Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism
E. Virginia Armbrust,1*John A. Berges,2Chris Bowler,3,4Beverley R. Green,5Diego Martinez,6Nicholas H. Putnam,6Shiguo Zhou,7Andrew E. Allen,8,4Kirk E. Apt,9Michael Bechner,7Mark A. Brzezinski,10Balbir K. Chaal,5Anthony Chiovitti,11Aubrey K. Davis,12Mark S. Demarest,10J. Chris Detter,6Tijana Glavina,6David Goodstein,6Masood Z. Hadi,13Uffe Hellsten,6Mark Hildebrand,12Bethany D. Jenkins,14Jerzy Jurka,15Vladimir V. Kapitonov,15Nils Kröger,16Winnie W. Y. Lau,1Todd W. Lane,17Frank W. Larimer,18,6J. Casey Lippmeier,9,19Susan Lucas,6Mónica Medina,6Anton Montsant,3,4Miroslav Obornik,5Micaela Schnitzler Parker,1Brian Palenik,12Gregory J. Pazour,20Paul M. Richardson,6Tatiana A. Rynearson,1Mak A. Saito,21David C. Schwartz,7Kimberlee Thamatrakoln,12Klaus Valentin,22Assaf Vardi,4Frances P. Wilkerson,23Daniel S. Rokhsar6,24*
Diatoms are unicellular algae with plastids acquired by secondaryendosymbiosis. They are responsible for 20% of global carbonfixation. We report the 34 million–base pair draft nucleargenome of the marine diatom Thalassiosira pseudonana and its129 thousand–base pair plastid and 44 thousand–basepair mitochondrial genomes. Sequence and optical restrictionmapping revealed 24 diploid nuclear chromosomes. We identifiednovel genes for silicic acid transport and formation of silica-basedcell walls, high-affinity iron uptake, biosynthetic enzymesfor several types of polyunsaturated fatty acids, use of a rangeof nitrogenous compounds, and a complete urea cycle, all attributesthat allow diatoms to prosper in aquatic environments.
1 School of Oceanography, University of Washington, Seattle, WA 98195, USA. 2 Department of Biological Sciences, University of Wisconsin–Milwaukee, Milwaukee, WI 53201, USA. 3 Laboratory of Molecular Plant Biology, Stazione Zoologica, Villa Comunale, I 80121 Naples, Italy. Organismes Photosynthétiques et Environnement, Département de Biologie, 75230 Paris, France. 4 Ecole Normale Supérieure, 75230 Paris, France. 5 Department of Botany, University of British Columbia, Vancouver, B.C., Canada, V6T 1Z4. 6 Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. 7 Departments of Genetics and Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA. 8 Department of Geosciences, Princeton University, Princeton, NJ 08540, USA. 9 Martek Biosciences Corp, 6480 Dobbin Road, Columbia, MD 21045, USA. 10 Department of Ecology, Evolution, and Marine Biology and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA. 11 School of Botany, University of Melbourne, Victoria 3010, Australia. 12 Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA. 13 Lockheed Martin Corporation, Sandia National Laboratory, Post Office Box 969, MS-9951, Livermore, CA 94551, USA. 14 Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA. 15 Genetic Information Research Institute, Mountain View, CA 94043, USA. 16 Lehrstuhl Biochemie I, Universität Regensburg, D-93053, Regensburg, Germany. 17 Biosystems Research Department, Sandia National Laboratories, Livermore, CA 94551–0969. 18 Genome Analysis Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. 19 Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK. 20 Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA. 21 Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. 22 Alfred Wegener Institute, 27570 Bremerhaven, Germany. 23 Romberg Tiburon Center, San Francisco State University, Tiburon, CA 94920, USA. 24 Center for Integrative Genomics, University of California at Berkeley, Berkeley, CA, USA
Present address: Institute of Parasitology, Academy of Sciencesof the Czech Republic, Branisovska 31, 370 05 Ceske Budejovice,Czech Republic.
* To whom correspondence should be addressed. E-mail: armbrust{at}ocean.washington.edu (E.V.A.), dsrokhsar{at}lbl.gov (D.S.R.)
The editors suggest the following Related Resources on Science sites:
In Science Magazine
NEWS OF THE WEEK
Elizabeth Pennisi (1 October 2004) Science306 (5693), 31a.
[DOI: 10.1126/science.306.5693.31a] |Summary »|Full Text »|PDF »
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
From the Cover: Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses.
T. Mock, M. P. Samanta, V. Iverson, C. Berthiaume, M. Robison, K. Holtermann, C. Durkin, S. S. BonDurant, K. Richmond, M. Rodesch, et al. (2008)
PNAS
105, 1579-1584
|Abstract »|Full Text »|PDF »
Mining the diatom genome for the mechanism of biosilicification.
Thiamine biosynthesis in algae is regulated by riboswitches.
M. T. Croft, M. Moulin, M. E. Webb, and A. G. Smith (2007)
PNAS
104, 20770-20775
|Abstract »|Full Text »|PDF »
AUREOCHROME, a photoreceptor required for photomorphogenesis in stramenopiles.
F. Takahashi, D. Yamagata, M. Ishikawa, Y. Fukamatsu, Y. Ogura, M. Kasahara, T. Kiyosue, M. Kikuyama, M. Wada, and H. Kataoka (2007)
PNAS
104, 19625-19630
|Abstract »|Full Text »|PDF »
The Major Route for Chlorophyll Synthesis Includes [3,8-divinyl]-chlorophyllide a Reduction in Arabidopsis thaliana.
N. Nagata, R. Tanaka, and A. Tanaka (2007)
Plant Cell Physiol.
48, 1803-1808
|Abstract »|Full Text »|PDF »
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions.
S. S. Merchant, S. E. Prochnik, O. Vallon, E. H. Harris, S. J. Karpowicz, G. B. Witman, A. Terry, A. Salamov, L. K. Fritz-Laylin, L. Marechal-Drouard, et al. (2007)
Science
318, 245-250
|Abstract »|Full Text »|PDF »
C3 and C4 Pathways of Photosynthetic Carbon Assimilation in Marine Diatoms Are under Genetic, Not Environmental, Control.
K. Roberts, E. Granum, R. C. Leegood, and J. A. Raven (2007)
Plant Physiology
145, 230-235
|Abstract »|Full Text »|PDF »
Salinity-dependent diatom biosilicification implies an important role of external ionic strength.
E. G. Vrieling, Q. Sun, M. Tian, P. J. Kooyman, W. W. C. Gieskes, R. A. van Santen, and N. A. J. M. Sommerdijk (2007)
PNAS
104, 10441-10446
|Abstract »|Full Text »|PDF »
Genomic and Biochemical Analysis of Lipid Biosynthesis in the Unicellular Rhodophyte Cyanidioschyzon merolae: Lack of a Plastidic Desaturation Pathway Results in the Coupled Pathway of Galactolipid Synthesis.
The Membrane-Associated CpcG2-Phycobilisome in Synechocystis: A New Photosystem I Antenna.
K. Kondo, Y. Ochiai, M. Katayama, and M. Ikeuchi (2007)
Plant Physiology
144, 1200-1210
|Abstract »|Full Text »|PDF »
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
B. Palenik, J. Grimwood, A. Aerts, P. Rouze, A. Salamov, N. Putnam, C. Dupont, R. Jorgensen, E. Derelle, S. Rombauts, et al. (2007)
PNAS
104, 7705-7710
|Abstract »|Full Text »|PDF »
PhyloGena a user-friendly system for automated phylogenetic annotation of unknown sequences.
K. Hanekamp, U. Bohnebeck, B. Beszteri, and K. Valentin (2007)
Bioinformatics
23, 793-801
|Abstract »|Full Text »|PDF »
Tracing the Evolution of the Light-Harvesting Antennae in Chlorophyll a/b-Containing Organisms.
A. G. Koziol, T. Borza, K.-I. Ishida, P. Keeling, R. W. Lee, and D. G. Durnford (2007)
Plant Physiology
143, 1802-1816
|Abstract »|Full Text »|PDF »
A single-molecule barcoding system using nanoslits for DNA analysis.
K. Jo, D. M. Dhingra, T. Odijk, J. J. de Pablo, M. D. Graham, R. Runnheim, D. Forrest, and D. C. Schwartz (2007)
PNAS
104, 2673-2678
|Abstract »|Full Text »|PDF »
Analysis of Thalassiosira pseudonana Silicon Transporters Indicates Distinct Regulatory Levels and Transport Activity through the Cell Cycle.
Evolutionary Processes During the Formation of the Plant-Specific Dof Transcription Factor Family.
M. Shigyo, N. Tabei, T. Yoneyama, and S. Yanagisawa (2007)
Plant Cell Physiol.
48, 179-185
|Abstract »|Full Text »|PDF »
Chimeric Plastid Proteome in the Florida "Red Tide" Dinoflagellate Karenia brevis.
T. Nosenko, K. L. Lidie, F. M. Van Dolah, E. Lindquist, J.-F. Cheng, US Department of Energy-Joint Genome Institute, and D. Bhattacharya (2006)
Mol. Biol. Evol.
23, 2026-2038
|Abstract »|Full Text »|PDF »
Dimethylsulfoniopropionate uptake by marine phytoplankton..
M. Vila-Costa, R. Simo, H. Harada, J. M. Gasol, D. Slezak, and R. P. Kiene (2006)
Science
314, 652-654
|Abstract »|Full Text »|PDF »
Algae need their vitamins..
M. T. Croft, M. J. Warren, and A. G. Smith (2006)
Eukaryot. Cell
5, 1175-1183
|Full Text »|PDF »
From the Cover: Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.
E. Derelle, C. Ferraz, S. Rombauts, P. Rouze, A. Z. Worden, S. Robbens, F. Partensky, S. Degroeve, S. Echeynie, R. Cooke, et al. (2006)
PNAS
103, 11647-11652
|Abstract »|Full Text »|PDF »
Gene Expression Induced by Copper Stress in the Diatom Thalassiosira pseudonana..
A. K. Davis, M. Hildebrand, and B. Palenik (2006)
Eukaryot. Cell
5, 1157-1168
|Abstract »|Full Text »|PDF »
In Diatoms, the Transthylakoid Proton Gradient Regulates the Photoprotective Non-photochemical Fluorescence Quenching Beyond its Control on the Xanthophyll Cycle.
From the Cover: Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus.
P. R. Gilson, V. Su, C. H. Slamovits, M. E. Reith, P. J. Keeling, and G. I. McFadden (2006)
PNAS
103, 9566-9571
|Abstract »|Full Text »|PDF »
Membrane transporters in the relict plastid of malaria parasites.
K. A. Mullin, L. Lim, S. A. Ralph, T. P. Spurck, E. Handman, and G. I. McFadden (2006)
PNAS
103, 9572-9577
|Abstract »|Full Text »|PDF »
Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra.
R. F. Waller, N. J. Patron, and P. J. Keeling (2006)
Int J Syst Evol Microbiol
56, 1439-1447
|Abstract »|Full Text »|PDF »
Oceanographic basis of the global surface distribution of Prochlorococcus ecotypes..
H. A. Bouman, O. Ulloa, D. J. Scanlan, K. Zwirglmaier, W. K. W. Li, T. Platt, V. Stuart, R. Barlow, O. Leth, L. Clementson, et al. (2006)
Science
312, 918-921
|Abstract »|Full Text »|PDF »
A "Holistic" Kinesin Phylogeny Reveals New Kinesin Families and Predicts Protein Functions.
Phylogenomic Analysis Identifies Red Algal Genes of Endosymbiotic Origin in the Chromalveolates.
S. Li, T. Nosenko, J. D. Hackett, and D. Bhattacharya (2006)
Mol. Biol. Evol.
23, 663-674
|Abstract »|Full Text »|PDF »
Ancient Origin of Elicitin Gene Clusters in Phytophthora Genomes.
R. H. Y. Jiang, B. M. Tyler, S. C. Whisson, A. R. Hardham, and F. Govers (2006)
Mol. Biol. Evol.
23, 338-351
|Abstract »|Full Text »|PDF »
Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi.
S. T. Dyhrman, S. T. Haley, S. R. Birkeland, L. L. Wurch, M. J. Cipriano, and A. G. McArthur (2006)
Appl. Envir. Microbiol.
72, 252-260
|Abstract »|Full Text »|PDF »
Identification of Proteins from a Cell Wall Fraction of the Diatom Thalassiosira pseudonana: Insights into Silica Structure Formation.
L. G. Frigeri, T. R. Radabaugh, P. A. Haynes, and M. Hildebrand (2006)
Mol. Cell. Proteomics
5, 182-193
|Abstract »|Full Text »|PDF »
Cooccurrence of ScDSP Gene Expression, Cell Death, and DNA Fragmentation in a Marine Diatom, Skeletonema costatum.
C.-C. Chung, S.-P. L. Hwang, and J. Chang (2005)
Appl. Envir. Microbiol.
71, 8744-8751
|Abstract »|Full Text »|PDF »
Sequence and Comparative Genomic Analysis of Actin-related Proteins.
J. Muller, Y. Oma, L. Vallar, E. Friederich, O. Poch, and B. Winsor (2005)
Mol. Biol. Cell
16, 5736-5748
|Abstract »|Full Text »|PDF »
Mosaic Origin of the Heme Biosynthesis Pathway in Photosynthetic Eukaryotes.
Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum.
S. Reslewic, S. Zhou, M. Place, Y. Zhang, A. Briska, S. Goldstein, C. Churas, R. Runnheim, D. Forrest, A. Lim, et al. (2005)
Appl. Envir. Microbiol.
71, 5511-5522
|Abstract »|Full Text »|PDF »
Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life.
S. N. Vinogradov, D. Hoogewijs, X. Bailly, R. Arredondo-Peter, M. Guertin, J. Gough, S. Dewilde, L. Moens, and J. R. Vanfleteren (2005)
PNAS
102, 11385-11389
|Abstract »|Full Text »|PDF »
Reciprocal Fusions of Two Genes in the Formaldehyde Detoxification Pathway in Ciliates and Diatoms.
N. A. Stover, A. R. O. Cavalcanti, A. J. Li, B. C. Richardson, and L. F. Landweber (2005)
Mol. Biol. Evol.
22, 1539-1542
|Abstract »|Full Text »|PDF »
Genomes, phylogeny, and evolutionary systems biology.
Genome-Based Examination of Chlorophyll and Carotenoid Biosynthesis in Chlamydomonas reinhardtii.
M. Lohr, C.-S. Im, and A. R. Grossman (2005)
Plant Physiology
138, 490-515
|Abstract »|Full Text »|PDF »
Diatom Plastids Possess a Phosphoribulokinase with an Altered Regulation and No Oxidative Pentose Phosphate Pathway.
A. K. Michels, N. Wedel, and P. G. Kroth (2005)
Plant Physiology
137, 911-920
|Abstract »|Full Text »|PDF »
Paths toward Algal Genomics.
A. R. Grossman (2005)
Plant Physiology
137, 410-427
|Full Text »|PDF »
Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum.
A. Montsant, K. Jabbari, U. Maheswari, and C. Bowler (2005)
Plant Physiology
137, 500-513
|Abstract »|Full Text »|PDF »
The Diatom EST Database.
U. Maheswari, A. Montsant, J. Goll, S. Krishnasamy, K. R. Rajyashri, V. M. Patell, and C. Bowler (2005)
Nucleic Acids Res.
33, D344-D347
|Abstract »|Full Text »|PDF »
Comment on "The Evolution of Modern Eukaryotic Phytoplankton".
P. J. Keeling, J. M. Archibald, N. M. Fast, and J. D. Palmer (2004)
Science
306, 2191b
|Full Text »|PDF »
Genome Update: correlation of bacterial genomic properties.
P. F. Hallin, T. Coenye, T. T. Binnewies, H. Jarmer, H.-H. Staerfeldt, and D. W. Ussery (2004)
Microbiology
150, 3899-3903
|Full Text »|PDF »
20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand–base pair plastid and 44 thousand–base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments. 
Present address: Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic. 
