First published online June 14, 2002; 10.1104/pp.010713
Plant Physiol, July 2002, Vol. 129, pp. 993-1002
Genome Properties of the Diatom Phaeodactylum
tricornutum[w]
Simona
Scala,14
Nicolas
Carels,12
Angela
Falciatore,3
Maria Luisa
Chiusano, and
Chris
Bowler*
Laboratories of Molecular Plant Biology (S.S., A.F., C.B.) and
Molecular Evolution (N.C., M.L.C.), Stazione Zoologica "Anton
Dohrn," Villa Comunale, I-80121 Naples, Italy
Diatoms are a ubiquitous class of microalgae of extreme
importance for global primary productivity and for the biogeochemical cycling of minerals such as silica. However, very little is known about
diatom cell biology or about their genome structure. For diatom
researchers to take advantage of genomics and post-genomics technologies, it is necessary to establish a model diatom species. Phaeodactylum tricornutum is an obvious candidate
because of its ease of culture and because it can be genetically
transformed. Therefore, we have examined its genome composition by the
generation of approximately 1,000 expressed sequence tags. Although
more than 60% of the sequences could not be unequivocally identified by similarity to sequences in the databases, approximately 20% had
high similarity with a range of genes defined functionally at the
protein level. It is interesting that many of these sequences are more
similar to animal rather than plant counterparts. Base composition at
each codon position and GC content of the genome were compared
with Arabidopsis, maize (Zea mays), and
Chlamydomonas reinhardtii. It was found that
distribution of GC within the coding sequences is as homogeneous in
P. tricornutum as in Arabidopsis, but with a slightly
higher GC content. Furthermore, we present evidence that the P.
tricornutum genome is likely to be small (less than 20 Mb).
Therefore, this combined information supports the development of this
species as a model system for molecular-based studies of diatom
biology. The nucleotide sequence data reported has been deposited in
GenBank Nucleotide Sequence Database (dbEST section) under accession
nos. BI306757 through BI307753.
1
These authors contributed equally to the paper.
2
Present address: Centro de Astrobiologia, Consejo
Superior de Investigaciones Científicas-Instituto Nacional de
Tecnica Aerospacial, Carretera de Torrejon a Ajalvir km4, E-28850
Torrejon de Ardoz, Madrid, Spain.
3
Present address: Department of Molecular Biology,
University of Geneva, 30, Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
4
Present address: Centro di Biotecnologie A. O. Cardarelli, Via S. Giacomo Dei Capri 66, I-80131 Naples, Italy.
[w]
The online version of this article contains Web-only
data. The supplemental material is available at www.plantphysiol.org.
*
Corresponding author; e-mail chris{at}alpha.szn.it; fax
39-081- 764-1355.
© 2002 American Society of Plant Physiologists
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