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Systematics and Evolution of the Algae. I. Genomics Meets Phylogeny

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Progress in Botany

Part of the book series: Progress in Botany ((BOTANY,volume 62))

Abstract

The enormous amount of data generated by the various genome-sequencing projects has led to a plethora of studies addressing the evolutionary history of life on Earth.

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References

  • Akhmanova A, Voncken F, Van Alen T, Van Hoek A, Boxma B, Vogels G, Veenhuiss M, Hackstein JHP (1998) A hydrogenosome with a genome. Nature 396:527–528

    PubMed  CAS  Google Scholar 

  • Allen JF (1993) Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 165:609–631

    PubMed  CAS  Google Scholar 

  • Andersson SGE (1998) Bioenergetics of the obligate intracellular parasite Rickettsia prowazeki. Biochim Biophys Acta 1385:105–111

    Google Scholar 

  • Andersson SGE, Kurland CG (1998) Reductive evolution of resident genomes. Trends Microbiol 6:263–268

    PubMed  CAS  Google Scholar 

  • Andersson SGE, Kurland CG (1999) Origins of mitochondria and hydrogenosomes. Curr Opin Microbiol 2:535–541

    PubMed  CAS  Google Scholar 

  • Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Pontén T, Aismark UCM, Podowski RM, Näslund AK, Eriksson AS, Winkler HH, Kurland CG (1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133–140

    PubMed  CAS  Google Scholar 

  • Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet 14:442–444

    PubMed  CAS  Google Scholar 

  • Baldauf SL, Palmer JD, Doolittle WF (1996) The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc Natl Acad Sci USA 93:7749–7754

    PubMed  CAS  Google Scholar 

  • Barbrook AC, Lockhart PJ, Howe CJ (1998) Phylogenetic analysis of plastid origins based on secA sequences. Curr Genet 34:336–341

    PubMed  CAS  Google Scholar 

  • Bell SD, Jackson SP (1998) Transcription and translation in Archaea: a mosaic of eu-karyal and bacterial features. Trends Microbiol 6:222–228

    PubMed  CAS  Google Scholar 

  • Bernard C, Fenchel T (1994) Chemosensory behavior of Strombidium purpureum, an anaerobic oligotroph with endosymbiotic purple nonsulfur bacteria. J Eukaryot Microbiol 41:391–396

    Google Scholar 

  • Bhattacharya D (1997) Origins of algae and their plastids. Springer, Berlin Heidelberg New York

    Google Scholar 

  • Bhattacharya D, Medlin L (1995) The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. J Phycol 31:489–498

    CAS  Google Scholar 

  • Bhattacharya D, Schmidt HA (1997) Division Glaucocystophyta. Plant Syst Evol Suppl 11:139–148

    Google Scholar 

  • Bhattacharya D, Helmchen T, Bibeau C, Melkonian M (1995) Comparisons of nuclear-encoded small-subunit ribosomal RNAs reveal the evolutionary position of the Glaucocystophyta. Mol Biol Evol 12:415–420

    PubMed  CAS  Google Scholar 

  • Bhaya D, Grossman A (1991) Targeting proteins to diatom plastids involves transport through an endoplasmic reticulum. Mol Gen Genet 229:400–404

    PubMed  CAS  Google Scholar 

  • Blanchard JL, Schmidt GW (1995) Pervasive migration of organellar DNA to the nucleus in plants. J Mol Evol 41:397–406

    PubMed  CAS  Google Scholar 

  • Bodyl A (1997) Mechanism of protein targeting to the chlorarachniophyte plastids and the evolution of complex plastids with four membranes — a hypothesis. Bot Acta 110: 395–400

    Google Scholar 

  • Bölter B, Soll J, Schulz A, Hinnah S, Wagner R (1998) Origin of a chloroplast protein importer. Proc Natl Acad Sci USA 95:15831–15836

    PubMed  Google Scholar 

  • Brinkmann H, Martin W (1996) Higher-plant chloroplast and cytosolic 3-phospho-glycerate kinases: a case of endosymbiotic gene replacement. Plant Mol Biol 30:65–75

    PubMed  CAS  Google Scholar 

  • Brinkmann H, Philippe H (1999) Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol 16:817–825

    PubMed  CAS  Google Scholar 

  • Brocks JJ, Logan GA, Buick R, Summons RE (1999) Archean molecular fossils and the early rise of eukaryotes. Science 285:1033–1036

    PubMed  CAS  Google Scholar 

  • Brown JR, Doolittle WF (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92:2441–2445

    PubMed  CAS  Google Scholar 

  • Brown JR, Doolittle WF (1997) Archaea and the prokaryote-to-eukaryote transition. Microbiol Rev 61:456–502

    CAS  Google Scholar 

  • Bui ETN, Bradley PJ, Johnson PJ (1996) A common evolutionary origin for mitochondria and hydrogenosomes. Proc Natl Acad Sci USA 93:9651–9656

    PubMed  CAS  Google Scholar 

  • Burger G, Plante I, Lonergan KM, Gray MW (1995) The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: Complete sequence, gene content and genome organization. J Mol Biol 245:522–537

    PubMed  CAS  Google Scholar 

  • Caron L, Douady D, Quinet-Szely M, De Goër S, Berkaloff C (1996) Gene structure of a chlorophyll a/c-binding protein from a brown alga: Presence of an intron and phylogenetic implications. J Mol Evol 43:270–280

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T (1989) Archaebacteria and archezoa. Nature 339:100–101

    Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Cavalier-Smith T, Chao EE (1996) 18S rRNA sequence of Heterosigma carterae (Raphidophyceae), and the phylogeny of heterokont algae (Ochrophyta). Phycologia 35:500–510

    Google Scholar 

  • Cavalier-Smith T, Couch JA, Thorsteinsen KE, Gilson P, Deane JA, Hill DRA, McFadden GI (1996) Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny. Eur J Phycol 31:315–328

    Google Scholar 

  • Chen XJ, Schnell DJ (1999) Protein import into chloroplasts. Trends Cell Biol 9:222–227

    PubMed  CAS  Google Scholar 

  • Clay BL, Kugrens P (1999) Characterization of Hemiselmis amylosa sp. nov and phylogenetic placement of the blue-green cryptomonads H. amylosa and Falcomonas daucoides. Protist 150:297–310

    PubMed  CAS  Google Scholar 

  • Clayton RA, White O, Fraser CM (1998) Findings emerging from complete microbial genome sequences. Curr Opin Microbiol 1:562–566

    PubMed  CAS  Google Scholar 

  • Daugbjerg N, Andersen RA (1997) Phylogenetic analyses of the rbcL sequences from haptophytes and heterokont algae suggest their chloroplasts are unrelated. Mol Biol Evol 14:1242–1251

    PubMed  CAS  Google Scholar 

  • Deane JA, Fraunholz M, Su V, Maier U-G, Martin W, Durnford DG, McFadden GI (2000) Evidence for nucleomorph to host nucleus gene transfer: light-harvesting complex proteins from cryptomonads and chlorarachniophytes. Protist 151 (in press)

    Google Scholar 

  • Delwiche CF (1999) Tracing the thread of plastid diversity through the tapestry of life. Am Nat 154:S164–S177

    PubMed  Google Scholar 

  • Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and duplication of Rubisco genes in eubacteria and plastids. Mol Biol Evol 13:873–882

    PubMed  CAS  Google Scholar 

  • Delwiche CF, Palmer JD (1997) The origin of plastids and their spread via secondary symbiosis. Plant Syst Evol Suppl 11:53–86

    CAS  Google Scholar 

  • Denny P, Preiser P, Williamson D, Wilson I (1998) Evidence for a single origin of the 35-kb plastid DNA in apicomplexans. Protist 149:51–59

    PubMed  CAS  Google Scholar 

  • Denovan-Wright EM, Nedelcu AM, Lee RW (1998) Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos. Plant Mol Biol 36:285–295

    PubMed  CAS  Google Scholar 

  • Doolittle RF (1998a) Microbial genomes opened up. Nature 392:339–342

    PubMed  CAS  Google Scholar 

  • Doolittle RF, Feng DF, Tsang S, Cho G, Little E (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470–477

    PubMed  CAS  Google Scholar 

  • Doolittle WF (1997) Fun with genealogy. Proc Natl Acad Sci USA 94:12751–12753

    PubMed  CAS  Google Scholar 

  • Doolittle WF (1998b) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14:307–311

    PubMed  CAS  Google Scholar 

  • Doolittle WF, Logsdon JM Jr (1998) Archaeal genomics: do archaea have a mixed heritage. Curr Biol 8:R209–R211

    PubMed  CAS  Google Scholar 

  • Douglas SE (1998) Plastid evolution: origins, diversity, trends. Curr Opin Genet Devel 8:655–661

    CAS  Google Scholar 

  • Douglas SE, Penny SL (1999) The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. J Mol Evol 48:236–244

    PubMed  CAS  Google Scholar 

  • Durnford DG, Deane JA, Tan S, McFadden GI, Gantt E, Green BR (1999) A phylogenetic assessment of the eukaryotic light-harvesting antenna proteins, with implications for plastid evolution. J Mol Evol 48:59–68

    PubMed  CAS  Google Scholar 

  • Edgell DR, Doolittle WF (1997) Archaea and the origin(s) of DNA replication proteins. Cell 89:995–998

    PubMed  CAS  Google Scholar 

  • Embley TM, Martin W (1998) Molecular evolution: a hydrogen-producing mitochondrion. Nature 396:517–519

    PubMed  CAS  Google Scholar 

  • Embley TM, Finlay BJ, Dyal PL, Hirt RP, Wilkinson M, Williams AG (1995) Multiple origins of anaerobic ciliates with hydrogenosomes within the radiation of aerobic ciliates. Proc R Soc Lond B Biol Sci 262:87–93

    CAS  Google Scholar 

  • Embley TM, Horner DA, Hirt RP (1997) Anaerobic eukaryote evolution: hydrogenosomes as biochemically modified mitochondria. Trends Ecol Evol 12:437–441

    PubMed  CAS  Google Scholar 

  • Fagan T, Hastings JW, Morse D (1998) The phylogeny of glyceraldehyde-3-phosphate dehydrogenase indicates lateral gene transfer from cryptomonads to dinoflagellates. J Mol Evol 47:633–639

    PubMed  CAS  Google Scholar 

  • Fast NM, Logsdon JM Jr, Doolittle WF (1999) Phylogenetic analysis of the TATA box binding protein (TBP) gene from Nosema locustae: evidence for a microsporidia-fungi relationship and spliceosomal intron loss. Mol Biol Evol 16:1415–1419

    PubMed  CAS  Google Scholar 

  • Feagin JE (1994) The extrachromosomal DNAs of apicomplexan parasites. Annu Rev Microbiol 48:81–104

    PubMed  CAS  Google Scholar 

  • Felsenstein J (1977) The evolutionary advantage of recombination. Genetics 78:157–159

    Google Scholar 

  • Feng DF, Cho G, Doolittle RF (1997) Determining divergence times with a protein clock: update and reevaluation. Proc Natl Acad Sci USA 94:13028–13033

    PubMed  CAS  Google Scholar 

  • Fichera ME, Roos DS (1997) A plastid organelle as a drug target in apicomplexan parasites. Nature 390:407–409

    PubMed  CAS  Google Scholar 

  • Finlay BJ, Fenchel T (1989) Hydrogenosomes in some anaerobic protozoa resemble mitochondria. FEMS Microbiol Lett 65:311–314

    CAS  Google Scholar 

  • Fitch WM, Markowitz E (1970) An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet 4:579–593

    PubMed  CAS  Google Scholar 

  • Fitz-Gibbon ST, House CH (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27:4218–4222

    PubMed  CAS  Google Scholar 

  • Flechner A, Dressen U, Westhoff P, Henze K, Schnarrenberger C, Martin W (1996) Molecular characterization of transketolase (EC 2.2.1.1) active in the Calvin cycle of spinach chloroplasts. Plant Mol Biol 32:475–484

    PubMed  CAS  Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al. (1995) Whole-genome random sequence of Haemophilus influenzae Rd. Science 269:496–512

    PubMed  CAS  Google Scholar 

  • Forterre P (1995) Thermoreduction, a hypothesis for the origin of prokaryotes. C R Acad Sci III 318:415–422

    Google Scholar 

  • Forterre P (1997) Archaea: what can we learn from their sequences. Curr Opin Genet Dev 7:764–770

    PubMed  CAS  Google Scholar 

  • Forterre P (1999) Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol Microbiol 33:457–465

    PubMed  CAS  Google Scholar 

  • Forterre P, Philippe H (1999) Where is the root or the universal tree of life? Bioessays 21:871–879

    PubMed  CAS  Google Scholar 

  • Gaasterland T (1999) Archaeal genomics. Curr Opin Microbiol 2:542–547

    PubMed  CAS  Google Scholar 

  • Germot A, Philippe H, Le Guyader H (1996) Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial en-dosymbiosis in eukaryotes. Proc Natl Acad Sci USA 93:14614–14617

    PubMed  CAS  Google Scholar 

  • Germot A, Philippe H, Le Guyader H (1997) Evidence for loss of mitochondria in Aficrosporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol Biochem Parasitol 87:159–168

    PubMed  CAS  Google Scholar 

  • Gibbs SP (1979) The route of entry of cytoplasmically synthesized proteins into chloroplasts of algae possessing chloroplast ER. J Cell Sci 35:253–266

    PubMed  CAS  Google Scholar 

  • Gilson PR, McFadden GI (1996) The miniaturized nuclear genome of a eukaryotic endo-symbiont contains genes that overlap, genes that are cotranscribed, and the smallest known spliceosomal introns. Proc Natl Acad Sci USA 93:7737–7742

    PubMed  CAS  Google Scholar 

  • Gilson PR, Maier UG, McFadden GI (1997) Size isn’t everything: lessons in genetic miniaturisation from nucleomorphs. Curr Opin Genet Dev 7:800–806

    PubMed  CAS  Google Scholar 

  • Gogarten JP, Kibak H, Dittrich P, Taiz L, Bowman EJ, Bowman BJ, Manolson MF, Poole RJ, Date T, Oshima T, Konishi J, Denda K, Yoshida M (1989) Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86:6661–6665

    PubMed  CAS  Google Scholar 

  • Gogarten JP, Olendzenski L, Hilario E, Simon C, Holsinger KE (1996) Dating the cenan-cestor of organisms. Science 274:1751–1753

    Google Scholar 

  • Golding GB, Gupta RS (1995) Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol Biol Evol 12:1–6

    PubMed  CAS  Google Scholar 

  • Graur D, Li W-H (1999) Fundamentals of molecular evolution. Sinauer, Sunderland

    Google Scholar 

  • Gray MW (1998) Rickettsia, typhus and the mitochondrial connection. Nature 396:109–110

    PubMed  CAS  Google Scholar 

  • Gray MW, Lang BF (1998) Transcription in chloroplasts and mitochondria: a tale of two polymerases. Trends Microbiol 6:1–3

    PubMed  CAS  Google Scholar 

  • Gray MW, Spencer DF (1996). Organellar evolution. In: Roberts DM, Sharp P, Alderson G, Collins MA (eds) Evolution of microbial life. 54th Symposium of the Society of General Microbiology. Cambridge Univeristy, Cambridge, pp 109–126

    Google Scholar 

  • Gray MW, Lang BF, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Brossard N, Delage E, Littlejohn TG, Plante I, Rioux P, Saint-Louis D, Zhu Y, Burger G (1998) Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res 26:865–878

    PubMed  CAS  Google Scholar 

  • Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283:1476–1481

    PubMed  CAS  Google Scholar 

  • Gribaldo S, Cammarano P (1998) The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. J Mol Evol 47:508–516

    PubMed  CAS  Google Scholar 

  • Grishin NV (1995) Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J Mol Evol 41:675–679

    PubMed  CAS  Google Scholar 

  • Guillou L, Chretiennot-Dinet MJ, Boulben S, Moon-Van Der Staay SY, Vaulot D (1999) Symbiomonas scintillans gen. et sp. nov. and Picophagus flagellatus gen. et sp. nov. (Heterokonta): two new heterotrophic flagellates of picoplanktonic size. Protist 150:383–398

    Google Scholar 

  • Gunderson JH, Goss SH, Coats DW (1999) The phylogenetic position of Amoebophrya sp. infecting Gymnodinium sanguineum. J Eukaryot Microbiol 46:194–197

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Gupta RS, Golding GB (1996) The origin of the eukaryotic cell. Trends Biochem Sci 21:166–171

    PubMed  CAS  Google Scholar 

  • Hasegawa M, Fitch WM (1996) Dating the cenancestor of organisms. Science 274:1751–1753

    Google Scholar 

  • Häuber MM, Müller SB, Speth V, Maier U-G (1994) How to involve a complex plastis? A hypothesis. Bot Acta 107:383–386

    Google Scholar 

  • Heins L, Collinson I, Soll J (1998) The protein translocation apparatus of chloroplast envelopes. Trends Plant Sci 3:56–60

    Google Scholar 

  • Helmchen TA, Bhattacharya D, Melkonian M (1995) Analyses of ribosomal RNA sequences from Glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids. J Mol Evol 41:203–210

    PubMed  CAS  Google Scholar 

  • Henze K, Badr A, Wettern M, Cerff R, Martin W (1995) A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc Natl Acad Sci USA 92:9122–9126

    PubMed  CAS  Google Scholar 

  • Hess WR, Partensky F, Van der Staay GWM, Garcia-Fernandez JM, Börner T, Vaulot D (1996) Coexistence of phycoerythrin and a chlorophyll a/b antenna in a marine prokaryote. Proc Natl Acad Sci USA 93:11126–11130

    PubMed  CAS  Google Scholar 

  • Hess WR, Steglich C, Lichtlé C, Partensky F (1999) Phycoerythrins of the oxyphotobacterium Prochlorococcus marinus are associated to the thylakoid membrane and are encoded by a single large gene cluster. Plant Mol Biol 40:507–521

    PubMed  CAS  Google Scholar 

  • Hillis DM, Moritz C, Mable BK (1996) Molecular systematics, vol 2. Sinauer, Sunderland

    Google Scholar 

  • Hinnah SC, Hill K, Wagner R, Schlicher T, Soll J (1997) Reconstitution of a chloroplast protein import channel. EMBO J 16:7351–7360

    PubMed  CAS  Google Scholar 

  • Hirt RP, Logsdon JM, Healy B, Dorey MW, Doolittle WF, Embley TM (1999) Microsporidia are related to fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci USA 96:580–585

    PubMed  CAS  Google Scholar 

  • Hodges PE, McKee AHZ, Davis BP, Pasyne WEB, Garreis JI (1999) Yeast Protein Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res 27:69–73

    PubMed  CAS  Google Scholar 

  • Honda D, Yokota A, Sugiyama J (1999a) Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. J Mol Evol 48:723–739

    PubMed  CAS  Google Scholar 

  • Honda D, Yokochi T, Nakahara T, Raghukumar S, Nakagiri A, Schaumann K, Higashihara T (1999b) Molecular phylogeny of labyrinthulids and thraustochytrids based on the sequencing of 18S ribosomal RNA gene. J Eukayot Microbiol 46:637–647

    CAS  Google Scholar 

  • Horner DS, Hirt RP, Kilvington S, Lloyd D, Embley TM (1996) Molecular data suggest an early acquisition of the mitochondrion endosymbiont. Proc R Soc Lond B Biol Sci 263:1053–1059

    CAS  Google Scholar 

  • Horner DS, Hirt RP, Embley TM (1999) A single eubacterial origin of eukaryotic pyruvate:ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes. Mol Biol Evol 16:1280–1291

    PubMed  CAS  Google Scholar 

  • Hu Q, Miyashita H, Iwasaki I, Kurano N, Miyachi S, Iwaki M, Itoh S (1998) A photosystem I reaction center driven by chlorophyll d in oxygenic photosynthesis. Proc Natl Acad Sci USA 95:13319–13323

    PubMed  CAS  Google Scholar 

  • Hu Q, Marquardt J, Iwasaki I, Miyashita H, Kurano N, Mörschel E, Miyachi S (1999) Molecular structure, localization and function of biliproteins in the chlorophyll a/d containing oxygenic photosynthetic prokaryote Acaryochloris marina. Biochim Biophys Acta 1412:250–261

    PubMed  CAS  Google Scholar 

  • Ishida K, Cao Y, Hasegawa M, Okada N, Hara Y (1997) The origin of chlorarachniophyte plastids, as inferred from phylogenetic comparisons of amino acid sequences of EF- Tu. J Mol Evol 45:682–687

    PubMed  CAS  Google Scholar 

  • Iwabe N, Kuwa K, Hasegawa M, Osawa S, Miyata T (1989) Evolutionary relationships of archaebacteria, eubacteria, and eucaryotes inferred from phylogenic trees of duplicated genes. Proc Natl Acad Sci USA 86:9355–9359

    PubMed  CAS  Google Scholar 

  • Jermiin LS, Olsen GJ, Mengersen KL, Easteal S (1997) Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis. Mol Biol Evol 14:1296–1302

    CAS  Google Scholar 

  • Judd WS, Campbell CS, Kellogg EA, Stevens PF (1999) Plant systematics. A phylogenetic approach. Sinauer, Sunderland

    Google Scholar 

  • Kaneko T, Matsubayashi T, Sugita M, Sugiura M (1996a) Physical and gene maps of the unicellular cyanobacterium Synechococcus sp. strain PCC6301 genome. Plant Mol Biol 31:193–201

    PubMed  CAS  Google Scholar 

  • Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, et al. (1996b) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136

    PubMed  CAS  Google Scholar 

  • Karpov SA, Kersanach R, Williams DM (1998) Ultrastructure and 18S rRNA gene sequence of a small heterotrophic flagellate Siluania monomastiga gen. et sp. nov. (Bicosoecida). Eur J Protistol 34:415–425

    Google Scholar 

  • Katz LA (1998) Changing perspectives on the origin of eukaryotes. Trends Ecol Evol 13:493–497

    PubMed  CAS  Google Scholar 

  • Keegstra K, Cline K (1999) Protein import and routing systems of chloroplasts. Plant Cell 11:557–570

    PubMed  CAS  Google Scholar 

  • Keegstra K, Froehlich JE (1999) Protein import into chloroplasts. Curr Opin Plant Biol 2:471–476

    PubMed  CAS  Google Scholar 

  • Keeling PJ, Doolittle WF (1997) Evidence that eukaryotic triosephosphate isomerase is of α-proteobacterial origin. Proc Natl Acad Sci USA 94:1270–1275

    PubMed  CAS  Google Scholar 

  • Keeling PJ, McFadden GI (1998) Origins of microsporidia. Trends Microbiol 6:19–23

    PubMed  CAS  Google Scholar 

  • Keeling PJ, Deane JA, Hink-Schauer C, Douglas SE, Maier UG, McFadden GI (1999) The secondary endosymbiont of the cryptomonad Guillardia theta contains α-, β-, and γ-tubulin genes. Mol Biol Evol 16:1308–1313

    PubMed  CAS  Google Scholar 

  • Kenrick P, Crane PR (1997) The origin and early diversification of land plants. A cladistic study. Smithsonian Institution, Washington

    Google Scholar 

  • Kishore R, Muchhal US, Schwartzbach SD (1993) The presequence of Euglena LHCPII, a cytoplasmically synthesized chloroplast protein, contains a functional endoplasmic reticulum-targeting domain. Proc Natl Acad Sci USA 90:11845–11849

    PubMed  CAS  Google Scholar 

  • Köhler S, Delwiche CF, Denny PW, Tilney LG, Webster P, Wilson RJM, Palmer JD, Roos DS (1997) A plastid of probable green algal origin in apicomplexan parasites. Science 275:1485–1489

    PubMed  Google Scholar 

  • Koonin EV, Galperin MY (1997) Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr Opin Genet Dev 7:757–763

    PubMed  CAS  Google Scholar 

  • Koonin EV, Mushegian AR (1996) Complete genome sequences of cellular life forms: Glimpses of theoretical evolutionary genomics. Curr Opin Genet Dev 6:757–762

    PubMed  CAS  Google Scholar 

  • Kotani H, Tabata S (1998) Lessons from sequencing of the genome of a unicellular cya-nobacterium, Synechocystis sp. PCC6803. Annu Rev Plant Physiol Plant Mol Biol 49:151–171

    PubMed  CAS  Google Scholar 

  • Kowallik KV (1997) Origin and evolution of chloroplasts: Current status and future perspectives. In: Schenk HEA, Herrmann RG, Jeon KW, Müller NE, Schwemmler W (eds) Eukaryotism and symbiosis. Intertaxonic combination versus symbiotic adaptation. Springer, Berlin Heidelberg New York, pp 3–23

    Google Scholar 

  • La Roche J, Van der Staay GWM, Partensky F, Ducret A, Aebersold R, Li R, Golden SS, Hiller RG, Wrench PM, Larkum AWD, Green BR (1996) Independent evolution of the prochlorophyte and green plant chlorophyll a/b light-harvesting proteins. Proc Natl Acad Sci USA 93:15244–15248

    PubMed  Google Scholar 

  • Lang BF, Burger G, O’Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387:493–497

    PubMed  CAS  Google Scholar 

  • Lang BF, O’Kelly CJ, Burger G (1998a) Mitochondrial genomics in protists, an approach to probing eukaryotic evolution. Protist 149:313–322

    Google Scholar 

  • Lang BF, Seif E, Gray MW, O’Kelly CJ, Burger G (1999a) Comparative genomics approach to the evolution of eukaryotes and their mitochondria. J Eukaryot Microbiol 46:320–326

    PubMed  CAS  Google Scholar 

  • Lang BF, Gray MW, Burger G (1999b) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33:351–397

    PubMed  CAS  Google Scholar 

  • Lang M, Apt KE, Kroth PG (1998b) Protein transport into “complex” diatom plastids utilizes two different targeting signals. J Biol Chem 273:30973–30978

    PubMed  CAS  Google Scholar 

  • Lawson VA, McPhee DA, Deacon NJ (1996) Elimination of sequence ambiguities by a single-step modification of a solid-phase, single-stranded sequencing protocol. Biotechniques 21:356–358

    PubMed  CAS  Google Scholar 

  • Leipe DD, Wainright PO, Gunderson JH, Porter D, Patterson DJ, Valois F, Himmerich S, Sogin ML (1994) The stramenopiles from a molecular perspective: 16S-like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 33:369–377

    Google Scholar 

  • Leitsch CEW, Kowallik KV, Douglas S (1999) The atpA gene cluster of Guillardia theta (Cryptophyta): a piece in the puzzle of chloroplast genome evolution. J Phycol 35:128–135

    CAS  Google Scholar 

  • Lemieux C, Otis C, Turmel M (2000) Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature 403:649–652

    PubMed  CAS  Google Scholar 

  • Li W-H (1997) Molecular Evolution. Sinauer, Sunderland

    Google Scholar 

  • Linton EW, Hittner D, Lewandowski C, Auld T, Triemer RE (1999) A molecular study of euglenoid phylogeny using small subunit rDNA. J Eukaryot Microbiol 46:217–223

    PubMed  CAS  Google Scholar 

  • Lockhart PJ, Steel MA, Barbrook AC, Huson DH, Charleston MA, Howe CJ (1998) A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol Biol Evol 15:1183–1188

    PubMed  CAS  Google Scholar 

  • Löffelhardt W, Bohnert H J, Bryant DA (1997) The complete sequence of the Cyanophora paradoxa cyanelle genome (Glaucocystophyceae). Plant Syst Evol 11:149–162

    Google Scholar 

  • Lokstein H, Steglich C, Hess WR (1999) Light-harvesting antenna function of phycoerythrin in Prochlorococcus marinus. Biochim Biophys Acta 1410:97–98

    PubMed  CAS  Google Scholar 

  • Lopez P, Forterre P, Philippe H (1999) The root of the tree of life in the light of the covarion model. J Mol Evol 49:496–508

    PubMed  CAS  Google Scholar 

  • López-García P, Moreira D (1999) On hydrogen transfer and a chimeric origin of eukaryotes. Trends Biochem Sci 24:424–424

    Google Scholar 

  • Lorimer GH, Chen Y-R, Hartman FC (1993) A role for the â-amino group of lysine-334 of ribulose-l,5-bisphosphate carboxylase in the addition of carbon dioxide to the 2,3-enediol(ate) of ribulose 1,5-bisphosphate. Biochemistry 32:9018–9024

    PubMed  CAS  Google Scholar 

  • Marin B, Klingberg M, Melkonian M (1998) Phylogenetic relationships among the Cryptophyta: analyses of nuclear-encoded SSU rRNA sequences support the monophyly of extant plastid-containing lineages. Protist 149:265–276

    PubMed  CAS  Google Scholar 

  • Martin W, Herrmann RG (1998) Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol 118:9–17

    PubMed  CAS  Google Scholar 

  • Martin W, Müller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392:37–41

    PubMed  CAS  Google Scholar 

  • Martin W, Schnarrenberger C (1997) The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis. Curr Genet 32:1–18

    PubMed  CAS  Google Scholar 

  • Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162–165

    PubMed  CAS  Google Scholar 

  • Martin WF (1996) Is something wrong with the tree of life? Bioessays 18:523–527

    CAS  Google Scholar 

  • May T, Soll J (1999) Chloroplast precursor protein translocon. FEBS Lett 452:52–56

    PubMed  CAS  Google Scholar 

  • McFadden GI (1999a) Endosymbiosis and evolution of the plant cell. Curr Opin Plant Biol 2:513–519

    PubMed  CAS  Google Scholar 

  • McFadden GI (1999b) Plastids and protein targeting. J Eukaryot Microbiol 46:339–346

    PubMed  CAS  Google Scholar 

  • McFadden GI, Gilson P (1997) What’s eating eu? The role of eukaryote/eukaryote endo-symbioses in plastid origins. In: Müller NE, Schwemmler W, Schenk HEA, Herrmann R, Jeon KW (eds) Eukaryotism and symbiosis. Intertaxonic combination versus symbiotic adaption. Springer, Berlin Heidelberg New York, pp 24–39

    Google Scholar 

  • McFadden GI, Roos DS (1999) Apicomplexan plastids as drug targets. Trends Microbiol 7:328–333

    PubMed  CAS  Google Scholar 

  • McFadden GI, Waller RF (1997) Plastids in parasites of humans. Bioessays 19:1033–1040

    PubMed  CAS  Google Scholar 

  • McFadden GI, Gilson PR, Hill DRA (1994) Goniomonas: rRNA sequences indicate that this phagotrophic flagellate is a close relative of the host component of cryptomonads. Eur J Phycol 29:29–32

    Google Scholar 

  • McFadden GI, Gilson PR, Waller RF (1995) Molecular phylogeny of chlorarachniophytes based on plastid rRNA and rbcL sequences. Arch Protistenkd 145:231–239

    Google Scholar 

  • McFadden GI, Gilson PR, Douglas SE, Cavalier-Smith T, Hofmann CJB, Maier UG (1997a) Bonsai genomics: sequencing the smallest eukaryotic genomes. Trends Genet 13:46–49

    PubMed  CAS  Google Scholar 

  • McFadden GI, Waller RE, Reith ME, Lang-Unnasch N (1997b) Plastids in apicomplexan parasites. Plant Syst Evol Suppl 11:261

    CAS  Google Scholar 

  • Medlin LK, Kooistra WHCF, Potter D, Saunders GW, Andersen RA (1997) Phylogenetic relationships of the “golden algae” (haptophytes, heterokont chromophytes) and their plastids. Plant Syst Evol Suppl 11:187–220

    CAS  Google Scholar 

  • Melkonian M (1996) Phylogeny of photosynthetic protists and their plastids. Verh Dtsch Ges Zool 89:71–96

    Google Scholar 

  • Melkonian M, Marin B, Surek B (1995) Phylogeny and evolution of the algae. In: Arai R, Kato M, Doi Y (eds) Biodiversity and evolution. The National Science Museum Foundation, Tokyo, pp 153–176

    Google Scholar 

  • Meyer-Gauen G, Schnarrenberger C, Cerff R, Martin W (1994) Molecular characterization of a novel, nuclear-encoded, NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase in plastids of the gymnosperm Pinus sylvestris L. Plant Mol Biol 26:1155–1166

    PubMed  CAS  Google Scholar 

  • Mimuro M, Akimoto S, Yamazaki I, Miyashita H, Miyachi S (1999) Fluorescence properties of chlorophyll d-dominating prokaryotic alga, Acaryochloris marina: studies using time-resolved fluorescence spectroscopy on intact cells. Biochim Biophys Acta 1412:37–46

    PubMed  CAS  Google Scholar 

  • Mimuro M, Hirayama K, Uezono K, Miyashita H, Miyachi S (2000) Uphill energy transfer in a chlorophyll d-dominating oxygenic prokaryote, Acaryochloris marina. Biochim Biophys Acta 1456:27–34

    PubMed  CAS  Google Scholar 

  • Miyachi S, Strassdat K, Miyashita H, Senger H (1997) Quantum requirement of photosynthesis in the primarily chlorophyll d containing prokaryote Acaryochloris marina. Z Naturforsch [C] 52:636–638

    CAS  Google Scholar 

  • Miyamoto MM, Fitch WM (1996) Constraints on protein evolution and the age of the eubacteria/eukaryote split. Syst Biol 45:568–575

    PubMed  CAS  Google Scholar 

  • Miyashita H, Ikemoto H, Kurano N, Adachi K, Chihara M, Miyachi S (1996) Chlorophyll d as a major pigment. Nature 383:402–402

    CAS  Google Scholar 

  • Miyashita H, Adachi K, Kurano N, Ikemoto H, Chihara M, Miyachi S (1997) Pigment composition of a novel oxygenic photosynthetic prokaryote containing chlorophyll d as the major chlorophyll. Plant Cell Physiol 38:274–281

    CAS  Google Scholar 

  • Moreira D, López-García P (1998) Symbiosis between methanogenic archaea and 8-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J Mol Evol 47:517–530

    PubMed  CAS  Google Scholar 

  • Morse D, Salois P, Markovic P, Hastings JW (1995) Nuclear-encoded form II Rubisco in dinoflagellates. Science 268:1622–1624

    PubMed  CAS  Google Scholar 

  • Müller M (1997) Evolutionary origins of trichomonad hydrogenosomes. Parasitol Today 13:166–167

    PubMed  Google Scholar 

  • Müller M, Martin W (1999) The genome of Rickettsia prowazekii and some thoughts on the origin of mitochondria and hydrogenosomes. Bioessays 21:377–381

    PubMed  Google Scholar 

  • Nelissen B, Van de Peer Y, Wilmotte A, De Wachter R (1995) An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences. Mol Biol Evol 12:1166–1173

    PubMed  CAS  Google Scholar 

  • Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson LD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM (1999) Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399:323–329

    PubMed  CAS  Google Scholar 

  • Nielsen H, Engelbrecht J, Brunak S, Von Heijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10:1–6

    PubMed  CAS  Google Scholar 

  • Norén F, Moestrup Ø, Rehnstam-Holm AS (1999) Parvilucifera infectans Norén et Moestrup gen. et sp nov (Perkinsozoa phylum nov.): a parasitic flagellate capable of killing toxic microalgae. Eur J Protistol 35:233–254

    Google Scholar 

  • Nowitzki U, Flechner A, Kellerman J, Hasegawa M, Schnarrenberger C, Martin W (1998) Eubacterial origin of nuclear genes for chloroplast and cytosolic glucose-6-phosphate isomerase from spinach: sampling eubacterial gene diversity in eukaryotic chromosomes through symbiosis. Gene 214:205–213

    PubMed  CAS  Google Scholar 

  • Ohta N, Sato N, Nozaki H, Kuroiwa T (1997) Analysis of the cluster of ribosomal protein genes in the plastid genome of a unicellular red alga Cyanidioschyzon merolae: Translocation of the str cluster as an early event in the rhodophyte-chromophyte lineage of plastid evolution. J Mol Evol 45:688–695

    PubMed  CAS  Google Scholar 

  • Olsen GJ, Woese CR (1997) Archaeal genomics: an overview. Cell 89:991–994

    PubMed  CAS  Google Scholar 

  • Osafune T, Schiff JA, Hase E (1991) Stage-dependent localization of LHCP II apoprotein in the Golgi of synchronized cells of Euglena gracilis by immunogold electron microscopy. Exp Cell Res 193:320–330

    PubMed  CAS  Google Scholar 

  • Page RDM, Holmes EC (1998) Molecular evolution, a phylogenetic approach. Blackwell, Oxford

    Google Scholar 

  • Palenik B, Swift H (1996) Cyanobacterial evolution and prochlorophyte diversity as seen in DNA-dependent RNA polymerase gene sequences. J Phycol 32:638–646

    CAS  Google Scholar 

  • Palmer JD (1996) Rubisco surprises in dinoflagellates. Plant Cell 8:343–345

    PubMed  CAS  Google Scholar 

  • Palmer JD (1997a) Genome evolution — the mitochondrion that time forgot. Nature 387:454–455

    PubMed  Google Scholar 

  • Palmer JD (1997b) Organelle genomes: going, going, gone. Science 275:790–791

    PubMed  CAS  Google Scholar 

  • Palmer JD, Delwiche CF (1998) The origin and evolution of plastids and their genomes. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants, vol 2. Kluwer, Boston, pp 375–409

    Google Scholar 

  • Paquin B, Laforest MJ, Forget L, Roewer I, Wang Z, Longcore J, Lang BF (1997) The fungal mitochondrial genome project: Evolution of fungal mitochondrial genomes and their gene expression. Curr Genet 31:380–395

    PubMed  CAS  Google Scholar 

  • Partensky F, Hess WR, Vaulot D (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev 63:1–106

    Google Scholar 

  • Philippe H, Adoutte A (1998) The molecular phylogeny of Eukaryota: solid facts and uncertainties. In: Coombs G, Vickerman K, Sleigh MA, Warren A (eds) Evolutionary relationships among protozoa. Chapman and Hall, London, pp 25–56

    Google Scholar 

  • Philippe H, Forterre P (1999) The rooting of the universal tree of life is not reliable. J Mol Evol 49:509–523

    PubMed  CAS  Google Scholar 

  • Philippe H, Laurent J (1998) How good are deep phylogenetic trees. Curr Opin Genet Dev 8:616–623

    PubMed  CAS  Google Scholar 

  • Plaumann M, Pelzer-Reith B, Martin WF, Schnarrenberger C (1997) Multiple recruitment of class-I aldolase to chloroplasts and eubacterial origin of eukaryotic class-II aldolases revealed by cDNAs from Euglena gracilis. Curr Genet 31:430–438

    PubMed  CAS  Google Scholar 

  • Poole A, Jeffares D, Penny D (1998) The path from the RNA world. J Mol Evol 46:1–17

    PubMed  CAS  Google Scholar 

  • Poole A, Jeffares D, Penny D (1999) Early evolution: prokaryotes, the new kids on the block. Bioessays 21:880–889

    PubMed  CAS  Google Scholar 

  • Race HL, Herrmann RG, Martin W (1999) Why have organelles retained genomes? Trends Genet 15:364–370

    PubMed  CAS  Google Scholar 

  • Reumann S, Keegstra K (1999) The endosymbiotic origin of the protein import machinery of chloroplastic envelope membranes. Trends Plant Sci 4:302–307

    PubMed  Google Scholar 

  • Reumann S, Davila-Aponte J, Keegstra K (1999) The evolutionary origin of the protein-translocating channel of the chloroplastic envelope membranes: identification of a cyanobacterial homolog. Proc Natl Acad Sci USA 96:784–789

    PubMed  CAS  Google Scholar 

  • Rivera MC, Jain R, Moore JE, Lake JA (1998) Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA 95:6239–6244

    PubMed  CAS  Google Scholar 

  • Roger AJ, Clark CG, Doolittle WF (1996) A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis. Proc Natl Acad Sci USA 93:14618–14622

    PubMed  CAS  Google Scholar 

  • Roger AJ, Svärd SG, Tovar J, Clark CG, Smith MW, Gillin FD, Sogin ML (1998) A mitochondrial-like chaperonin 60 gene in Giardia lamblia: Evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. Proc Natl Acad Sci USA 95:229–234

    PubMed  CAS  Google Scholar 

  • Roger AJ, Sandblom O, Doolittle WF, Philippe H (1999) An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes. Mol Biol Evol 16:218–233

    PubMed  CAS  Google Scholar 

  • Roos DS, Crawford MJ, Donald RGK, Kissinger JC, Klimczak LJ, Striepen B (1999) Origin, targeting, and function of the apicomplexan plastid. Curr Opin Microbiol 2:426–432

    PubMed  CAS  Google Scholar 

  • Rosenthal B, Mai ZM, Caplivski D, Ghosh S, De la Vega H, Graf T, Samuelson J (1997) Evidence for the bacterial origin of genes encoding fermentation enzymes of the amitochondriate protozoan parasite Entamoeba histolytica. J Bacteriol 179:3736–3745

    PubMed  CAS  Google Scholar 

  • Rowan R, Whitney SM, Fowler A, Yellowlees D (1996) Rubisco in marine symbiotic dinoflagellates: form II enzymes in eukaryotic oxygenic phototrophs encoded by a nuclear multigene family. Plant Cell 8:539–553

    PubMed  CAS  Google Scholar 

  • Saunders GW, Hill DRA, Sexton JP, Andersen RA (1997) Small-subunit ribosomal RNA sequences from selected dinoflagellates: testing classical evolutionary hypotheses with molecular systematic methods. Plant Syst Evol Suppl 11:237–259

    CAS  Google Scholar 

  • Schiller H, Senger H, Miyashita H, Miyachi S, Dau H (1997) Light-harvesting in Acaryochloris marina. Spectroscopic characterization of a chlorophyll d-dominated photosynthetic antenna system. FEBS Lett 410:433–436

    PubMed  CAS  Google Scholar 

  • Schmidt M, Svendsen I, Feierabend J (1995) Analysis of the primary structure of the chloroplast isozyme of triosephosphate isomerase from rye leaves by protein and cDNA sequencing indicates a eukaryotic origin of its gene. Biochim Biophys Acta 1261:257–264

    PubMed  Google Scholar 

  • Schnarrenberger C, Pelzer-Reith B, Yatsuki H, Freund S, Jacobshagen S, Hori K (1994) Expression and sequence of the only detectable aldolase in Chlamydomonas rein-hardtii. Arch Biochem Biophys 313:173–178

    PubMed  CAS  Google Scholar 

  • Schnepf E (1993) From prey via endosymbiont to plastid: comparative studies in dinoflagellates. In: Lewin RA (ed) Origins of plastids. Symbiogenesis, prochlorophytes, and the origins of chloroplasts. Chapman and Hall, New York, pp 53–76

    Google Scholar 

  • Schopf JW (1993) Microfossils of the early Archaean apex chart: new evidence of the antiquity of life. Science 260:640–646

    PubMed  CAS  Google Scholar 

  • Schwartzbach SD, Osafune T, Löffelhardt W (1998) Protein import into cyanelles and complex chloroplasts. Plant Mol Biol 38:247–263

    PubMed  CAS  Google Scholar 

  • Settles AM, Martienssen R (1998) Old and new pathways of protein export in chloroplasts and bacteria. Trends Cell Biol 8:494–501

    PubMed  CAS  Google Scholar 

  • Sicheritz-Pontén T, Kurland CG, Andersson SGE (1998) A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae. Biochim Biophys Acta 1365:545–551

    PubMed  Google Scholar 

  • Sogin ML (1997) History assignment: when was the mitochondrion found. Curr Opin Genet Dev 7:792–799

    PubMed  CAS  Google Scholar 

  • Soll J, Tien R (1998) Protein translocation into and across the chloroplastic envelope membranes. Plant Mol Biol 38:191–207

    PubMed  CAS  Google Scholar 

  • Soltis DE, Soltis PS, Doyle JC (eds) (1998) Molecular systematics of plants, vol 2. Kluwer, Boston

    Google Scholar 

  • Springer N, Ludwig W, Amann R, Schmidt HJ, Görtz, HD, Schleifer KH (1993) Occurrence of fragmented 16S ribosomal RNA in an obligate bacterial endosymbiont of Paramecium caudatum. Proc Natl Acad Sci USA 90:9892–9895

    PubMed  CAS  Google Scholar 

  • Stiller JW, Hall BD (1997) The origin of red algae: Implications for plasmid evolution. Proc Natl Acad Sci USA 94:4520–4525

    PubMed  CAS  Google Scholar 

  • Stiller JW, Hall BD (1998) Sequences of the largest subunit of RNA polymerase II from two red algae and their implications for rhodophyte evolution. J Phycol 34:857–864

    CAS  Google Scholar 

  • Stiller JW, Hall BD (1999) Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol Biol Evol 16:1270–1279

    PubMed  CAS  Google Scholar 

  • Stoebe B, Kowallik KV (1999) Gene-cluster analysis in chloroplast genomics. Trends Genet 15:344–347

    PubMed  CAS  Google Scholar 

  • Sugita M, Sugishita H, Fujishiro T, Tsuboi M, Sugita C, Endo T, Sugiura M (1997) Organization of a large gene cluster encoding ribosomal proteins in the cyanobacterium Synechococcus sp. strain PCC 6301: comparison of gene clusters among cyanobacteria, eubacteria and chloroplast genomes. Gene 195:73–79

    PubMed  CAS  Google Scholar 

  • Sulli C, Schwartzbach SD (1995) The polyprotein percursor to the Euglena light-harvesting chlorophyll a/b-binding protein is transported to the Golgi apparatus prior to chloroplast import and polyprotein processing. J Biol Chem 270:13084–13090

    PubMed  CAS  Google Scholar 

  • Sulli C, Fang ZW, Muchhal U, Schwartzbach SD (1999) Topology of Euglena chloroplast protein precursors within endoplasmic reticulum to Golgi to chloroplast transport vesicles. J Biol Chem 274:457–463

    PubMed  CAS  Google Scholar 

  • Tomitani A, Okada K, Miyashita H, Matthijs HCP, Ohno T, Tanaka A (1999) Chlorophyll b and phycobilins in the common ancestor of cyanobacteria and chloroplasts. Nature 400:159–162

    PubMed  CAS  Google Scholar 

  • Turmel M, Otis C, Lemieux C (1999) The complete chloroplast DNA sequence of the green alga Nephroselmis olivácea: Insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci USA 96:10248–10253

    PubMed  CAS  Google Scholar 

  • Turner S (1997) Molecular systematics of oxygenic photosynthetic bacteria. Plant Syst Evol Suppl 11:13–52

    CAS  Google Scholar 

  • Turner S, Pryer KM, Miao VPW, Palmer JD (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small submit rRNA sequence analysis. J Eukaryot Microbiol 46:327–338

    PubMed  CAS  Google Scholar 

  • Unseld M, Marienfeld JR, Brandt P, Brennicke A (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet 15:57–61

    PubMed  CAS  Google Scholar 

  • Urbach E, Scanlan DJ, Distel DL, Waterbury JB, Chisholm SW (1998) Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria). J Mol Evol 46:188–201

    PubMed  CAS  Google Scholar 

  • Valentin K (1997) Phylogeny and expression of the secA gene from a chromophytic alga. Implications for the evolution of plastids and sec-dependent protein translocation. Curr Genet 32:300–307

    PubMed  CAS  Google Scholar 

  • Van de Peer Y, De Wachter R (1997) Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA. J Mol Evol 45:619–630

    PubMed  Google Scholar 

  • Van de Peer Y, Rensing SA, Maier UG, De Wachter R (1996) Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc Natl Acad Sci USA 93:7732–7736

    PubMed  Google Scholar 

  • Van der Auwera G, De Wachter R (1998) Structure of the large subunit rDNA from a diatom, and comparison between small and large subunit ribosomal RNA for studying stramenopile evolution. J Eukaryot Microbiol 45:521–527

    PubMed  Google Scholar 

  • Vellai T, Takács K, Vida G (1998) A new aspect to the origin and evolution of eukaryotes. J Mol Evol 46:499–507

    PubMed  CAS  Google Scholar 

  • Wakasugi T, Nagai T, Kapoor M, Sugita M, Ito M, Ito S, Tsudzuki J, Nakashima K, Tsudzuki T, Suzuki Y, Hamada A, Ohta T, Inamura A, Yoshinaga K, Sugiura M (1997) Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc Natl Acad Sci USA 94:5967–5972

    PubMed  CAS  Google Scholar 

  • Waller RF, Keeling PJ, Donald RGK, Striepen B, Handman E, Lang-Unnasch N, Cowman AF, Bersa GS, Roos DS, McFadden GI (1998) Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum. Proc Natl Acad Sci USA 95:12352–12357

    PubMed  CAS  Google Scholar 

  • Wang SL, Liu XQ, Douglas SE (1997) The large ribosomal protein gene cluster of a cryptomonad plastid: gene organization, sequence and evolutionary implications. Biochem Mol Biol Int 41:1035–1044

    PubMed  CAS  Google Scholar 

  • Watson GMF, Tabita FR (1997) Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiol Lett 146:13–22

    PubMed  CAS  Google Scholar 

  • Whatley JM, John P, Whatley FR (1979) From extracellular to intracellular: the establishment of mitochondria and chloroplasts. Proc R Soc Lond B Biol Sci 204:165–187

    PubMed  CAS  Google Scholar 

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Melkonian, M. (2001). Systematics and Evolution of the Algae. I. Genomics Meets Phylogeny. In: Esser, K., Lüttge, U., Kadereit, J.W., Beyschlag, W. (eds) Progress in Botany. Progress in Botany, vol 62. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56849-7_15

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