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

Armbrust, E. Virginia
Berges, John A.
Bowler, Chris
Green, Beverley R.
Martinez, Diego
Putnam, Nicholas H.
Zhou, Shiguo
Allen, Andrew E.
Apt, Kirk E.
Bechner, Michael
Brzezinski, Mark A.
Chaal, Balbir K.
Chiovitti, Anthony
Davis, Aubrey K.
Demarest, Mark S.
Detter, J. Chris
Glavina, Tijana
Goodstein, David
Hadi, Masood Z.
Hellsten, Uffe
Hildebrand, Mark
Jenkins, Bethany D.
Jurka, Jerzy
Kapitonov, Vladimir V.
Kröger, Nils
Lau, Winnie W. Y.
Lane, Todd W.
Larimer, Frank W.
Lippmeier, J. Casey
Lucas, Susan
Medina, Mónica
Montsant, Anton
Obornik, Miroslav
Parker, Micaela Schnitzler
Palenik, Brian
Pazour, Gregory J.
Richardson, Paul M.
Rynearson, Tatiana A.
Saito, Mak A.
Schwartz, David C.
Thamatrakoln, Kimberlee
Valentin, Klaus
Vardi, Assaf
Wilkerson, Frances P.
Rokhsar, Daniel S.

¹School of Oceanography, University of Washington, Seattle, WA 98195, USA. ²Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA. ³Laboratory of Molecular Plant Biology, Stazione Zoologica, Villa Comunale, I 80121 Naples, Italy. Organismes Photosynthétiques et Environnement, Département de Biologie, ⁴Ecole Normale Supérieure, 75230 Paris, France. ⁵Department of Botany, University of British Columbia, Vancouver, B.C., Canada, V6T 1Z4. ⁶Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. ⁷Departments of Genetics and Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA. ⁸Department of Geosciences, Princeton University, Princeton, NJ 08540, USA. ⁹Martek Biosciences Corp, 6480 Dobbin Road, Columbia, MD 21045, USA. ¹⁰Department of Ecology, Evolution, and Marine Biology and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA. ¹¹School of Botany, University of Melbourne, Victoria 3010, Australia. ¹²Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA. ¹³Lockheed Martin Corporation, Sandia National Laboratory, Post Office Box 969, MS-9951, Livermore, CA 94551, USA. ¹⁴Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA. ¹⁵Genetic Information Research Institute, Mountain View, CA 94043, USA. ¹⁶Lehrstuhl Biochemie I, Universität Regensburg, D-93053, Regensburg, Germany. ¹⁷Biosystems Research Department, Sandia National Laboratories, Livermore, CA 94551-0969. ¹⁸Genome Analysis Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. ¹⁹Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK. ²⁰Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA. ²¹Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. ²²Alfred Wegener Institute, 27570 Bremerhaven, Germany. ²³Romberg Tiburon Center, San Francisco State University, Tiburon, CA 94920, USA. ²⁴Center for Integrative Genomics, University of California at Berkeley, Berkeley, CA, USA

*To whom correspondence should be addressed. E-mail: [email protected] (E.V.A.), [email protected] (D.S.R.)

†Present address: Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.

Supporting Online Material: www.sciencemag.org/cgi/content/full/306/5693/79/DC1; Materials and Methods; Figs. S1 to S7; Tables S1 to S4; References

7 June 2004; accepted 17 August 2004

Science 306(5693):p 79-86, October 1, 2004.

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.