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Genome properties of the diatom Phaeodactylum tricornutum.

TitleGenome properties of the diatom Phaeodactylum tricornutum.
Publication TypeJournal Article
Year of Publication2002
AuthorsScala, S, Carels, N, Falciatore, A, Chiusano, MLuisa, Bowler, C
JournalPlant Physiol
Volume129
Issue3
Pagination993-1002
Date Published2002 Jul
ISSN0032-0889
KeywordsAnimals, Arabidopsis, Base Composition, Centrifugation, Density Gradient, Chlamydomonas reinhardtii, Diatoms, DNA, DNA, Complementary, Evolution, Molecular, Expressed Sequence Tags, Gene Library, Genome, Molecular Sequence Data, Phytoplankton, Sequence Analysis, DNA, Zea mays
Abstract

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.

DOI10.1104/pp.010713
Alternate JournalPlant Physiol.
PubMed ID12114555
PubMed Central IDPMC166495