The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes

Diatoms are photosynthetic secondary endosymbionts found throughout marine andfreshwater environments, and are believed to be responsible for around one fifth of theprimary productivity on Earth 1-3. Here we report the complete genome sequence of themarine pennate diatom Phaeodactylum tricornutum. By comparison with the sequence ofthe centric diatom Thalassiosira pseudonana 4-6 we have explored the evolutionaryorigins, functional significance, and ubiquity throughout diatoms of their generepertoires. In spite of the fact that the pennate and centric lineages have only beendiverging for 90 million years, their genome structures are dramatically different and asubstantial fraction of genes (~40%) are not shared by these representatives of the twolineages. Analysis of molecular divergence compared with yeasts and metazoans revealsrapid rates of gene diversification in diatoms. Contributing factors include selectiveexpansion of gene families, gains of introns, and differential losses of genes andmobilization of transposable elements. Most significantly, we document theunprecedented presence of hundreds of genes from bacteria. The ancient origins of theselateral gene transfers is testified by the finding that more than 300 are found in bothdiatoms, and many are likely to provide novel possibilities for metabolite managementand for the perception of environmental signals. These findings go a long way towardexplaining the incredible diversity and success of the diatoms in contemporary oceans.

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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