Digital expression profiling of novel diatom transcripts provides insight into their biological functions

Type Article
Date 2010
Language English
Author(s) Maheswari Uma1, Jabbari Kamel1, 2, 9, Petit Jean-Louis2, 9, Porcel Betina M.2, 9, Allen Andrew E.1, Cadoret Jean-Paul3, de Martino Alessandra1, Heijde Marc1, Kaas Raymond3, La Roche Julie4, Lopez P.1, Martin-Jezequel Veronique5, Meichenin Agnes1, Mock Thomas6, 7, Parker Micaela Schnitzler6, Vardi Assaf1, 8, Armbrust E. Virginia6, Weissenbach Jean2, 9, Katinka Michael2, 9, Bowler Chris1
Affiliation(s) 1 : Ecole Normale Super, Inst Biol, CNRS UMR 8197, INSERM U1024, F-75005 Paris, France.
2 : CEA Inst Genom, F-91057 Evry, France.
3 : IFREMER, Physiol & Biotechnol Algues, F-44311 Nantes, France.
4 : IFM GEOMAR Leibniz Inst Meereswissensch, D-24105 Kiel, Germany.
5 : Univ Nantes, EA 2160, Lab Mer, Fac Sci & Tech, F-44322 Nantes 3, France.
6 : Univ Washington, Sch Oceanog, Seattle, WA 98105 USA.
7 : Univ E Anglia, Sch Environm Sci, Norwich NR4 7TJ, Norfolk, England.
8 : Weizmann Inst Sci, Dept Plant Sci, IL-76100 Rehovot, Israel.
9 : Genoscope & CNRS UMR 8030, F-91057 Evry, France.
Source Genome Biology (1474-760X) (Biomed Central Ltd), 2010 , Vol. 11 , N. 8 , P. 1-19
DOI 10.1186/gb-2010-11-8-r85
WOS© Times Cited 74
Abstract Background: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. Results: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. Conclusions: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.
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Maheswari Uma, Jabbari Kamel, Petit Jean-Louis, Porcel Betina M., Allen Andrew E., Cadoret Jean-Paul, de Martino Alessandra, Heijde Marc, Kaas Raymond, La Roche Julie, Lopez P., Martin-Jezequel Veronique, Meichenin Agnes, Mock Thomas, Parker Micaela Schnitzler, Vardi Assaf, Armbrust E. Virginia, Weissenbach Jean, Katinka Michael, Bowler Chris (2010). Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biology, 11(8), 1-19. Publisher's official version : , Open Access version :