
  31. Picelli S, Bjorklund AK, Faridani OR, Sagasser S, Winberg G, Sandberg R. 2013. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature Methods, 10(11), 1096-1098. [CrossRef] [PubMed] [Google Scholar]
  32. Rice PM, Bleasby AJ, Ison JC. 2011. EMBOSS User's Guide: Practical Bioinformatics. Cambridge University Press. [Google Scholar]
  33. Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature, 425, 798-804. [CrossRef] [PubMed] [Google Scholar]
  34. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna 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. Systematic Biology, 61(3), 539-542. [CrossRef] [PubMed] [Google Scholar]
  35. Roure B, Rodriguez-Ezpeleta N, Philippe H. 2007. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evolutionary Biology, 7 Suppl 1, S2. [CrossRef] [Google Scholar]
  36. Shi X, Frankel J. 1990. Morphology and development of mirror image doubles of Stylonychia mytilus. Journal of Protozoology, 37(1), 1-13. [CrossRef] [Google Scholar]
  37. Shin MK, Hwang UW, Kim W, Wright A-DG, Krawczyk C, Lynn DH. 2000. Phylogenetic position of the ciliates Phacodinium (Order Phacodiniida) and Protocruzia (Subclass Protocruziidia) and systematics of the spirotrich ciliates examined by small subunit ribosomal RNA gene sequences. European Journal of Protistology, 36(3), 293-302. [CrossRef] [Google Scholar]
  38. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21), 2688-2690. [CrossRef] [PubMed] [Google Scholar]
  39. Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF. 2013. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16, 000 tiny chromosomes. PLoS Biology, 11(1), e1001473. [CrossRef] [PubMed] [Google Scholar]
  40. Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56(4), 564-577. [CrossRef] [Google Scholar]
  41. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725-2729. [CrossRef] [PubMed] [Google Scholar]
  42. Woese CR. 1987. Bacterial Evolution. Microbiological Research, 51(2), 221-271. [Google Scholar]
  43. Xiong J, Wang G, Cheng J, Tian M, Pan X, Warren A, Jiang C, Yuan D, Miao W. 2015. Genome of the facultative scuticociliatosis pathogen Pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer. Scientific Reports, 5, 15470. [CrossRef] [PubMed] [Google Scholar]
  44. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J. 2006. WEGO: a web tool for plotting GO annotations. Nucleic Acids Research, 34(Web Server issue), W293-7. [Google Scholar]

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