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Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage

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Abstract

The chloroplast genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been completely sequenced and are compared with those of other secondary plastids of the red lineage: the centric diatom Odontella sinensis, the haptophyte Emiliania huxleyi, and the cryptophyte Guillardia theta. All five chromist genomes are compact, with small intergenic regions and no introns. The three diatom genomes are similar in gene content with 127–130 protein-coding genes, and genes for 27 tRNAs, three ribosomal RNAs and two small RNAs (tmRNA and signal recognition particle RNA). All three genomes have open-reading frames corresponding to ORFs148, 355 and 380 of O. sinensis, which have been assigned the names ycf88, ycf89 and ycf90. Gene order is not strictly conserved, but there are a number of conserved gene clusters showing remnants of red algal origin. The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process.

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Notes

  1. The gene was incorrectly referred to as psbW (psb28) in Armbrust et al. 2004. The name psbW should be used only for a 6 kDa hydrophobic protein that is always nuclear-encoded (Shi and Schroeder 2004). The gene annotated as psbW in the Synechocystis 6803 genome and the plastid genomes of O. sinensis, G. theta and several red algae encodes a hydrophilic 13 kDa protein and should be called psb28 (Kashino et al. 2002).

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Acknowledgements

Financial support was provided by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) to BRG and the Centre National de Recherche Scientifique (CNRS) to CB. We thank Drs. I. Grigoriev, A. Kuo and R. Otillar at the Joint Genome Institute (Walnut Ceek, CA, USA) for help with sequence analysis, and Dr. Jijun Tang for the GRAPPA-IR analysis.

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Authors and Affiliations

  1. Department of Botany, University of British Columbia, #3529-6270 University Blvd., Vancouver, BC, Canada, V6T 1Z4

    Marie-Pierre Oudot-Le Secq & Beverley R. Green

  2. Stanford/JGI, Stanford Human Genome Center, 975 California Avenue, Palo Alto, CA, 94304, USA

    Jane Grimwood

  3. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA

    Harris Shapiro

  4. School of Oceanography, University of Washington, Seattle, WA, 98195, USA

    E. Virginia Armbrust

  5. Cell Signalling Laboratory, Stazione Zoologica, Villa Comunale, 80121, Naples, Italy

    Chris Bowler

  6. CNRS FRE2910, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75230, Paris, France

    Chris Bowler

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  1. Marie-Pierre Oudot-Le Secq
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Correspondence to Beverley R. Green.

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Communicated by R. Herrmann.

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Supplementary Table 1. Chromist Protein-coding Genes (DOC 112 kb)

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Oudot-Le Secq, MP., Grimwood, J., Shapiro, H. et al. Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Mol Genet Genomics 277, 427–439 (2007). https://doi.org/10.1007/s00438-006-0199-4

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