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

Abstract

BackgroundStudying 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.ResultsFor 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2610-9) contains supplementary material, which is available to authorized users.

A MADS‐box transcription factor regulates a central step in sporulation of the oomycete Phytophthora infestans

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Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs

“…Significant frequency differences have been shown for particular families in various eukaryotic lineages (Charoensawan et al, 2010b; de Mendoza et al, 2013; Thiriet-Rupert et al, 2016) and specifically in two fungal phyla, Ascomycota and Basidiomycota (Todd et al, 2014). These observations are confirmed by the present study for a larger set of genomes, including some of animals and protists.…”

Charting oat (Avena sativa) embryo and endosperm transcription factor expression reveals differential expression of potential importance for seed development

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