Phaeodactylum tricornutum

Taxonomy: Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Naviculales; Phaeodactylaceae; Phaeodactylum

Introduction

Phaeodactylum belongs to the unicellular brown algal class Bacillariophyceae, or the diatoms. Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are one of the most important constituents of phytoplankton communities in aquatic environments; it is estimated that 20% to 25% of all organic carbon fixation on the planet is carried out by diatoms.
The genome sequence of the pennate diatom Phaeodactylum tricornutum was the second diatom genome to be sequenced, after the centric diatom Thalassiosira pseudonana. The completed P. tricornutum genome, sequenced by the Joint Genome Institute (JGI), is approximately 27.4 megabases (Mb) in size and is predicted to contain fewer genes than T. pseudonana (10,402 as opposed to 11,776).

Our involvement

Our main contribution was the comparative analysis of P. tricornutum with other chromalveolates (including T. pseudonana), viridiplantae, red algae and opisthokonta. Our analyses indicated that, in spite of the fact that the pennate and centric diatoms have only been diverging for 90 million years, a substantial fraction of genes (40%) are not shared by these representatives of the two lineages. Other important observations include selective gene family expansions in the diatoms, differential losses and gains of genes. We were also involved in the in silico annotation of the core cell cycle genes.

In collaboration with

Publications

2010

Huysman, M., Martens, C., Vandepoele, K., Gillard, J., Rayko, E., Heijde, M., Bowler, C., Inzé, D., Van de Peer, Y., De Veylder, L., Vyverman, W. (2010) Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signalling. Genome Biol. 11(2):R17.

2008

Bowler, C., * Allen, A., * Badger, J., * Grimwood, J., * Jabbari, K., * Kuo, Y.-C., * Maheswari, U., * Martens, C., * Maumus, F., * Otillar, R., * Rayko, E., * Salamov, A., * Vandepoele, K., Beszteri, B., Gruber, A., Heijde, M., Katinka, M., Mock, T., Valentin, K., Vérret, F., Berges, J., Brownlee, C., Cadoret, J., Chiovitti, A., Jae Choi, C., Coesel, S., Martino, A., Detter, J., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M., Jenkins, B., Jiroutova, K., Jorgensen, R., Joubert, Y., Kaplan, A., Kroeger, N., Kroth, P., Roche, J., Lindquist, E., Lommer, M., Martin-Jézéquel, V., Lopez, P., Lucas, S., Mangogna, M., McGinnis, K., Medlin, L., Montsant, A., Oudot-Secq, M., Napoli, C., Obornik, M., Petit, J., Porcel, B., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T., Schmutz, J., Schnitzler Parker, M., Shapiro, H.J., Siaut, M., Stanley, M., J.Sussman, M., Taylor, J.S., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L., Rokhsar, D., Weissenbach, J., Armbrust, V., Green, P.J., Van de Peer, Y., Grigoriev, I. (2008) The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature 456(7219):239-44. *contributed equally











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