The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

PLoS Biology

Volumn 12, Issue 6, 2014, Pages

  Keeling, Patrick J ^a,b   Burki, Fabien ^a   Wilcox, Heather M ^c   Allam, Bassem ^d   Allen, Eric E ^e   Amaral Zettler, Linda A ^f,g   Armbrust, E Virginia ^h   Archibald, John M ^b,i   Bharti, Arvind K ^j   Bell, Callum J ^j   Beszteri, Bank ^k   Bidle, Kay D ^l   Cameron, Connor T ^j   Campbell, Lisa ^m   Caron, David A ⁿ   Cattolico, Rose Ann ^o   Collier, Jackie L ^d   Coyne, Kathryn ^p   Davy, Simon K ^q   Deschamps, Phillipe ^r   Dyhrman, Sonya T ^s   Edvardsen, Bente ^t   Gates, Ruth D ^u   Gobler, Christopher J ^d   Greenwood, Spencer J ^v   Guida, Stephanie M ^j   Jacobi, Jennifer L ^j   Jakobsen, Kjetill S ^t   James, Erick R ^a   Jenkins, Bethany ^w,x   John, Uwe ^k   Johnson, Matthew D ^y   Juhl, Andrew R ^s   Kamp, Anja ^z,aa   Katz, Laura A ^ab   Kiene, Ronald ^ac   Kudryavtsev, Alexander ^ad,ae   Leander, Brian S ^a   Lin, Senjie ^af   Lovejoy, Connie ^ag   Lynn, Denis ^a,ah   Marchetti, Adrian ^ai   McManus, George ^af   Nedelcu, Aurora M ^aj   Menden Deuer, Susanne ^x   Miceli, Cristina ^ak   Mock, Thomas ^al   Montresor, Marina ^am   Moran, Mary Ann ^an   Murray, Shauna ^ao   Nadathur, Govind ^ap   Nagai, Satoshi ^aq   Ngam, Peter B ^j   Palenik, Brian ^e   Pawlowski, Jan ^ae   Petroni, Giulio ^ar   Piganeau, Gwenael ^as,at   Posewitz, Matthew C ^au   Rengefors, Karin ^av   Romano, Giovanna ^am   Rumpho, Mary E ^aw   Rynearson, Tatiana ^x   Schilling, Kelly B ^j   Schroeder, Declan C ^ax   Simpson, Alastair G B ^b,ay   Slamovits, Claudio H ^b,i   Smith, David R ^az   Smith, G Jason ^ba   Smith, Sarah R ^e   Sosik, Heidi M ^y   Stief, Peter ^z   Theriot, Edward ^bb   Twary, Scott N ^bc   Umale, Pooja E ^j   Vaulot, Daniel ^bd   Wawrik, Boris ^be   Wheeler, Glen L ^ax,bf   Wilson, William H ^bg   Xu, Yan ^bh   Zingone, Adriana ^am   Worden, Alexandra Z ^b,c   more..

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b CANADIAN INSTITUTE FOR ADVANCED RESEARCH   (Canada)

^c MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^d STONY BROOK UNIVERSITY   (United States)

^e UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^f MARINE BIOLOGICAL LABORATORY   (United States)

^g BROWN UNIVERSITY   (United States)

^h UNIVERSITY OF WASHINGTON   (United States)

ⁱ DALHOUSIE UNIVERSITY   (Canada)

^j NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^k ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^l RUTGERS UNIVERSITY   (United States)

^m TEXAS A AND M UNIVERSITY   (United States)

ⁿ UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^o UNIVERSITY OF WASHINGTON   (United States)

^p UNIVERSITY OF DELAWARE   (United States)

^q VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

^r UNIVERSITÉ PARIS SUD   (France)

^s Department of Earth and Environmental Sciences   (United States)

^t UNIVERSITY OF OSLO   (Norway)

^u UNIVERSITY OF HAWAII   (United States)

^v UNIVERSITY OF PRINCE EDWARD ISLAND   (Canada)

^w UNIVERSITY OF RHODE ISLAND   (United States)

^x UNIVERSITY OF RHODE ISLAND   (United States)

^y WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^z MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^aa JACOBS UNIVERSITY BREMEN   (Germany)

^ab SMITH COLLEGE   (United States)

^ac UNIVERSITY OF SOUTH ALABAMA   (United States)

^ad ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^ae UNIVERSITY OF GENEVA   (Switzerland)

^af UNIVERSITY OF CONNECTICUT   (United States)

^ag UNIVERSITÉ LAVAL   (Canada)

^ah UNIVERSITY OF GUELPH   (Canada)

^ai UNIVERSITY OF NORTH CAROLINA   (United States)

^aj UNIVERSITY OF NEW BRUNSWICK   (Canada)

^ak UNIVERSITY OF CAMERINO   (Italy)

^al UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^am STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

^an UNIVERSITY OF GEORGIA   (United States)

^ao UNIVERSITY OF TECHNOLOGY SYDNEY   (Australia)

^ap UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^aq FISHERIES RESEARCH AGENCY   (Japan)

^ar UNIVERSITY OF PISA   (Italy)

^as France   (France)

^at SORBONNE UNIVERSITÉ   (France)

^au Department of Geology and Geological Engineering   (United States)

^av LUND UNIVERSITY   (Sweden)

^aw UNIVERSITY OF CONNECTICUT   (United States)

^ax THE LABORATORY   (United Kingdom)

^ay DALHOUSIE UNIVERSITY   (Canada)

^az UNIVERSITY OF WESTERN ONTARIO   (Canada)

^ba MOSS LANDING MARINE LABORATORIES   (United States)

^bb UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^bc LOS ALAMOS NATIONAL LABORATORY   (United States)

^bd CNRS   (France)

^be UNIVERSITY OF OKLAHOMA   (United States)

^bf PLYMOUTH MARINE LABORATORY   (United Kingdom)

^bg BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

^bh PRINCETON UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

RNA 18S; SMALL SUBUNIT RIBOSOMAL RNA; TRANSCRIPTOME;

ARTICLE; CLADISTICS; CRYPTOPHYTA; DINOFLAGELLATE; FORAMINIFER; MARINE BIOLOGY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; PRASINOPHYCEAE; RED ALGA; REFERENCE DATABASE; RNA SEQUENCE; SEA; STRAMENOPILE; TRANSCRIPTOMICS; TREE OF LIFE; BIODIVERSITY; EUKARYOTE; FACTUAL DATABASE; MICROBIOLOGY; MOLECULAR GENETICS; SEQUENCE ANALYSIS;

BIODIVERSITY; DATABASES, FACTUAL; ENVIRONMENTAL MICROBIOLOGY; EUKARYOTA; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; SEQUENCE ANALYSIS; TRANSCRIPTOME;

EID: 84903286893     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1001889     Document Type: Article

References (32)

1. Worden AZ, Allen AE, (2010) The voyage of the microbial eukaryote. Curr Opin Microbiol 13: 652-660.
2. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.
3. Burki F, Keeling PJ, (2014) Rhizaria. Curr Biol 24: R103-107.
4. del Campo J, Sieracki ME, Molestina R, Keeling PJ, Massana R, et al. (2014) The others: our biased perspective on eukaryotic genomes. Trends Ecol Evol 29: 252-259.
5. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, et al. (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306: 79-86.
6. Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, et al. (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.
7. Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, et al. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A 104: 7705-7710.
8. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456: 239-244.
9. Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, et al. (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324: 268-272.
10. Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, et al. (2011) Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci U S A 108: 4352-4357.
11. Nichols SA, Roberts BW, Richter DJ, Fairclough SR, King N, (2012) Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/beta-catenin complex. Proc Natl Acad Sci U S A 109: 13046-13051.
12. Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, et al. (2012) Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492: 59-65.
13. Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, et al. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499: 209-213.
14. Marin B, Melkonian M, (2010) Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons. Protist 161: 304-336.
15. Fensome RA, Taylor FJR, Norris G, Sarjeant WAS, Wharton DI, et al. (1993) A classification of living and fossil dinoflagellates. Hanover (Pennsylvania): Sheridan Press. 351 p.
16. Saldarriagaa JF, Taylor FJR, Cavalier-Smith T, Menden-Deuer S, Keeling PJ, (2004) Molecular data and the evolutionary history of dinoflagellates. Eur J Protist 40: 85-111.
17. Sun S, Chen J, Li W, Altintas I, Lin A, et al. (2011) Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res 39: D546-D551.
18. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, et al. (2006) Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
19. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, et al. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 4: e286.
20. Swart EC, Bracht JR, Magrini V, Minx P, Chen X, et al. (2013) The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 11: e1001473.
21. Amin SA, Parker MS, Armbrust EV, (2012) Interactions between diatoms and bacteria. Microbiol Molec Biol Rev 76: 667-684.
22. Massana R, Pedros-Alio C, (2008) Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiol 11: 213-218.
23. Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, et al. (2008) Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 10: 3349-3365.
24. Lopez-Garcia P, Rodriguez-Valera F, Pedros-Alio C, Moreira D, (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603-607.
25. Cuvelier ML, Allen AE, Monier A, McCrow JP, Messié M, et al. (2010) Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Nat Acad Sci U S A 107: 14679-14684.
26. Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, et al. (2012) Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environ Microbiol 14: 162-176.
27. Vaulot D, Lepere C, Toulza E, De la Iglesia R, Poulain J, et al. (2012) Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. PLoS ONE 7: e39648.
28. Cameron Thrash J, Temperton B, Swan BK, Landry ZC, Woyke T, et al. (2014) Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J E-pub ahead of print. doi:10.1038/ismej.2013.243.
29. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, et al. (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
30. Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, et al. (2014) Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 11: 41-46.
31. Massana R, Karniol B, Pommier T, Bodaker I, Beja O, (2008) Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate. Environ Microbiol 10: 1335-1343.
32. Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ, (2007) Vertical distribution of picoeukaryotic diversity in the open ocean. Environ Microbiol 9: 1233-1252.