title: Digital expression profiling of novel diatom transcripts provides insight into their biological functions.
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.
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France. uma@ebi.ac.uk
authors.forename: Uma
authors.initials: U
authors.lastname: Maheswari
authors.forename: Kamel
authors.initials: K
authors.lastname: Jabbari
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Petit
authors.forename: Betina M
authors.initials: BM
authors.lastname: Porcel
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Cadoret
authors.forename: Alessandra
authors.initials: A
authors.lastname: De Martino
authors.forename: Marc
authors.initials: M
authors.lastname: Heijde
authors.forename: Raymond
authors.initials: R
authors.lastname: Kaas
authors.forename: Julie
authors.initials: J
authors.lastname: La Roche
authors.forename: Pascal J
authors.initials: PJ
authors.lastname: Lopez
authors.forename: Véronique
authors.initials: V
authors.lastname: Martin-Jézéquel
authors.forename: Agnès
authors.initials: A
authors.lastname: Meichenin
authors.forename: Thomas
authors.initials: T
authors.lastname: Mock
authors.forename: Micaela
authors.initials: M
authors.lastname: Schnitzler Parker
authors.forename: Assaf
authors.initials: A
authors.lastname: Vardi
authors.forename: E Virginia
authors.initials: EV
authors.lastname: Armbrust
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
authors.forename: Michaël
authors.initials: M
authors.lastname: Katinka
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D002245:Carbon Dioxide / Q000378:metabolism; D017377:Diatoms / Q000235:genetics*; D004777:Environment; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D007501:Iron / Q000378:metabolism; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000378:metabolism; D012333:RNA, Messenger / Q000032:analysis*; D054712:Salinity; D017640:Silicates / Q000378:metabolism; D013696:Temperature
chemical_list: D012333:RNA, Messenger; D017640:Silicates; D002245:Carbon Dioxide; D007501:Iron; D009584:Nitrogen