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

(2010) GENOME BIOLOGY. 11(8).
Author
Organization
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.
Keywords
PHAEODACTYLUM-TRICORNUTUM, MARINE DIATOM, THALASSIOSIRA-PSEUDONANA, GENOME REVEALS, EST DATABASE, NITRIC-OXIDE, TRANSFORMATION, EVOLUTION, GENES, OCEAN

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MLA
Maheswari, Uma, Kamel Jabbari, Jean-Louis Petit, et al. “Digital Expression Profiling of Novel Diatom Transcripts Provides Insight into Their Biological Functions.” GENOME BIOLOGY 11.8 (2010): n. pag. Print.
APA
Maheswari, U., Jabbari, K., Petit, J.-L., Porcel, B. M., Allen, A. E., Cadoret, J.-P., De Martino, A., et al. (2010). Digital expression profiling of novel diatom transcripts provides insight into their biological functions. GENOME BIOLOGY, 11(8).
Chicago author-date
Maheswari, Uma, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, et al. 2010. “Digital Expression Profiling of Novel Diatom Transcripts Provides Insight into Their Biological Functions.” Genome Biology 11 (8).
Chicago author-date (all authors)
Maheswari, Uma, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Julie La Roche, Pascal J Lopez, Véronique Martin-Jézéquel, Agnès Meichenin, Thomas Mock, Micaela Schnitzler Parker, Assaf Vardi, E Virginia Armbrust, Jean Weissenbach, Michaël Katinka, and Chris Bowler. 2010. “Digital Expression Profiling of Novel Diatom Transcripts Provides Insight into Their Biological Functions.” Genome Biology 11 (8).
Vancouver
1.
Maheswari U, Jabbari K, Petit J-L, Porcel BM, Allen AE, Cadoret J-P, et al. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. GENOME BIOLOGY. 2010;11(8).
IEEE
[1]
U. Maheswari et al., “Digital expression profiling of novel diatom transcripts provides insight into their biological functions,” GENOME BIOLOGY, vol. 11, no. 8, 2010.
@article{8551770,
  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.},
  articleno    = {R85},
  author       = {Maheswari, Uma and Jabbari, Kamel and Petit, Jean-Louis and Porcel, Betina M and Allen, Andrew E and Cadoret, Jean-Paul and De Martino, Alessandra and Heijde, Marc and Kaas, Raymond and La Roche, Julie and Lopez, Pascal J and Martin-Jézéquel, Véronique and Meichenin, Agnès and Mock, Thomas and Schnitzler Parker, Micaela and Vardi, Assaf and Armbrust, E Virginia and Weissenbach, Jean and Katinka, Michaël and Bowler, Chris},
  issn         = {1465-6906},
  journal      = {GENOME BIOLOGY},
  keywords     = {PHAEODACTYLUM-TRICORNUTUM,MARINE DIATOM,THALASSIOSIRA-PSEUDONANA,GENOME REVEALS,EST DATABASE,NITRIC-OXIDE,TRANSFORMATION,EVOLUTION,GENES,OCEAN},
  language     = {eng},
  number       = {8},
  pages        = {19},
  title        = {Digital expression profiling of novel diatom transcripts provides insight into their biological functions},
  url          = {http://dx.doi.org/10.1186/gb-2010-11-8-r85},
  volume       = {11},
  year         = {2010},
}

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