Diatoms are eukaryotic, photosynthetic microorganisms found throughout marine and freshwater ecosystems that are responsible for around 20% of global primary productivity. A defining feature of diatoms is their ornately patterned silicified cell wall (known as frustule), which display species-specific nanoscale-structures. These organisms therefore play major roles in global carbon and silicon cycles.

The whole genome sequencing of the marine pennate diatom Phaeodactylum tricornutum has been recently performed by the Joint Genome Institute (Walnut Creek, CA, USA) (http://genome.jgi-psf.org/Phatr2/Phatr2.home.html). Although not considered to be of great ecological significance, P. tricornutum has been found in several locations around the world, typically in coastal areas with wide fluctutations in salinity. Unlike other diatoms it can exist in different morphotypes, and changes in cell shape can be stimulated by environmental conditions. This feature can be used to explore the molecular basis of cell shape control and morphogenesis. Furthermore the species can grow in the absence of silicon, and the biogenesis of silicified frustules is facultative, thereby providing opportunities for experimental exploration of silicon-based nanofabrication in diatoms. P. tricornutum has been used in laboratory-based studies of diatom physiology for several decades, and it is currently the only diatom that can routinely be genetically transformed.

In a joint project with Genoscope (Evry, France) we have generated approximately 90,000 ESTs from P. tricornutum cells grown in a range of conditions. Here we present a database of these sequences, that can be used for digital gene expression studies to explore this organism’s responses to a range of environmental conditions. Such studies should provide a foundation for interpreting the ecological success of diatoms.

  Phaeodactylum Digital Gene Expression Database
  Phaeodactylum Digital Gene Expression Database (V.2)
  Phaeodactylum Digital Gene Expression Database (V.3)

Further Reading:
 Falciatore, A. and Bowler, C. (2002) Revealing the molecular secrets of marine diatoms. Annu. Rev. Plant Biol. 53: 109-130.  pdf

 Scala, S., Carels, N., Falciatore, A., Chiusano, M. L. and Bowler, C. (2002) Genome properties of the diatom Phaeodactylum tricornutum. Plant Physiology 129: 993-1002.pdf
 

Armbrust, E.V., Berges, J.B., Bowler, C., Green, B.R., Martinez, D., Putnam, N.H., Zhou, S., Allen, A.E., Apt, K.E., Bechner, M., Brzezinski, M.A., Chaal, B.K., Chiovitti, A., Davis, A.K., Demarest, M.S., Detter, J.C., Glavina, T., Goodstein, D., Hadi, M.Z., Hellsten, U., Hildebrand, M., Jenkins, B.D., Jurka, J., Kapitonov, V.V., Kröger, N., Lau, V.V.Y., Lane, T.W., Larimer, F.W., Lippmeier, J.C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Schnitzler-Parker, M., Palenik, B., Pazour, G.J., Richardson, P.M., Rynearson, T.A., Saito, M.A., Schwartz, D.C., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F.P. and Rokhsar, D.S. (2004) The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science, 304: 79-86.pdf

Maheswari, U., Montsant,, A., Goll, J., Krishnasamy, S., Rajyashri, K.R., Morawala Patell, V. and Bowler, C. (2005) The Diatom EST Database. Nucl. Acids. Res. 33: D344-D347.pdf

Montsant, A., Jabbari, K., Maheswari, U. and Bowler, C. (2005) Comparative genomics of the pennate diatom Phaeodactylum tricornutum. Plant Physiol. 137: 500-513. pdf

For Queries:
Chris Bowler cbowler@biologie.ens.fr

Acknowledgments:
Thalassiosira pseudonana sequences were generated and kindly provided by Joint Genome Institute,Walnut Creek,CA,USA

Funding for this database was obtained from the EU-funded FP5 MarGenes project (QLRT-2001-01226), the EU-FP6 Diatomics project (LSHG-CT-2004-512035), the EU-FP6 Marine Genomics Network of Excellence (GOCE-CT-2004-505403), Genoscope (France), the Agence Nationale de la Recherche (France), the CNRS (France) and the Stazione Zoologica (Italy).

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