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Transcription factor families inferred from genome sequences of photosynthetic stramenopiles
Article first published online: 14 JUL 2010
DOI: 10.1111/j.1469-8137.2010.03371.x
© The Authors (2010). Journal compilation © New Phytologist Trust (2010)
Issue
New Phytologist
Special Issue: Featured papers on ‘The Ectocarpus genome sequence’
Volume 188, Issue 1, pages 52–66, October 2010
Additional Information
How to Cite
Rayko, E., Maumus, F., Maheswari, U., Jabbari, K. and Bowler, C. (2010), Transcription factor families inferred from genome sequences of photosynthetic stramenopiles. New Phytologist, 188: 52–66. doi: 10.1111/j.1469-8137.2010.03371.x
Publication History
- Issue published online: 2 SEP 2010
- Article first published online: 14 JUL 2010
- Received: 21 May 2010, Accepted: 23 May 2010
Keywords:
- diatom;
- Ectocarpus;
- expression analysis;
- haptophyte;
- heat shock transcription factor;
- heterokont;
- Myb transcription factor;
- stramenopile;
- stress;
- transcription factor;
- transposable elements;
- zinc finger
Summary
- •By comparative analyses we identify lineage-specific diversity in transcription factors (TFs) from stramenopile (or heterokont) genome sequences. We compared a pennate (Phaeodactylum tricornutum) and a centric diatom (Thalassiosira pseudonana) with those of other stramenopiles (oomycetes, Pelagophyceae, and Phaeophyceae (Ectocarpus siliculosus)) as well as to that of Emiliania huxleyi, a haptophyte that is evolutionarily related to the stramenopiles.
- •We provide a detailed description of diatom TF complements and report numerous peculiarities: in both diatoms, the heat shock factor (HSF) family is overamplified and constitutes the most abundant class of TFs; Myb and C2H2-type zinc finger TFs are the two most abundant TF families encoded in all the other stramenopile genomes investigated; the presence of diatom and lineage-specific gene fusions, in particular a class of putative photoreceptors with light-sensitive Per-Arnt-Sim (PAS) and DNA-binding (basic-leucine zipper, bZIP) domains and an HSF-AP2 domain fusion.
- •Expression data analysis shows that many of the TFs studied are transcribed and may be involved in specific responses to environmental stimuli.
- •Evolutionary and functional relevance of these observations are discussed.