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

Author

Maheswari, Uma, Jabbari, Kamel, Petit, Jean-Louis, Porcel, Betina M, Allen, Andrew E, Cadoret, Jean-Paul, De Martino, Alessandra, Heijde, Marc, Kaas, Raymond, LaRoche, Julie, Lopez, Pascal J, Martin-Jézéquel, Véronique, Meichenin, Agnès, Mock, Thomas, Schnitzler Parker, Micaela, Vardi, Assaf, Armbrust, E Virginia, Weissenbach, Jean, Katinka, Michaël, Bowler, Chris, Maheswari, Uma, Jabbari, Kamel, Petit, Jean-Louis, Porcel, Betina M, Allen, Andrew E, Cadoret, Jean-Paul, De Martino, Alessandra, Heijde, Marc, Kaas, Raymond, LaRoche, Julie, Lopez, Pascal J, Martin-Jézéquel, Véronique, Meichenin, Agnès, Mock, Thomas, Schnitzler Parker, Micaela, Vardi, Assaf, Armbrust, E Virginia, Weissenbach, Jean, Katinka, Michaël, and Bowler, Chris

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.

Published
2010
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2. The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

Author

Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, De Martino, Alessandra, Detter, John Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, Huysman, Marie J.J., Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, Kroth, Peter G., La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin–Jézéquel, Véronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Oudot–Le Secq, Marie-Pierre, Napoli, Carolyn, Obornik, Miroslav, Schnitzler Parker, Micaela, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele S., Sussman, Michael R., Taylor, Alison R., Vardi, Assaf, Dassow, Peter von, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Van de Peer, Yves, Grigoriev, Igor V., Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, De Martino, Alessandra, Detter, John Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, Huysman, Marie J.J., Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, Kroth, Peter G., La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin–Jézéquel, Véronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Oudot–Le Secq, Marie-Pierre, Napoli, Carolyn, Obornik, Miroslav, Schnitzler Parker, Micaela, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele S., Sussman, Michael R., Taylor, Alison R., Vardi, Assaf, Dassow, Peter von, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Van de Peer, Yves, and Grigoriev, Igor V.

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008

3. A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis.

Author

Kroth, Peter G., Chiovitti, Anthony, Gruber, Ansgar, Martin-Jezequel, Veronique, Mock, Thomas, Schnitzler Parker, Micaela, Stanley, Michele S., Kaplan, Aaron, Caron, Lise, Weber, Till, Maheswari, Uma, Armbrust, Elisabeth Virginia, Bowler, Chris, Kroth, Peter G., Chiovitti, Anthony, Gruber, Ansgar, Martin-Jezequel, Veronique, Mock, Thomas, Schnitzler Parker, Micaela, Stanley, Michele S., Kaplan, Aaron, Caron, Lise, Weber, Till, Maheswari, Uma, Armbrust, Elisabeth Virginia, and Bowler, Chris

Published
2008

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

Author

Maheswari, Uma, primary, Jabbari, Kamel, additional, Petit, Jean-Louis, additional, Porcel, Betina M, additional, Allen, Andrew E, additional, Cadoret, Jean-Paul, additional, De Martino, Alessandra, additional, Heijde, Marc, additional, Kaas, Raymond, additional, La Roche, Julie, additional, Lopez, Pascal J, additional, Martin-Jézéquel, Véronique, additional, Meichenin, Agnès, additional, Mock, Thomas, additional, Schnitzler Parker, Micaela, additional, Vardi, Assaf, additional, Armbrust, E Virginia, additional, Weissenbach, Jean, additional, Katinka, Michaël, additional, and Bowler, Chris, additional

Published
2010
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6. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, Chris, E. Allen, Andrew, H. Badger, Jonathan, Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, P. Otillar, Robert, Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, A. Berges, John, Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Jae Choi, Chang, Coesel, Sacha, De Martino, Alessandra, Chris Detter, J., Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, J. J. Huysman, Marie, D. Jenkins, Bethany, Jiroutova, Katerina, E. Jorgensen, Richard, Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, G. Kroth, Peter, La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin-jézéquel, Véronique, J. Lopez, Pascal, Lucas, Susan, Mangogna, Manuela, Mcginnis, Karen, K. Medlin, Linda, Montsant, Anton, Oudot-le Secq, Marie-Pierre, Napoli, Carolyn, Obornik, Miroslav, Schnitzler Parker, Micaela, Petit, Jean-Louis, M. Porcel, Betina, Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, A. Rynearson, Tatiana, Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele, R. Sussman, Michael, R. Taylor, Alison, Vardi, Assaf, Von Dassow, Peter, Vyverman, Wim, Willis, Anusuya, S. Wyrwicz, Lucjan, S. Rokhsar, Daniel, Weissenbach, Jean, Virginia Armbrust, E., R. Green, Beverley, Van de Peer, Yves, V. Grigoriev, Igor, Bowler, Chris, E. Allen, Andrew, H. Badger, Jonathan, Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, P. Otillar, Robert, Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, A. Berges, John, Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Jae Choi, Chang, Coesel, Sacha, De Martino, Alessandra, Chris Detter, J., Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, J. J. Huysman, Marie, D. Jenkins, Bethany, Jiroutova, Katerina, E. Jorgensen, Richard, Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, G. Kroth, Peter, La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin-jézéquel, Véronique, J. Lopez, Pascal, Lucas, Susan, Mangogna, Manuela, Mcginnis, Karen, K. Medlin, Linda, Montsant, Anton, Oudot-le Secq, Marie-Pierre, Napoli, Carolyn, Obornik, Miroslav, Schnitzler Parker, Micaela, Petit, Jean-Louis, M. Porcel, Betina, Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, A. Rynearson, Tatiana, Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele, R. Sussman, Michael, R. Taylor, Alison, Vardi, Assaf, Von Dassow, Peter, Vyverman, Wim, Willis, Anusuya, S. Wyrwicz, Lucjan, S. Rokhsar, Daniel, Weissenbach, Jean, Virginia Armbrust, E., R. Green, Beverley, Van de Peer, Yves, and V. Grigoriev, Igor

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (approx40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans

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