Molecular Genetics and Genomics

, Volume 277, Issue 4, pp 427–439 | Cite as

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

  • Marie-Pierre Oudot-Le Secq
  • Jane Grimwood
  • Harris Shapiro
  • E. Virginia Armbrust
  • Chris Bowler
  • Beverley R. GreenEmail author
Original Paper


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.


Chloroplast Plastid Genome Secondary endosymbiosis Diatom 



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.

Supplementary material

438_2006_199_MOESM1_ESM.doc (112 kb)
Supplementary Table 1. Chromist Protein-coding Genes (DOC 112 kb)


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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Marie-Pierre Oudot-Le Secq
    • 1
  • Jane Grimwood
    • 2
  • Harris Shapiro
    • 3
  • E. Virginia Armbrust
    • 4
  • Chris Bowler
    • 5
    • 6
  • Beverley R. Green
    • 1
    Email author
  1. 1.Department of BotanyUniversity of British ColumbiaVancouverCanada
  2. 2.Stanford/JGIStanford Human Genome CenterPalo AltoUSA
  3. 3.Department of EnergyJoint Genome InstituteWalnut CreekUSA
  4. 4.School of OceanographyUniversity of WashingtonSeattleUSA
  5. 5.Cell Signalling LaboratoryStazione ZoologicaNaplesItaly
  6. 6.CNRS FRE2910, Département de BiologieEcole Normale SupérieureParisFrance

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