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Genomics of Marine Algae

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Introduction to Marine Genomics

Part of the book series: Advances in Marine Genomics ((AMGE,volume 1))

Abstract

The algae are an extremely diverse group of organisms from several different perspectives; including their phylogeny, their basic biology and biochemistry, the range of complexity they exhibit and their adaptation to a large number of different habitats. As a result, algal research touches on a broad spectrum of questions ranging from the importance of algae as key species in marine ecosystems to algae as a source of novel biomolecules and bioprocesses. Two key developments have accelerated research in this field over the past few years. The first is the application of high-throughput sequencing approaches both to whole genome sequencing and to metagenomic exploration of marine environments. The second is the emergence of model organisms in several of the less well studied algal lineages. These model organisms are important because they permit efficient application of genomic approaches to these groups. This chapter will describe how genomic research is providing new insights into many aspects of algal biology and will attempt to outline where this research is likely to lead in the future.

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Abbreviations

DD:

(2E,4E/Z)-decadienal

kbp:

kilobase pairs

Mbp:

megabase pairs

NO:

nitric oxide

PCR:

polymerase chain reaction

pg:

picogramme

rDNA:

ribosomal DNA

References

  • Allen AE, Vardi A, Bowler C (2006) An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr Opin Plant Biol 9:264–273

    CAS  PubMed  Google Scholar 

  • Archibald JM (2007) Nucleomorph genomes: structure, function, origin and evolution. Bioessays 29:392–402

    CAS  PubMed  Google Scholar 

  • Archibald JM, Rogers MB, Toop M, Ishida K, Keeling PJ (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci U S A 100:7678–7683

    CAS  PubMed  Google Scholar 

  • Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kröger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004) The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306:79–86

    CAS  PubMed  Google Scholar 

  • Asamizu E, Nakajima M, Kitade Y, Saga N, Nakamura Y, Tabata S (2003) Comparison of RNA expression profiles between two generations of Porphyra yezoensis (Rhodophyta), based on expressed sequence tag frequency analysis. J Phycol 39:923–330

    Google Scholar 

  • Bachvaroff TR, Concepcion GT, Rogers CR, Herman EM, Delwiche CF (2004) Dinoflagellate expressed sequence tags data indicate massive transfer of chloroplast genes to the nuclear genome. Protist 155:65–78

    CAS  PubMed  Google Scholar 

  • Bachvaroff TR, Place AR (2008) From stop to start: tandem gene arrangement, copy number and trans-splicing sites in the dinoflagellate Amphidinium carterae. PLoS ONE 3:e2929

    PubMed  Google Scholar 

  • Baldauf SL (2008) An overview of the phylogeny and diversity of eukaryotes. J Syst Evol 46:263–273

    Google Scholar 

  • Bartsch I, Wiencke C, Bischof K, Buchholz CM, Buck BH, Eggert A, Feuerpfeil P, Hanelt D, Jacobsen S, Karez R, Karsten U, Molis M, Roleda M, Schubert H, Schumann R, Valentin K, Weinberger F, Wiese J (2008) The genus Laminaria sensu lato: recent insights and developments. Eur J Phycol 43:1–86

    Google Scholar 

  • Bauer I, Maranda L,Young KA, Shimizu Y, Fairchild C, Cornell L, MacBeth J, Huang S (1995) Isolation and structure of caribenolide I, a highly potent antitumor macrolide from a culture free-swimming Caribbean dinoflagellate, Amphidinium sp. S1-36-5. J Org Chem 60:1084–1086

    CAS  Google Scholar 

  • Berger F, Taylor A, Brownlee C (1994) Cell fate determination by the cell wall in early Fucus development. Science 263:1421–1423

    CAS  PubMed  Google Scholar 

  • Bhattacharya D, Yoon HS, Hackett JD (2004) Photosynthetic eukaryotes unite: endosymbiosis connects the dots. Bioessays 26:50–60

    PubMed  Google Scholar 

  • Bouarab K, Potin P, Correa J, Kloareg B (1999) Sulfated oligosaccharides mediate the interaction between a marine red alga and its green algal pathogenic endophyte. Plant Cell 11(9):1635–1650

    CAS  PubMed  Google Scholar 

  • Bouget FY, Berger F, Brownlee C (1998) Position dependent control of cell fate in the Fucus embryo: role of intercellular communication. Development 125:1999–2008

    CAS  PubMed  Google Scholar 

  • Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kröger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jézéquel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456:239–244

    CAS  PubMed  Google Scholar 

  • Brownlee C, Bouget FY, Corellou F (2001) Choosing sides: establishment of polarity in zygotes of fucoid algae. Semin Cell Dev Biol 12:345–351

    CAS  PubMed  Google Scholar 

  • Bryhni E (1974) Control of morphogenesis in the multicellular alga Ulva mutabilis. Defect in cell wall production. Dev Biol 37:273–277

    CAS  PubMed  Google Scholar 

  • Butterfield NJ (2000) Bangiomorpha pubescens n. gen., n. sp.; implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiol 26:386–404

    Google Scholar 

  • Charrier B, Coelho SM, Le Bail A, Tonon T, Michel G, Potin P, Kloareg B, Boyen C, Peters AF, Cock JM (2008) Development and physiology of the brown alga Ectocarpus siliculosus: two centuries of research. New Phytol 177:319–332

    CAS  PubMed  Google Scholar 

  • Cheney D, Metz B, Stiller J (2001) Agrobacterium-mediated genetic transformation in the macroscopic marine red alga Porphyra yezoensis. J Phycol 37:11

    Google Scholar 

  • Coelho S, Peters AF, Charrier B, Roze D, Destombe C, Valero M, Cock JM (2007) Complex life cycles of multicellular eukaryotes: new approaches based on the use of model organisms. Gene 406:152–170

    CAS  PubMed  Google Scholar 

  • Coelho SM, Taylor AR, Ryan KP, Sousa-Pinto I, Brown MT, Brownlee C (2002) Spatiotemporal patterning of reactive oxygen production and Ca(2+) wave propagation in Fucus rhizoid cells. Plant Cell 14:2369–2381

    CAS  PubMed  Google Scholar 

  • Coesel S, Oborník M, Varela J, Falciatore A, Bowler C (2008) Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms. PLoS ONE 3:e2896

    PubMed  Google Scholar 

  • Coleman FC, Williams SL (2002) Overexploiting marine ecosystem engineers: potential consequences for biodiversity. Trends Ecol Evol 17:40–44

    Google Scholar 

  • Collén J, Hervé C, Guisle-Marsollier I, Leger J, Boyen C (2006a) Expression profiling of Chondrus crispus (Rhodophyceae) after exposure to methyl jasmonate. J Exp Bot 57:3869–3881

    PubMed  Google Scholar 

  • Collén J, Roeder V, Rousvoal S, Collin O, Kloareg B, Boyen C (2006b) An expressed sequence tag analysis of thallus and regenerating protoplasts of Chondrus crispus (Gigartinales, Rhodophyceae). J Phycol 42:104–112

    Google Scholar 

  • Corellou F, Bisgrove SR, Kropf DL, Meijer L, Kloareg B, Bouget FY (2000) A S/M DNA replication checkpoint prevents nuclear and cytoplasmic events of cell division including centrosomal axis alignment and inhibits activation of cyclin-dependent kinase-like proteins in fucoid zygotes. Development 127:1651–1660

    CAS  PubMed  Google Scholar 

  • Corellou F, Brownlee C, Kloareg B, Bouget FY (2001) Cell cycle-dependent control of polarised development by a cyclin-dependent kinase-like protein in the Fucus zygote. Development 128:4383–4392

    CAS  PubMed  Google Scholar 

  • Coyer JA, Hoarau G, Stam WT, Olsen JL (2007) Hybridization and introgression in a mixed population of the intertidal seaweeds Fucus evanescens and F. serratus. J Evol Biol 20:2322–2333

    CAS  PubMed  Google Scholar 

  • Crépineau F, Roscoe T, Kaas R, Kloareg B, Boyen C (2000) Characterisation of complementary DNAs from the expressed sequence tag analysis of life cycle stages of Laminaria digitata (Phaeophyceae). Plant Mol Biol 43:503–513

    PubMed  Google Scholar 

  • Derelle E, Ferraz C, Escande ML, Eychenié S, Cooke R, Piganeau G, Desdevises Y, Bellec L, Moreau H, Grimsley N (2008) Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PLoS ONE 3:e2250

    PubMed  Google Scholar 

  • Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynie S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piegu B, Ball SG, Ral JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y, Moreau H (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A 103:11647–11652

    CAS  PubMed  Google Scholar 

  • Duggins DO, Simenstad CA, Estes JA (1989) Magnification of secondary production by kelp detritus in coastal marine ecosystems. Science 245:170–173

    CAS  PubMed  Google Scholar 

  • Durnford DG, Gray MW (2006) Analysis of Euglena gracilis plastid-targeted proteins reveals different classes of transit sequences. Eukaryot Cell 5:2079–2091

    CAS  PubMed  Google Scholar 

  • FAO (2003) A guide to the seaweed industry. FAO Fisheries technical paper 441

    Google Scholar 

  • Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O, Taylor FJ (2004) The evolution of modern eukaryotic phytoplankton. Science 305:354–360

    CAS  PubMed  Google Scholar 

  • Faust MA, Gulledge RA (2002) Identifying harmful marine dinoflagellates. Contributions from the United States National Herbarium 42:1–144

    Google Scholar 

  • Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237–240

    CAS  PubMed  Google Scholar 

  • Fjeld A, Løvle A (1976) Genetics of multicellular algae. In: Lewin, RA (ed) The genetics of algae, Blackwell Scientific Publications, Oxford, pp 219–235

    Google Scholar 

  • Gautier A, Michel-Salamin L, Tosi-Couture E, McDowall AW, Dubochet J (1986) Electron microscopy of the chromosomes of dinoflagellates in situ: confirmation of Bouligand’s liquid crystal hypothesis. J Ultrastruc Mol Struct Res 97:10–30

    Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63

    CAS  PubMed  Google Scholar 

  • Goddard H, Manison NF, Tomos D, Brownlee C (2000) Elemental propagation of calcium signals in response-specific patterns determined by environmental stimulus strength. Proc Natl Acad Sci USA 97:1932–1937

    CAS  PubMed  Google Scholar 

  • Guillou L, Eikrem W, Chrétiennot-Dinet MJ, Le Gall F, Massana R, Romari K, Pedrós-Alió C, Vaulot D (2004) Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems. Protist 155:193–214

    CAS  PubMed  Google Scholar 

  • Guillou L, Moon-Van Der Staay SY, Claustre H, Partensky F, Vaulot D (1999) Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions. Appl Environ Microbiol 65:4528–4536

    CAS  PubMed  Google Scholar 

  • Guiry MD, Guiry GM (2008) AlgaeBase. Worldwide electronic publication, National University of Ireland, Galway. http://www.algaebase.org.

  • Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D (2005) Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6:80

    PubMed  Google Scholar 

  • Hackett JD, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Nosenko T, Bhattacharya D (2004) Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr Biol 14:213–218

    CAS  PubMed  Google Scholar 

  • He P, Yao Q, Chen Q, Guo M, Xiong A, Wu W, Ma J (2001) Transferring and expression of glucose oxidase gene – gluc in Porphyra yezoensis. J Phycol 37(suppl):22

    Google Scholar 

  • Hutchinson GE (1961) The paradox of the plankton. Amer Nat 95:137–145

    Google Scholar 

  • Ianora A, Miralto A, Poulet SA, Carotenuto Y, Buttino I, Romano G, Casotti R, Pohnert G, Wichard T, Colucci-D’Amato L, Terrazzano G, Smetacek V (2004) Aldehyde suppression of copepod recruitment in blooms of a ubiquitous planktonic diatom. Nature 429:403–407

    CAS  PubMed  Google Scholar 

  • Inagaki Y, Dacks JB, Doolittle WF, Watanabe KI, Ohama T (2000) Evolutionary relationship between dinoflagellates bearing obligate diatom endosymbionts: insight into tertiary endosymbiosis. Int J Syst Evol Microbiol 50:2075–2081

    PubMed  Google Scholar 

  • Kapraun DF (2005) Nuclear DNA content estimates in multicellular green, red and brown algae: phylogenetic considerations. Ann Bot 95:7–44

    CAS  PubMed  Google Scholar 

  • Keeling PJ (2004) Diversity and evolutionary history of plastids and their hosts. Amer J Bot 91:1481–1493

    Google Scholar 

  • Keeling PJ (2007) Ostreococcus tauri: seeing through the genes to the genome. Trends Genet 23:151–154

    CAS  PubMed  Google Scholar 

  • Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9:605–628

    CAS  PubMed  Google Scholar 

  • Kilian O, Kroth PG (2005) Identification and characterization of a new conserved motif within the presequence of proteins targeted into complex diatom plastids. Plant J 41:175–183

    CAS  PubMed  Google Scholar 

  • Kitade Y, Asamizu E, Fukuda S, Nakajima M, Ootsuka S, Endo H, Tabata S, Saga N (2008) Identification of genes preferentially expressed during asexual sporulation in Porphyra yezoensis gametophytes (bangiales, rhodophyta). J Phycol 44:113–123

    CAS  Google Scholar 

  • Kitade Y, Iitsuka O, Fukuda S, Saga N (2004) Porphyra yezoensis as a model plant for genome sciences. Jpn J Phycol 52:129–131

    Google Scholar 

  • Klarzynski O, Plesse B, Joubert J-M, Yvin J-C, Kopp M, Kloareg B, Fritig B (2000) Linear b-1,3 glucans are elicitors of defense responses in tobacco. Plant Physiol 124:1027–1037

    CAS  PubMed  Google Scholar 

  • Kroth PG, Chiovitti A, Gruber A, Martin-Jezequel V, Mock T, Parker MS, Stanley MS, Kaplan A, Caron L, Weber T, Maheswari U, Armbrust EV, Bowler C (2008) A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS ONE 3:e1426

    PubMed  Google Scholar 

  • La Claire JW 2nd. (2006) Analysis of expressed sequence tags from the harmful alga, Prymnesium parvum (Prymnesiophyceae, Haptophyta). Mar Biotechnol 8:534–546

    CAS  PubMed  Google Scholar 

  • LaJeunesse TC, Lambert G, Andersen RA, Coffroth MA, Galbraith DW (2005) Symbiodinium (Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates. J Phycol 41:880–886

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Le Gall Y, Brown S, Marie D, Mejjad M, Kloareg B (1993) Quantification of nuclear DNA and G-C content in marine macroalgae by flow cytometry of isolated nuclei. Protoplasma 173:123–132

    Google Scholar 

  • Lee H, Lee HK, An G, Lee YK (2007) Analysis of expressed sequence tags from the red alga Griffithsia okiensis. J Microbiol 45:541–546

    CAS  PubMed  Google Scholar 

  • Lin CM, Larsen J, Yarish C, Chen T (2001) A novel gene transfer in Porphyra. J Phycol 37:31

    CAS  Google Scholar 

  • Lobanov AV, Fomenko DE, Zhang Y, Sengupta A, Hatfield DL, Gladyshev VN (2007) Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol 8(9):R198

    PubMed  Google Scholar 

  • Lovejoy C, Massana R, Pedrós-Alió C (2006) Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas. Appl Environ Microbiol 72:3085–3095

    CAS  PubMed  Google Scholar 

  • Manley SL (2002) Phytogenesis of halomethanes: A product of selection or a metabolic accident?. Biogeochem 60:163–180

    CAS  Google Scholar 

  • Massana R, Balague V, Guillou L, Pedros-Alio C (2004) Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiol Ecol 50:231–243

    CAS  PubMed  Google Scholar 

  • Massana R, Guillou L, Díez B, Pedrós-Alió C (2002) Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl Environ Microbiol 68:4554–4558

    CAS  PubMed  Google Scholar 

  • Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428:653–657

    CAS  PubMed  Google Scholar 

  • McGinn PJ, Morel FM (2008) Expression and inhibition of the carboxylating and decarboxylating enzymes in the photosynthetic C4 pathway of marine diatoms. Plant Physiol 146:300–309

    CAS  PubMed  Google Scholar 

  • McHugh DJ (2003) A guide to the seaweed industry. FAO Fisheries Technical Paper No. 441. FAO, Rome, 105 pp.

    Google Scholar 

  • Medlin LK, Metfies K, Mehl H, Wiltshire K, Valentin K (2006) Picoeukaryotic plankton diversity at the Helgoland time series site as assessed by three molecular methods. Microb Ecol 52:53–71

    CAS  PubMed  Google Scholar 

  • Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riaño-Pachón DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martínez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848):245–250

    CAS  PubMed  Google Scholar 

  • Metfies K, Medlin LK (2008) Feasibility of transferring fluorescent in situ hybridization probes to an 18S rRNA gene phylochip and mapping of signal intensities. Appl Environ Microbiol 74:2814–2821

    CAS  PubMed  Google Scholar 

  • Mitman GG, van der Meer JP (1994) Meiosis, blade development, and sex determination in Porphyra purpurea (Rhodophyta). J Phycol 30:147–159

    Google Scholar 

  • Mock T, Samanta MP, Iverson V, Berthiaume C, Robison M, Holtermann K, Durkin C, Bondurant SS, Richmond K, Rodesch M, Kallas T, Huttlin EL, Cerrina F, Sussman MR, Armbrust EV (2008) Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proc Natl Acad Sci U S A 105(5):1579–1584

    CAS  PubMed  Google Scholar 

  • Mock T, Thomas DN (2005) Recent advances in sea-ice microbiology. Environ Microbiol 7:605–619

    CAS  PubMed  Google Scholar 

  • Moreira D, López-García P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10:31–38

    CAS  PubMed  Google Scholar 

  • Morse D, Salois P, Markovic P, Hastings WJ (1995) A Nuclear-Encoded Form II RuBisCO in Dinoflagellates. Science 268:1622–1624

    CAS  PubMed  Google Scholar 

  • Moulager M, Monnier A, Jesson B, Bouvet R, Mosser J, Schwartz C, Garnier L, Corellou F, Bouget FY (2007) Light-dependent regulation of cell division in Ostreococcus: evidence for a major transcriptional input. Plant Physiol 144:1360–1369

    CAS  PubMed  Google Scholar 

  • Muhlin JF, Engel CR, Stessel R, Weatherbee RA, Brawley SH (2008) The influence of coastal topography, circulation patterns, and rafting in structuring populations of an intertidal alga. Mol Ecol 17:1198–1210

    CAS  PubMed  Google Scholar 

  • Müller DG (1967) Generationswechsel, Kernphasenwechsel und Sexualität der Braunalge Ectocarpus siliculosus im Kulturversuch. Planta 141:39–54

    Google Scholar 

  • Nagasaki K (2008) Dinoflagellates, diatoms, and their viruses. J Microbiol 46:235–243

    PubMed  Google Scholar 

  • Nassoury N, Cappadocia M, Morse D (2003) Plastid ultrastructure defines the protein import pathway in dinoflagellates. J Cell Sci 116:2867–2874

    CAS  PubMed  Google Scholar 

  • Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, Tabata S (2000) Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis. DNA Res 7:223–227

    PubMed  Google Scholar 

  • Nosenko T, Bhattacharya D (2007) Horizontal gene transfer in chromalveolates. BMC Evol Biol 7:173

    PubMed  Google Scholar 

  • Not F, Valentin K, Romari K, Lovejoy C, Massana R, Töbe K, Vaulot D, Medlin LK (2007) Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes. Science 315:253–255

    CAS  PubMed  Google Scholar 

  • Nowack EC, Melkonian M, Glöckner G (2008) Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Curr Biol 18:410–418

    CAS  PubMed  Google Scholar 

  • Ohme M, Miura A (1988) Tetrad analysis in conchospore germlings of Porphyra yezoensis (Rhodophyta, Bangiales). Plant Sci 57:135–140

    Google Scholar 

  • Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci USA 104:7705–7710

    CAS  PubMed  Google Scholar 

  • Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA (2006) Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2:e220

    PubMed  Google Scholar 

  • Park E-J, Fukuda S, Endo H, Kitade Y,Saga N (2007) Genetic polymorphism within Porphyra yezoensis (Bangiales, Rhodophyta) and related species from Japan and Korea detected by cleaved amplified polymorphic sequence analysis. Eur J Phycol 42:29–40

    CAS  Google Scholar 

  • Patron NJ, Waller RF, Archibald JM, Keeling PJ (2005) Complex protein targeting to dinoflagellate plastids. J Mol Biol 348(4):1015–1024

    CAS  PubMed  Google Scholar 

  • Peters AF, Marie D, Scornet D, Kloareg B, Cock JM (2004) Proposal of Ectocarpus siliculosus as a model organism for brown algal genetics and genomics. J Phycol 40:1079–1088

    Google Scholar 

  • Peters AF, Scornet D, Ratin M, Charrier B, Monnier A, Merrien Y, Corre E, Coelho SM, Cock JM (2008) Life-cycle-generation-specific developmental processes are modified in the immediate upright mutant of the brown alga Ectocarpus siliculosus. Development 135:1503–1512

    CAS  PubMed  Google Scholar 

  • Piganeau G, Desdevises Y, Derelle E, Moreau H (2008) Picoeukaryotic sequences in the Sargasso Sea metagenome. Genome Biol 9:R5

    PubMed  Google Scholar 

  • Piganeau G, Moreau H (2007) Screening the Sargasso Sea metagenome for data to investigate genome evolution in Ostreococcus (Prasinophyceae, Chlorophyta). Gene 406:184–190

    CAS  PubMed  Google Scholar 

  • Reddy CRK, Iima M, Fujita Y (1992) Induction of fastgrowing and morphologically different strains through intergeneric protoplast fusions of Ulva and Enteromorpha (Ulvales, Chlorophyta). J Appl Phycol 4:57–65

    Google Scholar 

  • Reyes-Prieto A, Moustafa A, Bhattacharya D (2008) Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Curr Biol 18:956–962

    CAS  PubMed  Google Scholar 

  • Reyes-Prieto A, Weber AP, Bhattacharya D (2007) The origin and establishment of the plastid in algae and plants. Annu Rev Genet 41:147–168

    CAS  PubMed  Google Scholar 

  • Rodriguez F, Derelle E, Guillou L, Le Gall F, Vaulot D, Moreau H (2005) Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae). Environ Microbiol 7:853–859

    CAS  PubMed  Google Scholar 

  • Roeder V, Collen J, Rousvoal S, Corre E, Leblanc C, Boyen C (2005) Identification of stress gene transcripts in Laminaria digitata (Phaeophyceae) protoplast cultures by expressed sequence tag analysis. J Phycol 41:1227–1235

    CAS  Google Scholar 

  • Romari K, Vaulot D (2004) Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol Oceanogr 49:784–798

    Google Scholar 

  • Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5:398–430

    CAS  Google Scholar 

  • Serrao EA, Pearson G, Kautsky L, Brawley SH (1996) Successful external fertilization in turbulent environments. Proc Natl Acad Sci U S A 93:5286–5290

    CAS  PubMed  Google Scholar 

  • Shimizu Y, Kitade Y, Saga N (2004) A nonradioactive whole-mount in situ hybridization protocol for Porphyra (Rhodophyta) gametophytic germlings. J Appl Phycol 16:329–333

    Google Scholar 

  • Siaut M, Heijde M, Mangogna M, Montsant A, Coesel S, Allen A, Manfredonia A, Falciatore A, Bowler C (2007) Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene 406:23–35

    CAS  PubMed  Google Scholar 

  • Siegel BZ, Siegel SM (1973) The chemical composition of algal cell walls. CRC Crit Rev Microbiol 3:1–26

    CAS  PubMed  Google Scholar 

  • Slapeta J, López-García P, Moreira D (2006) Global dispersal and ancient cryptic species in the smallest marine eukaryotes. Mol Biol Evol 23:23–29

    CAS  PubMed  Google Scholar 

  • Spector DL (1984) Dinoflagellate nuclei. In: Spector DL (ed) Dinoflagellates, Academic Press Inc, New York, pp 107–147

    Google Scholar 

  • Suttle CA (2005) Viruses in the sea. Nature 437:356–361

    CAS  PubMed  Google Scholar 

  • Tanikawa N, Akimoto H, Ogoh K, Chun W, Ohmiya Y (2004) Expressed sequence tag analysis of the dinoflagellate Lingulodinium polyedrum during dark phase. Photochem Photobiol 80:31–35

    CAS  PubMed  Google Scholar 

  • Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313:1261–1266

    CAS  PubMed  Google Scholar 

  • Vaulot D, Eikrem W, Viprey M, Moreau H (2008) The diversity of small eukaryotic phytoplankton (≤3 mum) in marine ecosystems. FEMS Microbiol Rev 32:795–820

    CAS  PubMed  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    CAS  PubMed  Google Scholar 

  • Waaland JR, Dickson LG, Watson BA (1990) Protoplast isolation and regeneration in the marine alga Porpyra nereocystis. Plantation 181:522–528

    Google Scholar 

  • Waaland JR, Stiller JW, Cheney DP (2004) Macroalgal candidates for genomics. J Phycol 40:26–33

    Google Scholar 

  • Wilson WH, Schroeder DC, Allen MJ, Holden MTG, Parkhill J, Barrell BG, Churcher C, Hamlin N, Mungall K, Norbertczak H, Quail MA, Price C, Rabbinowitsch E, Walker D, Craigon M, Roy D, Ghazal P (2005) Complete Genome Sequence and Lytic Phase Transcription Profile of a Coccolithovirus. Science 309:1090–1092

    CAS  PubMed  Google Scholar 

  • Worden AZ, Lee J-H, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KFX, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough EW, Van de Peer Y, Grigoriev IV (2009) Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes. Science 324:268–272

    CAS  PubMed  Google Scholar 

  • Yan X, Fujita Y, Aruga Y (2000) Induction and characterization of pigmentation mutants in Porphyra yezoensis (Bangiales, Rhodophyta). J Appl Phycol 12:69–81

    CAS  Google Scholar 

  • Yoon HS, Grant J, Tekle YI, Wu M, Chaon BC, Cole JC, Logsdon JM Jr, Patterson DJ, Bhattacharya D, Katz LA (2008) Broadly sampled multigene trees of eukaryotes. BMC Evol Biol 8:14

    PubMed  Google Scholar 

  • Yoon HS, Hackett JD, Bhattacharya D (2006) A genomic and phylogenetic perspective on endosymbiosis and algal origin. J Appl Phycol 18:475–481

    Google Scholar 

  • Yoon HS, Hackett JD, Ciniglia C, Pinto D, Bhattacharya D (2004) A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol 21:809–818

    CAS  PubMed  Google Scholar 

  • Zaslavskaia LA, Lippmeier JC, Kroth PG, Grossman AR, Apt KE (2000) Transformation of the diatom Phaeodactylum tricornutum (Bacillariophyceae) with a variety of selectable marker and reporter genes. J Phycol 36:379–386

    CAS  Google Scholar 

  • Zaslavskaia LA, Lippmeier JC, Shih C, Ehrhardt D, Grossman AR, Apt KE (2001) Trophic conversion of an obligate photoautotrophic organism through metabolic engineering. Science 292:2073–2075

    CAS  PubMed  Google Scholar 

  • Zhang Z, Green BR, Cavalier-Smith T (1999) Single gene circles in dinoflagellate chloroplast genomes. Nature 400:155–159

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, 29682, Roscoff Cedex, France

    Susana M. Coelho & Svenja Heesch

  2. Laboratoire International Associé Dispersal and Adaptation in Marine Species, CNRS, UMR 7139, 29682, Roscoff Cedex, France

    Svenja Heesch & J. Mark Cock

  3. Laboratoire ARAGO, UMR7628 Modèles en biologie cellulaire et évolutive, 66651, Banyuls-sur-mer, France

    Nigel Grimsley & Hervé Moreau

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  1. Susana M. Coelho
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  2. Svenja Heesch
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  3. Nigel Grimsley
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  4. Hervé Moreau
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  5. J. Mark Cock
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Correspondence to Susana M. Coelho .

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Editors and Affiliations

  1. CNRS UMR 7139, Labo. Végétaux Marins et Biomolécules, Université Paris VI, place Georges Teissier, Roscoff CX, 29682, France

    J. Mark Cock

  2. Max F. Perutz Laboratories GmbH, Dr. Bohr-gasse 9/4, Wien, 1030, Austria

    Kristin Tessmar-Raible

  3. CNRS UMR 7139, Labo. Végétaux Marins et Biomolécules, Université Paris VI, place Georges Teissier, Roscoff CX, 29682, France

    Catherine Boyen

  4. Equipe Diversité et Connectivité dans le, Paysage Marin Côtier (DIV&CO), Université Paris VI, place Georges Teissier, Roscoff CX, 29682, France

    Frédérique Viard

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Coelho, S.M., Heesch, S., Grimsley, N., Moreau, H., Cock, J.M. (2010). Genomics of Marine Algae. In: Cock, J., Tessmar-Raible, K., Boyen, C., Viard, F. (eds) Introduction to Marine Genomics. Advances in Marine Genomics, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-8639-6_6

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