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are a group of oleaginous microalgae that harbor an expanded array of lipid-synthesis related genes, yet how they are transcriptionally regulated remains unknown.Here a phylogenomic approach was employed to identify and functionally annotate the transcriptional factors (TFs) and TF binding-sites (TFBSs) in N. Among 36 microalgae and higher plants genomes, a two-fold reduction in the number of TF families plus a seven-fold decrease of average family-size in Nannochloropsis, Rhodophyta and Chlorophyta were observed.15 R2R3-MYB genes and 8 R1R2R3-MYB genes in IMET1), which appears to support the hypothesis of “loss” instead of “gain” in higher plants.It has been proposed that alterations in the expression of TF-encoding genes serve as one major source of the diversity and changes that underlie higher plant evolution, however the potential link between genome-wide TF-family profiles and plant evolution remains elusive.

Comparison of the IMET1 TFs and TFBSs to the reference plant TF-TFBS motif pairs in TRANSFAC enabled us to predict 78 interaction pairs between a TF and a TFBS motif, which consisted of 34 TFs (with 11 TFs potentially involved in the TAG biosynthesis pathway), 30 TFBSs and 950 target genes.As a result, several public databases of plant TFs have been established, such as Plant TFDB (v. These databases have cataloged the predicted TFs of over 50 species from the main lineages of the plant kingdom, including green algae, moss, fern, gymnosperm and angiosperm.We first performed a genome-wide identification of TFs in N. The results revealed 125, 119 and 85 TFs in the three Nannochloropsis strains respectively (1.26%, 0.99% and 0.94% of their proteomes; Supplemental Table S1, Supplemental Dataset S1).However, the molecular and cellular mechanisms underlying lipid metabolism in microalgae are still elusive, which has hampered rational approaches to screen for or genetically engineer superior production strains.Moreover, identification of the transcriptional factors (TF; trans elements) and their cognate transcriptional factor binding-sites (TFBS; cis elements) is one of the first steps in dissecting and engineering the regulatory network for enhanced productivity of the target molecules.

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