title: Transcription factors in microalgae: genome-wide prediction and comparative analysis.
abstract: BACKGROUND
  Studying transcription factors, which are some of the key players in gene expression, is of outstanding interest for the investigation of the evolutionary history of organisms through lineage-specific features. In this study we performed the first genome-wide TF identification and comparison between haptophytes and other algal lineages.
  
  
  RESULTS
  For TF identification and classification, we created a comprehensive pipeline using a combination of BLAST, HMMER and InterProScan software. The accuracy evaluation of the pipeline shows its applicability for every alga, plant and cyanobacterium, with very good PPV and sensitivity. This pipeline allowed us to identify and classified the transcription factor complement of the three haptophytes Tisochrysis lutea, Emiliania huxleyi and Pavlova sp.; the two stramenopiles Phaeodactylum tricornutum and Nannochloropsis gaditana; the chlorophyte Chlamydomonas reinhardtii and the rhodophyte Porphyridium purpureum. By using T. lutea and Porphyridium purpureum, this work extends the variety of species included in such comparative studies, allowing the detection and detailed study of lineage-specific features, such as the presence of TF families specific to the green lineage in Porphyridium purpureum, haptophytes and stramenopiles. Our comprehensive pipeline also allowed us to identify fungal and cyanobacterial TF families in the algal nuclear genomes.
  
  
  CONCLUSIONS
  This study provides examples illustrating the complex evolutionary history of algae, some of which support the involvement of a green alga in haptophyte and stramenopile evolution.
authors.affiliation: IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France. Stanislas.Thiriet.Rupert@ifremer.fr.
authors.forename: Stanislas
authors.initials: S
authors.lastname: Thiriet-Rupert
authors.affiliation: IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
authors.forename: Grégory
authors.initials: G
authors.lastname: Carrier
authors.affiliation: MicroMar, Mer Molécules Santé, IUML - FR 3473 CNRS, University of Le Mans, Le Mans, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Chénais
authors.affiliation: IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
authors.forename: Camille
authors.initials: C
authors.lastname: Trottier
authors.affiliation: IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
authors.forename: Gaël
authors.initials: G
authors.lastname: Bougaran
authors.affiliation: IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Cadoret
authors.affiliation: MicroMar, Mer Molécules Santé, IUML - FR 3473 CNRS, University of Le Mans, Le Mans, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Schoefs
authors.affiliation: IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Saint-Jean
mesh_terms: D005075:Biological Evolution; D016825:Chlamydomonas reinhardtii / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics; D058087:Haptophyta / Q000235:genetics; D058086:Microalgae / Q000235:genetics*; D005810:Multigene Family; D044665:Porphyridium / Q000235:genetics; D020543:Proteome; D058009:Stramenopiles / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D020543:Proteome; D014157:Transcription Factors
keywords: Algae; Endosymbiotic gene transfer; Haptophytes; Prediction pipeline; Stramenopiles; Tisochrysis lutea; Transcription factors