Draft Sequence of Marine Diatom Determined at JGI

Diatoms are eukaryotic algae found throughout the world's oceans and freshwater systems.

The Science

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ∼20% of global carbon fixation. Researchers 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. Researchers 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.


Diatoms are simple single-celled algae, covered with elegant and often very beautiful casings sculpted from silica. They share biochemical features of both plants and animals and are related to the organisms that make up the well known White Cliffs of Dover in England. A team of 45 biologists, lead by oceanographer Virginia Armbrust of the University of Washington, and including members of the DOE Joint Genome Institute, has taken a big step toward resolving the paradoxical nature of these odd microbes. They have sequenced the genome of the marine diatom Thalassiosira pseudonana. The draft genome consists of 34 million bases on 24 chromosomes.

The genome contains about 11,500 genes in all. Analyses of these genes and the proteins they encode confirm that diatoms, in their evolutionary history, apparently acquired new genes by engulfing microbial neighbors. Somewhere along this line, perhaps the most significant acquisition was an algal cell that provided the diatom with all the machinery necessary for photosynthesis. Diatoms date back 180 million years, and remnants of their silica shells make up a porous rock called diatomite that is used in industrial filters. Today diatoms occupy vast swaths of ocean and fresh water, where they play a key role in the global carbon cycle. Diatom photosynthesis yields 19 billion tons of organic carbon, about 40% of the marine carbon produced each year; by processing these amounts of carbon dioxide into solid matter, they represent a key defense against global warming. In addition, the newly analyzed genome is beginning to shed light on how a diatom constructs its intricately patterned glass shell. So far, a dozen proteins involved in the deposition of the silicon have been found and more are expected. Such progress could be a boon to materials scientists as well as climate change scientists.

Principal Investigator

Virginia Armbrust
University of Washington–Seattle

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Armbrust, V. E., J. A. Berges, C. Bowler, B. R. Green, D. Martinez, N. H. Putnam, S. Zhou, A. E. Allen, K. E. Apt, M. Bechner, M. A. Brzezinski, B. K. Chaal, A. Chiovitti, A. K. Davis, M. S. Demarest, J. C. Detter, T. Glavina, D. Goodstein, M. Z. Hadi, U. Hellsten, M. Hildebran, B. D. Jenkins, J. Jurka, V. V. Kapitonov, N. Kröger, W. W. Y. Lau, T. W. Lane, F. W. Larimer, J. C. Lippmeier, S. Lucas, M. Medina, A. Montsant, M. Obornik, M. Schnitzler Parker, B. Palenik, G. J. Pazour, P. M. Richardson, T. A. Rynearson, M. A. Saito, D. C. Schwartz, K. Thamatrakoln, K. Valentin, A. Vardi, F. P. Wilkerson, and D. S. Rokhsar. 2004. “The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism,” Science 306, 79–86. DOI:10.1126/science.1101156.