FN Archimer Export Format
PT J
TI Digital expression profiling of novel diatom transcripts provides insight into their biological functions
BT 
AF 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
AS 1:1;2:1,2,9;3:2,9;4:2,9;5:1;6:3;7:1;8:1;9:3;10:4;11:1;12:5;13:1;14:6,7;15:6;16:1,8;17:6;18:2,9;19:2,9;20:1;
FF 1:;2:;3:;4:;5:;6:PDG-DOP-DCN-BRM-PBA;7:;8:;9:PDG-DOP-DCN-BRM-PBA;10:;11:;12:;13:;14:;15:;16:;17:;18:;19:;20:;
C1 Ecole Normale Super, Inst Biol, CNRS UMR 8197, INSERM U1024, F-75005 Paris, France.
   CEA Inst Genom, F-91057 Evry, France.
   IFREMER, Physiol & Biotechnol Algues, F-44311 Nantes, France.
   IFM GEOMAR Leibniz Inst Meereswissensch, D-24105 Kiel, Germany.
   Univ Nantes, EA 2160, Lab Mer, Fac Sci & Tech, F-44322 Nantes 3, France.
   Univ Washington, Sch Oceanog, Seattle, WA 98105 USA.
   Univ E Anglia, Sch Environm Sci, Norwich NR4 7TJ, Norfolk, England.
   Weizmann Inst Sci, Dept Plant Sci, IL-76100 Rehovot, Israel.
   Genoscope & CNRS UMR 8030, F-91057 Evry, France.
C2 ENS, FRANCE
   CEA, FRANCE
   IFREMER, FRANCE
   IFM GEOMAR, GERMANY
   UNIV NANTES, FRANCE
   UNIV WASHINGTON, USA
   UNIV E ANGLIA, UK
   WEIZMANN INST SCI, ISRAEL
   GENOSCOPE, FRANCE
   CNRS, FRANCE
SI NANTES
SE PDG-DOP-DCN-BRM-PBA
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-europe
   copubli-univ-france
   copubli-int-hors-europe
IF 7.172
TC 74
UR https://archimer.ifremer.fr/doc/00017/12810/9758.pdf
LA English
DT Article
AB 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.
PY 2010
SO Genome Biology
SN 1474-760X
PU Biomed Central Ltd
VL 11
IS 8
UT 000283777600006
BP 1
EP 19
DI 10.1186/gb-2010-11-8-r85
ID 12810
ER

EF