Phylogenomics of non-model ciliates based on transcriptomic analyses

Xiao Chen, Xiaolu Zhao, Xiaohui Liu, Alan Warren, Fangqing Zhao, Miao Miao

PDF(1224 KB)
PDF(1224 KB)
Protein Cell ›› 2015, Vol. 6 ›› Issue (5) : 373-385. DOI: 10.1007/s13238-015-0147-3
RESEARCH ARTICLE

Phylogenomics of non-model ciliates based on transcriptomic analyses

Author information +
History +

Abstract

Ciliates are one of the oldest living eukaryotic unicellular organisms, widely distributed in the waters around the world. As a typical marine oligotrich ciliate, Strombidium sulcatum plays an important role in marine food webs and energy flow. Here we report the first deep sequencing and analyses of RNA-Seq data from Strombidium sulcatum. We generated 42,640 unigenes with an N50 of 1,451 bp after de novo assembly and removing rRNA, mitochondrial and bacteria contaminants. We employed SPOCS to detect orthologs from S. sulcatum and 17 other ciliates, and then carried out the phylogenomic reconstruction using 127 single copy orthologs. In phylogenomic analyses, concatenated trees have similar topological structures with concordance tree on the class level. Together with phylogenetic networks analysis, it aroused more doubts about the placement of Protocruzia, Mesodinium and Myrionecta. While epiplasmic proteins are known to be related to morphological characteristics, we found the potential relationship between gene expression of epiplasmic proteins and morphological characteristics. This work supports the use of high throughput approaches for phylogenomic analysis as well as correlation analysis between expression level of target genes and morphological characteristics.

Keywords

Strombidium / protozoa / transcriptome / non-model ciliate / phylogenomic analysis

Cite this article

Download citation ▾
Xiao Chen, Xiaolu Zhao, Xiaohui Liu, Alan Warren, Fangqing Zhao, Miao Miao. Phylogenomics of non-model ciliates based on transcriptomic analyses. Protein Cell, 2015, 6(5): 373‒385 https://doi.org/10.1007/s13238-015-0147-3

References

[1]
Adl SM, Simpson AG, Lane CE (2012) The revised classification of eukaryotes. J Eukaryot Microbiol59: 429−493
CrossRef Google scholar
[2]
Agatha S (2004) A cladistic approach for the classification of oligotrichid ciliates (Ciliophora: Spirotricha). Acta Protozool43: 201
[3]
Allali K, Dolan J, Rassoulzadegan F (1994) Culture characteristics and orthophosphate excretion of a marine oligotrich ciliate, Strombidium sulcatum, fed heat-killed bacteria. Mar Ecol Prog Ser105: 159
CrossRef Google scholar
[4]
Ane C, Larget B, Baum DA, Smith SD, Rokas A (2007) Bayesian estimationof concordanceamong genetrees. Mol Biol Evol24: 1575
CrossRef Google scholar
[5]
Aubusson-Fleury A, Bricheux G, Damaj R (2013) Epiplasmins and epiplasm in Paramecium: the building of a submembraneous cytoskeleton. Protist164: 451−469
CrossRef Google scholar
[6]
Aury J-M, Jaillon O, Duret L (2006) Global trends of wholegenome duplications revealed by the ciliate Paramecium tetraurelia. Nature444: 171−178
CrossRef Google scholar
[7]
Baum DA (2007) Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon56: 417−426
[8]
Bernard C, Rassoulzadegan F (1990) Bacteria or microflagellates as a major food source for marine ciliates: possible implications for the microzooplankton. Mar Ecol Prog Ser64: 147−155
CrossRef Google scholar
[9]
Bryant D, Moulton V (2004) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol21: 255−265
CrossRef Google scholar
[10]
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol17: 540−552
CrossRef Google scholar
[11]
Christaki U, Dolan JR, Pelegri S, Rassoulzadegan F (1998) Consumption of picoplankton-size particles by marine ciliates: effects of physiological state of the ciliate and particle quality. Limnol Oceanogr43: 458−464
CrossRef Google scholar
[12]
Corliss JO (1979) The ciliated protozoa. Characterization, classification and guide to the literature. Pergamon, Oxford
[13]
Coyne RS, Hannick L, Shanmugam D (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 Biol12: R100
CrossRef Google scholar
[14]
Curtis DS, Phillips AR, Callister SJ, Conlan S, McCue LA (2013) SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes. Bioinformatics29: 2641−2642
CrossRef Google scholar
[15]
Dale T, Lynn DH (1998) Stomatogenesis of the ciliate genus Strombidinopsis with an improved description of S. spiniferum and S. acuminatum. J Eukaryot Microbiol45: 210−217
CrossRef Google scholar
[16]
Damaj R, Pomel S, Bricheux G, Coffe G, Viguès B, Ravet V, Bouchard P (2009) Cross-study analysis of genomic data defines the ciliate multigenic epiplasmin family: strategies for functional analysis in Paramecium tetraurelia. BMC Evol Biol9: 125
CrossRef Google scholar
[17]
Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics27: 1164−1165
CrossRef Google scholar
[18]
Dolan JR, Sall N, Metcalfe A, Gasser B (2003) Effects of turbulence on the feeding and growth of a marine oligotrich ciliate. Aquat Microbial Ecol31: 183−192
CrossRef Google scholar
[19]
Dragesco J, Dragesco-Kernéis A, Fryd-Versavel G (1986) Ciliés libres de l’Afrique intertropicale: introduction à la connaissance et à l’étude des Ciliés. IRD Editions
[20]
Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform23: 205−211
CrossRef Google scholar
[21]
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res32: 1792−1797
CrossRef Google scholar
[22]
Eisen JA, Coyne RS, Wu M (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol4: e286
CrossRef Google scholar
[23]
Fauré-Fremiet E (1962) Le genre Paranassula Kahl (Ciliata, Cyrtophorina). Cah Biol Mar3: 61−77
[24]
Foissner W (1993) Colpodea (Ciliophora). In: Balogh scientific books. Gustav Fischer Verlag, Stuttgart, p 798
[25]
Foissner W, Müller H, Agatha S (2007) A comparative fine structural and phylogenetic analysis of resting cysts in oligotrich and hypotrich Spirotrichea (Ciliophora). Eur J Protistol43: 295−314
CrossRef Google scholar
[26]
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics28: 3150−3152
CrossRef Google scholar
[27]
Gentekaki E, Kolisko M, Boscaro V (2014) Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages. Mol Phylogenet Evol78: 36−42
CrossRef Google scholar
[28]
Gordon A, Hannon G (2010) Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished).
[29]
Gould SB, Tham W-H, Cowman AF, McFadden GI, Waller RF (2008) Alveolins, a new family of cortical proteins that define the protist infrakingdom Alveolata. Mol Biol Evol25: 1219−1230
CrossRef Google scholar
[30]
Grabherr MG, Haas BJ, Yassour M (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol29: 644−652
CrossRef Google scholar
[31]
Grant JR, Lahr DJ, Rey FE (2012) Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora. Protist Genomics1: 3−18
CrossRef Google scholar
[32]
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol59: 307−321
CrossRef Google scholar
[33]
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser41: 95−98
[34]
Hall BG (2011) Phylogenetic trees made easy. A how-to manual. Sinauer, Sunderland
[35]
Honts JE, Williams NE (2003) Novel cytoskeletal proteins in the cortex of Tetrahymena. J Eukaryot Microbiol50: 9−14
CrossRef Google scholar
[36]
Huson DH (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics14: 68−73
CrossRef Google scholar
[37]
Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol23: 254−267
CrossRef Google scholar
[38]
Huson DH, Rupp R, Scornavacca C (2010) Phylogenetic networks. Concepts, algorithms and applications. Cambridge University Press, Cambridge
CrossRef Google scholar
[39]
Huttenlauch I, Stick R (2003) Occurrence of articulins and epiplasmins in protists. J Eukaryot Microbiol50: 15−18
CrossRef Google scholar
[40]
Huttenlauch I, Geisler N, Plessmann U, Peck RK, Weber K, Stick R (1995) Major epiplasmic proteins of ciliates are articulins: cloning, recombinant expression, and structural characterization. J Cell Biol130: 1401−1412
CrossRef Google scholar
[41]
Huttenlauch I, Peck RK, Stick R (1998) Articulins and epiplasmins: two distinct classes of cytoskeletal proteins of the membrane skeleton in protists. J Cell Sci111: 3367−3378
[42]
Inc S (2007) SPSS 16.0 for Windows. SPSS Inc, Chicago
[43]
Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol99: 138−148
[44]
Kim S-J, Min G-S (2009) Taxonomic study of poorly-known marine pleurostomatid ciliates of Litonotus paracygnus and L. pictus (Ciliophora: Pleurostomatida) from Korea. Anim Syst Evol Divers25: 167−178
CrossRef Google scholar
[45]
Kim SY, Yang EJ, Gong J, Choi JK (2010a) Redescription of Favella ehrenbergii (Claparède and Lachmann, 1858) Jörgensen, 1924 (Ciliophora: Choreotrichia), with phylogenetic analyses based on small subunit rRNA gene sequences. J Eukaryot Microbiol57: 460−467
CrossRef Google scholar
[46]
Kim YO, Kim SY, Lee WJ, Choi JK (2010b) New Observations on the Choreotrich Ciliate Strombidinopsis acuminata Fauré-Fremiet 1924, and Comparison with Strombidinopsis jeokjo Jeong et al., 2004. J Eukaryot Microbiol57: 48−55
CrossRef Google scholar
[47]
Kloetzel JA, Baroin-Tourancheau A, Miceli C, Barcetta S, Farmar J, Banerjee D, Fleury-aubusson A (2003a) Plateins: a novel family of signal peptide-containing articulins in euplotid ciliates. J Eukaryot Microbiol50: 19−33
CrossRef Google scholar
[48]
Kloetzel JA, Baroin-Tourancheau A, Miceli C, Barchetta S, Farmar J, Banerjee D, Fleury-Aubusson A (2003b) Cytoskeletal proteins with N-terminal signal peptides: plateins in the ciliate Euplotes define a new family of articulins. J Cell Sc116: 1291−1303
CrossRef Google scholar
[49]
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol10: R25
CrossRef Google scholar
[50]
Larget BR, Kotha SK, Dewey CN, Ane C (2010) BUCKy: gene tree/ species tree reconciliation with Bayesian concordance analysis. Bioinformatics26: 2910−2911
CrossRef Google scholar
[51]
Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform12: 323
CrossRef Google scholar
[52]
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. Sci China Life Sci53: 131−138
CrossRef Google scholar
[53]
Li J, Liu W, Gao S, Warren A, Song W(2013) Multigene-based analyses of the phylogenetic evolution of oligotrich ciliates, with consideration of the internal transcribed spacer 2 secondary structure of three systematically ambiguous genera. Eukaryot Cell12: 430−437
CrossRef Google scholar
[54]
Lynn DH (2008) Ciliated protozoa: characterization, classification, and guide to the literature. Springer, Dordrecht
[55]
Lynn DH, Montagnes DJS, Dale T, Gilron GL, Strom SL (1991) A reassessment of the genus Strombidinopsis (Ciliophora, Choreotrichida) with descriptions of four new planktonic species and remarks in its taxonomy and phylogeny. J Mar Biol Assoc UK71: 597−612
CrossRef Google scholar
[56]
Marrs JA, Bouck GB (1992) The two major membrane skeletal proteins (articulins) of Euglena gracilis define a novel class of cytoskeletal proteins. J Cell Biol118: 1465−1475
CrossRef Google scholar
[57]
McManus GB, Xu D, Costas BA, Katz LA (2010) Genetic identities of cryptic species in the Strombidium stylifer/apolatum/oculatum cluster, including a description of Strombidium rassoulzadegani n. sp. J Eukaryot Microbiol57: 369−378
CrossRef Google scholar
[58]
Modeo L, Petroni G, Rosati G, Montagnes DJ (2003) A multidisciplinary approach to describe protists: redescriptions of Novistrombidium testaceum Anigstein 1914 and Strombidium inclinatum Montagnes, Taylor, and Lynn 1990 (Ciliophora, Oligotrichia). J Eukaryot Microbiol50: 175−189
CrossRef Google scholar
[59]
Montagnes DJ, Taylor F, Lynn D (1990) Strombidium inclinatum n. sp. and a reassessment of Strombidium sulcatum Claparède and Lachmann (Ciliophora). J Protozool37: 318−323
CrossRef Google scholar
[60]
Morrison DA (2011) An Introduction to phylogenetic networks. RJR Productions, Uppsala
[61]
Nahon P, Coffe G, Guyader H, Darmanaden-Delorme J, Jeanmaire-Wolf R, Clerot J-C, Adoutte A (1993) Identification of the epiplasmins, a new set of cortical proteins of the membrane cytoskeleton in Paramecium. J Cell Sci104: 975−990
[62]
Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D (2004) Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol21: 1740−1752
CrossRef Google scholar
[63]
Pomel S, Diogon M, Bouchard P, Pradel L, Ravet V, Coffe G, Viguès B (2006) The membrane skeleton in Paramecium: molecular characterization of a novel epiplasmin family and preliminary GFP expression results. Protist157: 61−75
CrossRef Google scholar
[64]
Qi J, Zhao F (2011) inGAP-sv: A novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res39: W567−W575
CrossRef Google scholar
[65]
Qi J, Zhao F, Buboltz A, Schuster SC (2010) inGAP: An integrated nextgeneration genome analysis pipeline. Bioinformatics26: 127−129
CrossRef Google scholar
[66]
Resources NCfG (2014) Marine Microbial Eukaryote Transcriptome Sequencing Project
[67]
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics19: 1572−1574
CrossRef Google scholar
[68]
Song W, Wilbert N (1997) Morphological investigations on some free living ciliates (Protozoa, Ciliophora) from China Sea with description of a new hypotrichous genus Hemigastrostyla nov. gen. Archiv für Protistenkunde148: 413−444
CrossRef Google scholar
[69]
Song W, Wang M, Warren A (2000) Redescriptions of three marine ciliates, Strombidium elegans Florentin, 1901, Strombidium sulcatum Claparède & Lachmann, 1859 and Heterostrombidium paracalkinsi Lei, Xu & Song, 1999 (Ciliophora, Oligotrichida). Eur J Protistol36: 327−342
CrossRef Google scholar
[70]
Swart EC, Nowacki M, Shum J (2012) The Oxytricha trifallax mitochondrial genome. Genome Biol Evol4: 136−154
CrossRef Google scholar
[71]
Swart EC, Bracht JR, Magrini V (2013) The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol11: e1001473
CrossRef Google scholar
[72]
Tamar H (1992) Four marine species of Mesodinium (Ciliophora: Mesodiniidae) II. Mesodinium pulex Clap. & Lachm., 1858. Archiv für Protistenkunde141: 284−303
CrossRef Google scholar
[73]
Wiadnyana NN, Rassoulzadegan F (1989) Selective feeding of Acartia clausi and Centropages typicus on microzooplankton. Mar Ecol Prog Ser53: 37−45
CrossRef Google scholar
[74]
Williams NE (2004) The epiplasm gene EPC1 influences cell shape and cortical pattern in Tetrahymena thermophila. J Eukaryot Microbiol51: 201−206
CrossRef Google scholar
[75]
Xiong J, Lu X, Zhou Z (2012) Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using deep RNA sequencing. PLoS One7: e30630
CrossRef Google scholar
[76]
Yang Y, Smith SA (2013) Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics14: 328
CrossRef Google scholar

RIGHTS & PERMISSIONS

2015 Higher Education Press and Springer-Verlag Berlin Heidelberg
AI Summary AI Mindmap
PDF(1224 KB)

Accesses

Citations

Detail

Sections
Recommended

/