Jump to ContentJump to Main Navigation
Show Summary Details

The complete mitochondrial genome from an unidentified Phalansterium species.

Jean-François Pombert
  • Department of Biological and Chemical Sciences, Illinois Institute of Technology, 3105 South Dearborn, Chicago, Illinois, 60616, USA
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Alexey Smirnov
  • Department of Invertebrate Zoology, Faculty of Biology & Soil Sciences, St.Petersburg State University, Universitetskaja nab. 7/9, 199034, St.Petersburg, Russia
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Erick R. James
  • Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Jan Janouškovec
  • Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Michael W. Gray
  • Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Room 8-F2, PO Box 15000, Halifax, NS, B3H 4R2, Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Patrick J. Keeling
  • Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2013-08-20 | DOI: https://doi.org/10.2478/prge-2013-0002


We describe the complete sequence and organization of the mitochondrial genome from an unidentified species of Phalansterium. This is the first sequenced mitochondrial genome of a member of Variosea clade (Amoebozoa, Conosa). The sequence was assembled from shotgun reads of DNA from a mixed culture containing the euglenid Monomorphina aenigmatica and an amoebozoan that we demonstrate here is closely related to Phalansterium (in nuclear SSU rRNA phylogenies, it branches between two sequences from described species of Phalansterium). Sequence assembly resulted in two distinct mitochondrial genome types, one fragmented and euglenid-like, and the second a single circularmapping contig of 53,614 bp with an amoebozoan-like set of genes. The Phalansterium sp. mitochondrial genome is gene-rich and densely packed, with a large number of tRNAs and an unusually low ratio of identifiable protein-coding genes to unidentified ORFs. These ORFs potentially encode ribosomal proteins exhibiting a divergent character at the sequence level, and whose identification may be hindered by the presence of RNA editing in Phalansterium mitochondria, as inferred from numerous acceptor stem mis-matches typical of amoebozoan tRNA 5’ editing.

Keywords: Phalansterium; Amoebozoa; Variosea; Mitochondrion; Genome

  • [1] Cienkowski L., Über palmellaceen und einige flagellaten, Arch. Mikrosk. Anat., 1970, 7, 421–438, (in German) Google Scholar

  • [2] Stein F. von, Der organismus der infusionthiere. III. Flagelatten I, Engelmann, Leipzig, 1878, (in German) Google Scholar

  • [3] Transon A., Théorie sociétaire de Charles Fourier: Exposition succincte, EVERAT, Paris, 1832, (in French) Google Scholar

  • [4] Sandon H., Some protozoa from the soils and mosses of Spitsbergen, J. Linn. Soc. Zool. 1924, 35, 449–495 CrossrefGoogle Scholar

  • [5] Smirnov A.V., Chao E., Nassonova E.S., Cavalier-Smith T., A revised classification of naked lobose amoebae (Amoebozoa: Lobosa), Protist, 2011, 162, 545–570 Web of SciencePubMedCrossrefGoogle Scholar

  • [6] Hibberd D.J., Ultrastructure of the colonial colourless flagellate Phalansterium digitatum Stein (Phalansteriida ord. nov.) and Spongomonas uvella Stein (Spongomonadida ord. nov.), Protistologica, 1983, 19, 523–535 Google Scholar

  • [7] Ekelund F., A study of the soil flagellate Phalansterium solitarium Sandon 1924 with preliminary data on its ultrastructure, Protistology, 2002, 2, 152–158 Google Scholar

  • [8] Cavalier-Smith T., The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa, Int. J. Syst. Evol. Microbiol., 2002, 52, 297–354 Google Scholar

  • [9] Cavalier-Smith T., Chao E.E.-Y., Oates B., Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium, Eur. J. Protistol., 2004, 40, 21–48 CrossrefGoogle Scholar

  • [10] Smirnov A.V., Nassonova E., Berney C., Fahrni J., Bolivar I., Pawlowski J., et al., Molecular phylogeny and classification of the lobose amoebae, Protist, 2005, 156, 129–142 PubMedCrossrefGoogle Scholar

  • [11] Nikolaev S.I., Berney C., Petrov N.B., Mylnikov A.P., Fahrni J.F., Pawlowski J., et al., Phylogenetic position of Multicilia marina and the evolution of Amoebozoa, Int. J. Syst. Evol. Microbiol., 2006, 56, 1449–1458 CrossrefGoogle Scholar

  • [12] Smirnov A.V., Nassonova E.S., Cavalier-Smith T., Correct identification of species makes the amoebozoan rRNA tree congruent with morphology for the order Leptomyxida Page 1987; with description of Acramoeba dendroida n. g., n. sp., originally misidentified as “Gephyramoeba sp.”, Eur. J. Protistol., 2008, 44, 35–44 Web of ScienceGoogle Scholar

  • [13] Tekle Y.I., Grant J., Anderson O.R., Nerad T.A., Cole J.C., Patterson, D.J., et al., Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within “Amoebozoa” upon removal of varying rate classes of SSU-rDNA, Mol. Phylogenet. Evol. 2008, 47, 339–352 Web of ScienceCrossrefGoogle Scholar

  • [14] Cavalier-Smith T., Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations, J. Eukaryot. Microbiol., 2009, 56, 26–33 CrossrefWeb of ScienceGoogle Scholar

  • [15] Pawlowski J., Burki F., Untangling the phylogeny of amoeboid protists, J. Eukaryot. Microbiol., 2009, 56, 16–25 Web of ScienceCrossrefGoogle Scholar

  • [16] Shadwick L.L., Spiegel F.W., Shadwick J.D.L., Brown M.W., Silberman J.D., Eumycetozoa = Amoebozoa?: SSUrDNA phylogeny of protosteloid slime molds and its significance for the amoebozoan supergroup, PloS ONE, 2009, 1, e6754 Google Scholar

  • [17] Cole J., Anderson O.R., Tekle Y.I., Grant J., Kat L.A., Nerad T., et al., A description of a new “Amoebozoan” isolated from the American lobster, Homarus americanus, J. Eukaryot. Microbiol., 2010, 57, 40–47 Web of ScienceCrossrefGoogle Scholar

  • [18] Fiore-Donno A.M., Kamono A., Meyer M., Schnittler M., Fukui M., Cavalier-Smith T., et al., 18S rDNA phylogeny of Lamproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa), PloS ONE, 2012, 7, e35359 Google Scholar

  • [19] Kudryavtsev A., Wylezich C., Pawlowski J., Ovalopodium desertum n. sp. and the phylogenetic relationships of Cochliopodiidae (Amoebozoa), Protist, 2011, 162, 571–589 PubMedCrossrefWeb of ScienceGoogle Scholar

  • [20] Kudryavtsev A., Pawlowski J., Squamamoeba japonica n. g. n. sp. (Amoebozoa): a deep-sea amoeba from the Sea of Japan with a novel cell coat structure, Protist, 2013, 164, 13–23 PubMedWeb of ScienceCrossrefGoogle Scholar

  • [21] Tovar J., Fischer A., Clark C.G., The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica, Mol. Microbiol., 1999, 32, 1013–1021 CrossrefPubMedGoogle Scholar

  • [22] Takano H., Abe T., Sakurai R., Moriyama Y., Miyazawa Y., Nozaki H., et al., The complete DNA sequence of the mitochondrial genome of Physarum polycephalum, Mol. Gen. Genet., 2001, 264, 539–545 Google Scholar

  • [23] Burger G., Plante I., Lonergan K.M., Gray M.W., The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization, J. Mol. Biol., 1995, 245, 522–537 CrossrefGoogle Scholar

  • [24] Heidel A.J., Glöckner G., Mitochondrial genome evolution in the social amoebae, Mol. Biol. Evol., 2008, 25, 1440–1450 PubMedCrossrefGoogle Scholar

  • [25] Ogawa S., Yoshino R., Angata K., Iwamoto M., Pi M., Kuroe K., et al., The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization, Mol. Gen. Genet., 2000, 263, 514–519 Google Scholar

  • [26] Pombert J.-F., James E.R., Janouškovec J., Keeling P.J., Evidence for transitional stages in the evolution of euglenid group II introns and twintrons in the Monomorphina aenigmatica plastid genome, PLoS ONE, 2012, 7, e53433 Web of ScienceGoogle Scholar

  • [27] Boisvert S., Laviolette F., Corbeil J., Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies, J. Comput. Biol., 2010, 17, 1519–1533 CrossrefWeb of ScienceGoogle Scholar

  • [28] Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A., et al., Artemis: sequence visualization and annotation, Bioinformatics, 2000, 16, 944–945 CrossrefGoogle Scholar

  • [29] Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J., Basic Local Alignment Search Tool, J. Mol. Biol., 1990, 215, 403–410 Google Scholar

  • [30] Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, 25, 3389–3402 CrossrefGoogle Scholar

  • [31] Lowe T.M., Eddy S.R., tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 1997, 25, 955–964 CrossrefGoogle Scholar

  • [32] Lohse M., Drechsel O., Bock R., OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes, Curr. Genet., 2007, 52, 267–274 Web of ScienceCrossrefPubMedGoogle Scholar

  • [33] Gouy M., Guindon S., Gascuel O., SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol., 2010, 27, 221–224 CrossrefWeb of ScienceGoogle Scholar

  • [34] Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O., et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol., 2010, 59, 307–321 Web of ScienceGoogle Scholar

  • [35] Lanave C., Preparata G., Saccone C., Serio G., A new method for calculating evolutionary substitution rates, J. Mol. Evol., 1984, 20, 86–93 CrossrefGoogle Scholar

  • [36] Ronquist F., Teslenko M., Van der Mark P., Ayres D.L., Darling A., Höhna S., et al., MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst. Biol., 2012, 61, 539–542 Web of ScienceCrossrefGoogle Scholar

  • [37] Katoh K., Toh H., Parallelization of the MAFFT multiple sequence alignment program, Bioinformatics, 2010, 26, 1899–1900 CrossrefGoogle Scholar

  • [38] Capella-Gutiérrez S., Silla-Martínez J.M., Gabaldón T., trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, 2009, 25, 1972–1973 Web of ScienceCrossrefGoogle Scholar

  • [39] Bundschuh R., Altmüller J., Becker C., Nürnberg P., Gott J.M., Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA, Nucleic Acids Res., 2011, 39, 6044– 6055 Web of ScienceCrossrefPubMedGoogle Scholar

  • [40] Byrne E.M., Visomirski-Robic L., Cheng Y.-W., Rhee A.C., Gott J.M., RNA editing in Physarum mitochondria: assays and biochemical approaches, Methods Enzymol., 2007, 424, 141–172 Web of ScienceGoogle Scholar

  • [41] Beargie C., Liu T., Corriveau M., Lee H.Y., Gott J., Bundschuh R., et al., Genome annotation in the presence of insertional RNA editing, Bioinformatics, 2008, 24, 2571–2578 Web of ScienceCrossrefGoogle Scholar

  • [42] Gott J.M., Parimi N., Bundschuh R., Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs, Nucleic Acids Res., 2005, 33, 5063–5072 CrossrefGoogle Scholar

  • [43] Gawryluk R.M.R., Gray M.W., An ancient fission of mitochondrial cox1, Mol. Biol. Evol., 2010, 27, 7–10 Web of ScienceGoogle Scholar

  • [44] Lonergan K.M., Gray M.W., Expression of a continuous open reading frame encoding subunits 1 and 2 of cytochrome c oxidase in the mitochondrial DNA of Acanthamoeba castellanii, J. Mol. Biol., 1996, 257, 1019–1030 Google Scholar

  • [45] Lonergan K.M., Gray M.W., Editing of transfer RNAs in Acanthamoeba castellanii mitochondria, Science, 1993, 259, 812–816 Google Scholar

  • [46] Gott J.M., Somerlot B.H., Gray M.W., Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria, RNA, 2010, 16, 482–488 CrossrefWeb of ScienceGoogle Scholar

  • [47] Abad M.G., Long Y., Willcox A., Gott J.M., Gray M.W., Jackman J.E., et al., A role for tRNA(His) guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5’-tRNA editing, RNA, 2011, 17, 613–623 CrossrefWeb of ScienceGoogle Scholar

  • [48] Jackman J., Gott J., Gray M. W., Doing it in reverse: 3’-to- 5’ polymerization by the Thg1 superfamily, RNA, 2012, 18, 886–899 Web of ScienceGoogle Scholar

  • [49] Gray MW, Lang BF, Burger G. Mitochondria of protists. Annu. Rev. Genet., 2004, 38, 477–524. CrossrefGoogle Scholar

  • [50] Bullerwell C.E., Burger G., Gott J.M., Kourennaia O., Schnare M.N., Gray M.W., et al., Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa, Eukaryot. Cell, 2010, 9, 762–773 Web of ScienceGoogle Scholar

About the article

Received: 2013-06-10

Accepted: 2013-08-16

Published Online: 2013-08-20

Citation Information: Protist Genomics, Volume 1, Pages 25–32, ISSN (Online) 2299-100X, DOI: https://doi.org/10.2478/prge-2013-0002.

Export Citation

©2013 Versita Sp. z o.o.. This content is open access.

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Natalya I. Bondarenko, Elena S. Nassonova, Olja Mijanovic, Anna A. Glotova, Oksana G. Kamyshatskaya, Alexander A. Kudryavtsev, Alexey E. Masharsky, Dmitrii E. Polev, and Alexey V. Smirnov
Journal of Eukaryotic Microbiology, 2018
Cédric Berney, Stefan Geisen, Jeroen Van Wichelen, Frank Nitsche, Pieter Vanormelingen, Michael Bonkowski, and David Bass
Protist, 2015, Volume 166, Number 2, Page 271

Comments (0)

Please log in or register to comment.
Log in