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.
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.
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.
A. and Bowler, C. (2002) Revealing the molecular secrets of marine
diatoms. Annu. Rev. Plant Biol. 53: 109-130. pdf
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
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
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
A., Jabbari, K., Maheswari, U. and Bowler, C. (2005) Comparative
genomics of the pennate diatom Phaeodactylum tricornutum. Plant
Physiol. 137: 500-513. pdf
Chris Bowler email@example.com
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).