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PLOS ONE  2008 

EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata

DOI: 10.1371/journal.pone.0002621

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Background Classification of eukaryotes provides a fundamental phylogenetic framework for ecological, medical, and industrial research. In recent years eukaryotes have been classified into six major supergroups: Amoebozoa, Archaeplastida, Chromalveolata, Excavata, Opisthokonta, and Rhizaria. According to this supergroup classification, Archaeplastida and Chromalveolata each arose from a single plastid-generating endosymbiotic event involving a cyanobacterium (Archaeplastida) or red alga (Chromalveolata). Although the plastids within members of the Archaeplastida and Chromalveolata share some features, no nucleocytoplasmic synapomorphies supporting these supergroups are currently known. Methodology/Principal Findings This study was designed to test the validity of the Archaeplastida and Chromalveolata through the analysis of nucleus-encoded eukaryotic translation elongation factor 2 (EEF2) and cytosolic heat-shock protein of 70 kDa (HSP70) sequences generated from the glaucophyte Cyanophora paradoxa, the cryptophytes Goniomonas truncata and Guillardia theta, the katablepharid Leucocryptos marina, the rhizarian Thaumatomonas sp. and the green alga Mesostigma viride. The HSP70 phylogeny was largely unresolved except for certain well-established groups. In contrast, EEF2 phylogeny recovered many well-established eukaryotic groups and, most interestingly, revealed a well-supported clade composed of cryptophytes, katablepharids, haptophytes, rhodophytes, and Viridiplantae (green algae and land plants). This clade is further supported by the presence of a two amino acid signature within EEF2, which appears to have arisen from amino acid replacement before the common origin of these eukaryotic groups. Conclusions/Significance Our EEF2 analysis strongly refutes the monophyly of the Archaeplastida and the Chromalveolata, adding to a growing body of evidence that limits the utility of these supergroups. In view of EEF2 phylogeny and other morphological evidence, we discuss the possibility of an alternative eukaryotic supergroup.


[1]  Bisby FA, Roskov YR, Ruggiero MA, Orrell TM, Paglinawan LE, et al. (2007) Species 2000 & ITIS catalogue of life: 2007 annual checklist. Species 2000. Retrieved Jan. 21, 2008 .
[2]  Patterson DJ (1999) The diversity of eukaryotes. Am Nat 154: S96–S124.
[3]  Patterson DJ (2000) The lineages of eukaryotes. Tree of life web project. Retrieved Jan 21, 2008 .
[4]  Stechmann A, Cavalier-Smith T (2002) Rooting the eukaryote tree by using a derived gene fusion. Science 297: 89–91.
[5]  Richards TA, Cavalier-Smith T (2005) Myosin domain evolution and the primary divergence of eukaryotes. Nature 436: 1113–1118.
[6]  Stechmann A, Cavalier-Smith T (2003) Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90. J Mol Evol 57: 408–419.
[7]  Makiuchi T, Nara T, Annoura T, Hashimoto T, Aoki T (2007) Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups. Gene 394: 78–86.
[8]  Kim E, Simpson AGB, Graham LE (2006) Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol Biol Evol 23: 2455–2466.
[9]  Nozaki H, Matsuzaki M, Misumi O, Kuroiwa H, Higashiyama T, et al. (2005) Phylogenetic implications of the CAD complex from the primitive red alga Cyanidioschyzon merolae (Cyanidiales, Rhodophyta). J Phycol 41: 652–657.
[10]  Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 52: 399–451.
[11]  Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, et al. (2005) The tree of eukaryotes. Trends Ecol Evol 20: 670–676.
[12]  Simpson AGB, Roger AJ (2004) The real ‘kingdoms’ of eukaryotes. Curr Biol 14: R693–R696.
[13]  Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, et al. (2006) Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2: e220.
[14]  Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, et al. (2007) Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE 2: e790.
[15]  Bodyl A (2005) Do plastid-related characters support the chromalveolate hypothesis? J Phycol 41: 712–719.
[16]  Stiller JW, Riley J, Hall BD (2001) Are red algae plants? A critical evaluation of three key molecular data sets. J Mol Evol 52: 527–539.
[17]  Keeling PJ, Archibald JM, Fast NM, Palmer JD (2004) Comment on “The evolution of modern eukaryotic phytoplankton”. Science 306: 2191b.
[18]  Palmer JD (2003) The symbiotic birth and spread of plastids: How many times and whodunit? J Phycol 39: 4–11.
[19]  Nozaki H, Matsuzaki M, Takahara M, Misumi O, Kuroiwa H, et al. (2003) The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J Mol Evol 56: 485–497.
[20]  Grzebyk D, Katz ME, Knoll AH, Quigg A, Raven JA, et al. (2004) Response to comment on “The evolution of modern eukaryotic phytoplankton”. Science 306: 2191c.
[21]  Yoon HS, Grant J, Tekle YI, Wu M, Chaon BC, et al. (2008) Broadly sampled multigene trees of eukaryotes. BMC Evol Biol 8: 14.
[22]  Jarvis P, Soll M (2001) Toc, Tic, and chloroplast protein import. Biochim Biophys Acta 1541: 64–79.
[23]  Marin B, Nowack ECM, Melkonian M (2005) A plastid in the making: primary endosymbiosis. Protist 156: 425–432.
[24]  Nowack ECM, Melkonian M, Glockner G (2008) Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Curr Biol 18: 410–418.
[25]  Bodyl A, Mackiewicz P, Stiller JW (2007) The intracellular cyanobacteria of Paulinelia chromatophora: endosymbionts or organelles? Trends Microbiol 15: 295–296.
[26]  Theissen U, Martin W (2006) The difference between organelles and endosymbionts. Curr Biol 16: R1016–R1017.
[27]  Bhattacharya D, Archibald JM (2006) The difference between organelles and endosymbionts - response to Theissen and Martin. Curr Biol 16: R1017–R1018.
[28]  Okamoto N, Inouye I (2005) The katablepharids are a distant sister group of the Cryptophyta: a proposal for Katablepharidophyta divisio nova/Kathablepharida phylum novum based on SSU rDNA and beta-tubulin phylogeny. Protist 156: 163–179.
[29]  Andersen RA (2004) Biology and systematics of heterokont and haptophyte algae. Am J Bot 91: 1508–1522.
[30]  Cavalier-Smith T (1999) Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol 46: 347–366.
[31]  Graham LE, Wilcox LW (2000) Algae. Upper Saddle River, NJ: Prentice Hall.
[32]  Schnepf E, Elbrachter M (1999) Dinophyte chloroplasts and phylogeny: a review. Grana 38: 81–97.
[33]  Kohler S, Delwiche CF, Denny PW, Tilney LG, Webster P, et al. (1997) A plastid of probable green algal origin in apicomplexan parasites. Science 275: 1485–1489.
[34]  Kohler S (2005) Multi-membrane-bound structures of Apicomplexa: I. the architecture of the Toxoplasma gondii apicoplast. Parasitol Res 96: 258–272.
[35]  Hopkins J, Fowler R, Krishna S, Wilson I, Mitchell G, et al. (1999) The plastid in Plasmodium falciparum asexual blood stages: a three-dimensional ultrastructural analysis. Protist 150: 283–295.
[36]  Tomova C, Geerts WJC, Muller-Reichert T, Entzeroth R, Humbel BM (2006) New comprehension of the apicoplast of Sarcocystis by transmission electron tomography. Biol Cell 98: 535–545.
[37]  Moore RB, Obornik M, Janouskovec J, Chrudimsky T, Vancova M, et al. (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451: 959–963.
[38]  Stiller JW, Reel DC, Johnson JC (2003) A single origin of plastids revisited: convergent evolution in organellar genome content. J Phycol 39: 95–105.
[39]  Larkum AWD, Lockhart PJ, Howe CJ (2007) Shopping for plastids. Trends Plant Sci 12: 189–195.
[40]  McFadden GI, van Dooren GG (2004) Evolution: red algal genome affirms a common origin of all plastids. Curr Biol 14: R514–R516.
[41]  Stiller JW, Hall BD (1997) The origin of red algae: implications for plasmid evolution. Proc Natl Acad Sci U S A 94: 4520–4525.
[42]  Sanchez-Puerta MV, Bachvaroff TR, Delwiche CF (2007) Sorting wheat from chaff in multi-gene analyses of chlorophyll c-containing plastids. Mol Phylogenet Evol 44: 885–897.
[43]  Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, et al. (2004) The evolution of modern eukaryotic phytoplankton. Science 305: 354–360.
[44]  Fast NM, Kissinger JC, Roos DS, Keeling PJ (2001) Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol Biol Evol 18: 418–426.
[45]  Bucknam J, Boucher Y, Bapteste E (2006) Refuting phylogenetic relationships. Biol Direct 1: 26.
[46]  Gupta RS, Golding GB (1993) Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J Mol Evol 37: 573–582.
[47]  Gupta RS, Singh B (1994) Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr Biol 4: 1104–1114.
[48]  Gomez-Lorenzo MG, Spahn CMT, Agrawal RK, Grassucci RA, Penczek P, et al. (2000) Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 angstrom resolution. EMBO J 19: 2710–2718.
[49]  Jorgensen R, Merrill AR, Andersen GR (2006) The life and death of translation elongation factor 2. Biochem Soc Trans 34: 1–6.
[50]  Moreira D, Le Guyader H, Philippe H (2000) The origin of red algae and the evolution of chloroplasts. Nature 405: 69–72.
[51]  Germot a, Philippe H (1999) Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family. J Eukaryot Microbiol 46: 116–124.
[52]  Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36: 541–562.
[53]  Wiens JJ (2006) Missing data and the design of phylogenetic analyses. J Biomed Inform 39: 34–42.
[54]  Philippe H, Snell EA, Bapteste E, Lopez P, Holland PWH, et al. (2004) Phylogenomics of eukaryotes: Impact of missing data on large alignments. Mol Biol Evol 21: 1740–1752.
[55]  Patron NJ, Inagaki Y, Keeling PJ (2007) Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol 17: 887–891.
[56]  Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, et al. (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of Rhizaria with Chromalveolates. Mol Biol Evol 24: 1702–1713.
[57]  McFadden GI (2001) Primary and secondary endosymbiosis and the origin of plastids. J Phycol 37: 951–959.
[58]  Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, et al. (2005) Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol 15: 1325–1330.
[59]  Nosenko T, Bhattacharya D (2007) Horizontal gene transfer in chromalveolates. BMC Evol Biol 7: 173.
[60]  Lane CE, van den Heuvel K, Korera C, Curtis BA, Parsons BJ, et al. (2007) Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc Natl Acad Sci U S A 104: 19908–19913.
[61]  Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, et al. (2001) The highly reduced genome of an enslaved algal nucleus. Nature 410: 1091–1096.
[62]  V?rs N (1992) Ultrastructure and autecology of the marine, heterotrophic flagellate Leucocryptos marina (Braaud) Butcher 1967 (Kathablepharidaceae/Kathablepharidae), with a discussion of the genera Leucocryptos and Katablepharis/Kathablepharis. Eur J Protistol 28: 369–389.
[63]  McFadden GI, Gilson PR, Hill DRA (1994) Goniomonas: ribosomal RNA sequences indicate that this phagotrophic flagellate is a close relative of the host component of cryptomonads. Eur J Phycol 29: 29–32.
[64]  Maddison WP (1997) Gene trees in species trees. Syst Biol 46: 523–536.
[65]  Stiller JW (2007) Plastid endosymbiosis, genome evolution and the origin of green plants. Trends Plant Sci 12: 391–396.
[66]  Steiner JM, Yusa F, Pompe JA, Loffelhardt W (2005) Homologous protein import machineries in chloroplasts and cyanelles. Plant J 44: 646–652.
[67]  Stoebe B, Kowallik KV (1999) Gene-cluster analysis in chloroplast genomics. Trends Genet 15: 344–347.
[68]  Durnford DG, Deane JA, Tan S, McFadden GI, Gantt E, et al. (1999) A phylogenetic assessment of the eukaryotic light-harvesting antenna proteins, with implications for plastid evolution. J Mol Evol 48: 59–68.
[69]  Rissler HM, Durnford DG (2005) Isolation of a novel carotenoid-rich protein in Cyanophora paradoxa that is immunologically related to the light-harvesting complexes of photosynthetic eukaryotes. Plant Cell Physiol 46: 416–424.
[70]  Stoebe B, Martin W, Kowallik KV (1998) Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes. Plant Mol Biol Rep 16: 243–255.
[71]  Loffelhardt W, Bohnert HJ, Bryant DA (1997) The complete sequence of the Cyanophora paradoxa cyanelle genome (Glaucocystophyceae). Plant Syst Evol 149–162.
[72]  O'Kelly C (1993) Relationships of eukaryotic algal groups to other protists. In: Berner T, editor. Ultrastructure of microalgae. Boca Raton, FL: CRC Press. pp. 269–294.
[73]  Stiller JW, Harrell L (2005) The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny. BMC Evol Biol 5: 71.
[74]  Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972–977.
[75]  Burger G, Saint-Louis D, Gray MW, Lang BF (1999) Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: cyanobacterial introns and shared ancestry of red and green algae. Plant Cell 11: 1675–1694.
[76]  Secq MPO, Goer SL, Stam WT, Olsen JL (2006) Complete mitochondrial genomes of the three brown algae (Heterokonta: Phaeophyceae) Dictyota dichotoma, Fucus vesiculosus and Desmarestia viridis. Curr Genet 49: 47–58.
[77]  Kim E, Lane CE, Curtis BA, Kozera C, Bowman S, et al. (2008) Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). BMC Genomics 9: 215.
[78]  Gibbs SP (1981) The Chloroplasts of some algal groups may have evolved from endosymbiotic eukaryotic algae. Ann N Y Acad Sci 361: 193–208.
[79]  Rumpho ME, Summer EJ, Manhart JR (2000) Solar-powered sea slugs. Mollusc/algal chloroplast symbiosis. Plant Physiol 123: 29–38.
[80]  Leander BS, Keeling PJ (2003) Morphostasis in alveolate evolution. Trends Ecol Evol 18: 395–402.
[81]  Moriya M, Nakayama T, Inouye I (2002) A new class of the stramenopiles, Placididea classis nova: description of Placidia cafeteriopsis gen. et sp nov. Protist 153: 143–156.
[82]  Kim E, Archibald JM (2008) Diversity and evolution of plastids and their genomes. In: Sandelius AS, Aronsson H, editors. The Chloroplast: Interactions with the environment. Heidelberg: Springer.
[83]  Harper JT, Keeling PJ (2003) Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 20: 1730–1735.
[84]  Takishita K, Ishida KI, Maruyama T (2004) Phylogeny of nuclear-encoded plastid-targeted GAPDH gene supports separate origins for the peridinin- and the fucoxanthin derivative-containing plastids of dinoflagellates. Protist 155: 447–458.
[85]  Takishita K, Kawachi M, Noel MH, Matsumoto T, Kakizoe N, et al. (2008) Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. Gene 410: 26–36.
[86]  Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, et al. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A 99: 12246–12251.
[87]  Ohta N, Matsuzaki M, Misumi O, Miyagishima S, Nozaki H, et al. (2003) Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Res 10: 67–77.
[88]  Bachvaroff TR, Puerta MVS, Delwiche CF (2005) Chlorophyll c-containing plastid relationships based on analyses of a multigene data set with all four chromalveolate lineages. Mol Biol Evol 22: 1772–1782.
[89]  Bodyl A, Moszczynski K (2006) Did the peridinin plastid evolve through tertiary endosymbiosis? A hypothesis. Eur J Phycol 41: 435–448.
[90]  Lee RE, Kugrens P (1991) Katablepharis ovalis, a colorless flagellate with interesting cytological characteristics. J Phycol 27: 505–513.
[91]  Lee RE, Kugrens P, Mylnikov AP (1992) The structure of the flagellar apparatus of two strains of Katablepharis (Cryptophyceae). Br Phycol J 27: 369–380.
[92]  Clay B, Kugrens P (1999) Systematics of the enigmatic kathablepharids, including EM characterization of the type species, Kathablepharis phoenikoston, and new observations on K. remigera com. nov. Protist 150: 43–59.
[93]  Domozych DS, Wells B, Shaw PJ (1992) Scale biogenesis in the green alga, Mesostigma viride. Protoplasma 167: 19–32.
[94]  Domozych DS, Stewart KD, Mattox KR (1981) Development of the cell wall in Tetraselmis: role of the Golgi apparatus and extracellular wall assembly. J Cell Sci 52: 351–371.
[95]  Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62: 1435–1491.
[96]  Boorstein WR, Ziegelhoffer T, Craig EA (1994) Molecular evolution of the HSP70 multigene family. J Mol Evol 38: 1–17.
[97]  Maddison DR, Maddison WP (2001) MacClade 4: analysis of phylogeny and character evolution. Sunderland, MA: Sinauer Associates Inc.
[98]  Inagaki Y, Simpson AGB, Dacks JB, Roger AJ (2004) Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Syst Biol 53: 582–593.
[99]  Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.
[100]  Lartillot N, Brinkmann H, Philippe H (2007) Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7: S4.
[101]  Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104–2105.
[102]  Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502–504.
[103]  Desper R, Gascuel O (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol 9: 687–705.
[104]  Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Seattle: Department of Genome Sciences, University of Washington.


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