title: Transcription factor families inferred from genome sequences of photosynthetic stramenopiles.
abstract: • 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.
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France.
authors.forename: Edda
authors.initials: E
authors.lastname: Rayko
authors.forename: Florian
authors.initials: F
authors.lastname: Maumus
authors.forename: Uma
authors.initials: U
authors.lastname: Maheswari
authors.forename: Kamel
authors.initials: K
authors.lastname: Jabbari
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
mesh_terms: D001483:Base Sequence; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics*; D010788:Photosynthesis / Q000235:genetics*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D058009:Stramenopiles / Q000235:genetics*; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors