1. Digital expression profiling of novel diatom transcripts provides insight into their biological functions
- Author
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Jean Weissenbach, Michael Katinka, Jean-Paul Cadoret, Pascal J. Lopez, Raymond Kaas, Agnès Meichenin, Marc Heijde, Véronique Martin-Jézéquel, Jean-Louis Petit, Betina M. Porcel, Assaf Vardi, Kamel Jabbari, Micaela S. Parker, Uma Maheswari, Thomas Mock, E. Virginia Armbrust, Alessandra De Martino, Chris Bowler, Andrew E. Allen, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Physiologie et biotechnologie des Algues (PBA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Marine Biogeochemistry, Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), School of Oceanography [Seattle], University of Washington [Seattle], School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Department of Plant Sciences, Weizmann Institute of Science [Rehovot, Israël], Funding for the Diatom Digital Gene Expression Database was from the European Union-funded Diatomics project and the Agence Nationale de la Recherche (France). cDNA construction and DNA sequencing was funded by Genoscope (France)., BMC, Ed., Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, and Université de Nantes (UN)-Université de Nantes (UN)-Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST)
- Subjects
0106 biological sciences ,Salinity ,[SDV.GEN] Life Sciences [q-bio]/Genetics ,MESH: Carbon Dioxide ,01 natural sciences ,Genome ,MESH: Nitrogen ,Expressed Sequence Tags ,Genetics ,0303 health sciences ,Expressed sequence tag ,MESH: Iron ,biology ,Temperature ,Adaptation, Physiological ,MESH: Gene Expression Regulation ,MESH: Temperature ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,MESH: Diatoms ,Nitrogen ,Iron ,Molecular Sequence Data ,Thalassiosira pseudonana ,Computational biology ,Environment ,MESH: Expressed Sequence Tags ,03 medical and health sciences ,MESH: Gene Expression Profiling ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,RNA, Messenger ,Phaeodactylum tricornutum ,MESH: Environment ,Gene ,030304 developmental biology ,MESH: RNA, Messenger ,Diatoms ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,MESH: Molecular Sequence Data ,Gene Expression Profiling ,Silicates ,Research ,fungi ,Carbon Dioxide ,biology.organism_classification ,MESH: Adaptation, Physiological ,Gene expression profiling ,Diatom ,Gene Expression Regulation ,MESH: Silicates ,Function (biology) ,MESH: Salinity ,010606 plant biology & botany - Abstract
International audience; 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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- 2010