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.

Keywords: Algae; Endosymbiotic gene transfer; Haptophytes; Prediction pipeline; Stramenopiles; Tisochrysis lutea; Transcription factors.

Fig. 1

Identification pipeline. The pipeline is divided into three steps. Step One uses two strategies: i) a similarity search against an algae-based self-built database of known TFs with BLAST software; ii) functional domain annotation with InterProScan and HMMER software. The protein list obtained is the subject of the Step Two: the filtration of false positives according to specific parameters (see Methods). The last step consists in the classification of the putative TF list obtained in Step Two using a homemade perl script followed by manual curation for specific cases (see Methods)

Fig. 2

Percentages of the predicted proteomes dedicated to transcription factors in the 7 algae

Fig. 3

Dendrogram representing the repartition of the four lineages according to the presence/absence of TF families. The green lineage is colored in green, stramenopiles in orange, red lineage in red and haptophytes in purple. The scale indicates distance measurement

Fig. 4

Heatmap showing the clustering of TF families according to their proportion in the algal genomes. Cluster 1 comprises TF families described as specific to the green lineage. Cluster 2 is composed of families with equivalent proportions across algal genomes. Cluster 3 is composed of families present in the 7 algae but in different proportions. Cluster 4 is composed of 3 families that are absent in stramenopiles

Fig. 5

Percentages of MYB-SHAQKYF among MYB-related TFs in algae

Fig. 6

Expansion, gain and loss of TF families during the evolutionary history of microalgae