Transcription factors in microalgae: genome-wide prediction and comparative analysis

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...

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Published in:BMC genomics 2016-04, Vol.17 (265), p.282-282, Article 282
Main Authors: Thiriet-Rupert, Stanislas, Carrier, Grégory, Chénais, Benoît, Trottier, Camille, Bougaran, Gaël, Cadoret, Jean-Paul, Schoefs, Benoît, Saint-Jean, Bruno
Format: Article
Language:English
Subjects:
Algae
Biochemistry, Molecular Biology
Biological Evolution
Chlamydomonas reinhardtii - genetics
Cyanobacteria - genetics
Evolutionary genetics
Genetic aspects
Genetic research
Genome-wide association studies
Genomics
Haptophyta - genetics
Identification and classification
Life Sciences
Methods
Microalgae - genetics
Microbiology and Parasitology
Multigene Family
Porphyridium - genetics
Proteome
Stramenopiles - genetics
Transcription factors
Transcription Factors - genetics
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Summary: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. 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. 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.
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-016-2610-9