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

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, Pascal J., Martin-Jézéquel, Véronique, Meichenin, Agnès, Mock, Thomas ORCID:, Schnitzler Parker, Micaela, Vardi, Assaf, Armbrust, E. Virginia, Weissenbach, Jean, Katinka, Michaël and Bowler, Chris (2010) Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biology, 11 (8). ISSN 1474-7596

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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.

Item Type: Article
Additional Information: Funding Information: 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). We are grateful to Pierre Vincens, Jean-Pierre Roux and Edouard Bray for managing the server and the software and for their help in web interface creation, Ikhlak Ahmed for his help with statistical analysis using R statistical language, as well as Igor Grigoriev and Alan Kuo from JGI. We would also like to thank Patrick Wincker, Julie Poulain and the technical staff of Genoscope for their essential contribution to the experimental part of the work, as well as Franck Anière and the entire system network team at Genoscope. The database is freely available on the web at [48]. The P. tricornutum cDNAs have been submitted to the NCBI dbEST (GenBank accession numbers [GenBank:CD374840] to [GenBank:CD384835] and [GenBank:BI306757] to [GenBank:BI307753]).
Uncontrolled Keywords: ecology, evolution, behavior and systematics,genetics,cell biology ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Environmental Sciences
UEA Research Groups: Faculty of Science > Research Groups > Environmental Biology
Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences
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Depositing User: LivePure Connector
Date Deposited: 08 Mar 2024 12:33
Last Modified: 08 Mar 2024 12:34
DOI: 10.1186/gb-2010-11-8-r85

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