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Science 1 October 2004:
Vol. 306. no. 5693, pp. 79 - 86
DOI: 10.1126/science.1101156
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Research Articles

The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism

E. Virginia Armbrust,1* John A. Berges,2 Chris Bowler,3,4 Beverley R. Green,5 Diego Martinez,6 Nicholas H. Putnam,6 Shiguo Zhou,7 Andrew E. Allen,8,4 Kirk E. Apt,9 Michael Bechner,7 Mark A. Brzezinski,10 Balbir K. Chaal,5 Anthony Chiovitti,11 Aubrey K. Davis,12 Mark S. Demarest,10 J. Chris Detter,6 Tijana Glavina,6 David Goodstein,6 Masood Z. Hadi,13 Uffe Hellsten,6 Mark Hildebrand,12 Bethany D. Jenkins,14 Jerzy Jurka,15 Vladimir V. Kapitonov,15 Nils Kröger,16 Winnie W. Y. Lau,1 Todd W. Lane,17 Frank W. Larimer,18,6 J. Casey Lippmeier,9,19 Susan Lucas,6 Mónica Medina,6 Anton Montsant,3,4 Miroslav Obornik,5{dagger} Micaela Schnitzler Parker,1 Brian Palenik,12 Gregory J. Pazour,20 Paul M. Richardson,6 Tatiana A. Rynearson,1 Mak A. Saito,21 David C. Schwartz,7 Kimberlee Thamatrakoln,12 Klaus Valentin,22 Assaf Vardi,4 Frances P. Wilkerson,23 Daniel S. Rokhsar6,24*

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ~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.

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


{dagger} Present address: Institute of Parasitology, Academy of Sciences of 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.)

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