Diatom Genomics - Team Leader: Angela Falciatore

Research

Diatoms are a key phytoplankton group in the contemporary ocean. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes, and studies of their biology promise to reveal many novel aspects. Major objective of our research is to fully exploit novel genetic tools and genomic information to identify the mechanisms controlling diatom growth and distribution in the marine environment. Ecological questions drive our molecular investigations.

Because light is a key environmental signal for photosynthetic organisms, we are performing a comprehensive characterization of diatom light responses by studying:

- the diatom photoreceptors, their signaling pathways and their function in vivo;

- the diatom response to light stress, dissecting key photoprotection mechanisms;

- the light regulated rhythmic processes and their unknown regulators;

- the genetic regulatory elements driving genome expression and light response regulation, characterizing the diatom small non-coding RNAs and gene silencing pathways through computational and experimental approaches.

Selected publications
Rogato A, Richard H, Sarazin A, Voss B, Cheminant Navarro S, Champeimont R, Navarro L, Carbone A, Heww WR, Falciatore A.
The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum.
BMC Genomics, 15 (2014).

Oliveri P, Fortunato AE, Petrone L, Ishikawa-Fujiwara T, Kobayashi Y, Todo T, Antonova O, Arboleda E, Zantke J, Tessmar-Raible K, Falciatore A.
The Cryptochrome/Photolyase Family in aquatic organisms.
Mar Genomics., Apr;14:23-37. doi: 10.1016/j.margen.2014.02.001. Epub 2014 Feb 23. (2014).

Daboussi F, Leduc S, Maréchal A, Dubois G, Guyot V, Perez-Michaut C, Amato A, Falciatore A, Juillerat A, Beurdeley M, Voytas DF, Cavarec L, Duchateau P.
Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology.
Nat Commun., May 29;5:3831. doi: 10.1038/ncomms4831. (2014).

Fortunato AE, Annunziata R, Jaubert M, Bouly JP, Falciatore A.
Dealing with light: The widespread and multitasking cryptochrome/photolyase family in photosynthetic organisms.
Journal of Plant Physiology., in press (2014).

Lepetit B, Sturm S, Rogato A, Gruber A, Sachse M, Falciatore A, Kroth P, Lavaud J.
High light acclimation in the secondary plastids containing diatom Phaeodactylum tricornutum is triggered by the redox state of the plastoquinone pool.
Plant Physiology., Feb;161(2):853-65. doi: 10.1104/pp.112.207811. Epub 2012 Dec 3. (2013).

Huysman MJ, Fortunato AE, Matthijs M, Costa BS, Vanderhaeghen R, Van den Daele H, Sachse M, Inzé D, Bowler C, Kroth PG, Wilhelm C, Falciatore A, Vyverman W, De Veylder L.
AUREOCHROME1a-Mediated Induction of the Diatom-Specific Cyclin dsCYC2 Controls the Onset of Cell Division in Diatoms (Phaeodactylum tricornutum)
Plant Cell, (2013).

Frauke A Depauw , Alessandra Rogato, Maurizio Ribera d'Alcalá, Angela Falciatore
Exploring the molecular basis of responses to light in marine diatoms
J Exp Bot, 63 (2012).

Bowler C., De Martino A., Falciatore A.
Diatom cell division in an environmental context
Curr Opin Plant Biol, 13 (2010).

Heijde, M. and Zabulon, G. and Corellou, F. and Ishikawa, T. and Brazard, J. and Usman, A. and Sanchez, F. and Plaza, P. and Martin, M. and Falciatore, A. and Todo, T. and Bouget, F. Y. and Bowler, C.
Characterization of two members of the cryptochrome/photolyase family from Ostreococcus tauri provides insights into the origin and evolution of cryptochromes
Plant Cell Environ, (2010).

Benjamin Bailleul, Alessandra Rogato, Alessandra de Martino, Sacha Coesel, Pierre Cardol, Chris Bowler, Angela Falciatore, Giovanni Finazziaf
An atypical member of the light-harvesting complex stress-related protein family modulates diatom responses to light
Proc Natl Acad Sci U S A, 107 (2010).

De Riso, V. and Raniello, R. and Maumus, F. and Rogato, A. and Bowler, C. and Falciatore, A.
Gene silencing in the marine diatom Phaeodactylum tricornutum
Nucleic Acids Res, 37 (2009).

Coesel, S. and Mangogna, M. and Ishikawa, T. and Heijde, M. and Rogato, A. and Finazzi, G. and Todo, T. and Bowler, C. and Falciatore, A.
Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity
EMBO Rep, 10 (2009).

Bowler, C. and Allen, A. E. and Badger, J. H. and Grimwood, J. and Jabbari, K. and Kuo, A. and Maheswari, U. and Martens, C. and Maumus, F. and Otillar, R. P. and Rayko, E. and Salamov, A. and Vandepoele, K. and Beszteri, B. and Gruber, A. and Heijde, M. and Katinka, M. and Mock, T. and Valentin, K. and Verret, F. and Berges, J. A. and Brownlee, C. and Cadoret, J. P. and Chiovitti, A. and Choi, C. J. and Coesel, S. and De Martino, A. and Detter, J. C. and Durkin, C. and Falciatore, A. and Fournet, J. and Haruta, M. and Huysman, M. J. and Jenkins, B. D. and Jiroutova, K. and Jorgensen, R. E. and Joubert, Y. and Kaplan, A. and Kroger, N. and Kroth, P. G. and La Roche, J. and Lindquist, E. and Lommer, M. and Martin-Jezequel, V. and Lopez, P. J. and Lucas, S. and Mangogna, M. and McGinnis, K. and Medlin, L. K. and Montsant, A. and Oudot-Le Secq, M. P. and Napoli, C. and Obornik, M. and Parker, M. S. and Petit, J. L. and Porcel, B. M. and Poulsen, N. and Robison, M. and Rychlewski, L. and Rynearson, T. A. and Schmutz, J. and Shapiro, H. and Siaut, M. and Stanley, M. and Sussman, M. R. and Taylor, A. R. and Vardi, A. and von Dassow, P. and Vyverman, W. and Willis, A. and Wyrwicz, L. S. and Rokhsar, D. S. and Weissenbach, J. and Armbrust, E. V. and Green, B. R. and Van de Peer, Y. and Grigoriev, I. V.
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
Nature, 456 (2008).

Coesel, S. and Obornik, M. and Varela, J. and Falciatore, A. and Bowler, C.
Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms
PLoS One, 3 (2008).

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