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Nannochloropsis spp. are a group of oleaginous microalgae that harbor an expanded array of lipid-synthesis related genes, yet how they were transcriptionally regulated remain unknown. Here we present a genome-wide in silico map of TFs and TFBSs and a computationally predicted, preliminary regulatory network that link TFs and target genes in Nannochloropsis. First, the TF-encoding genes in the genomes of N.oceanica IMET1, N.oceanica CCMP1779 and N.gaditana CCMP526 were identified. 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 apparent, as compared to those of the surveyed higher plants. The degree of similarity in TF-family profiles was found to be indicative of the phylogenetic relationship among the species, suggesting that the co-evolution of species and their TF-family profiles occurred largely at the level of TF-family. Furthermore, comparative analysis of six sequenced Nannochloropsis genomes was performed using an improved pipeline based on MERCED algorithm for TFBS identification. This analysis revealed 68 “most-conserved” TFBSs, with 11 of which predicted to be related to lipid accumulation or photosynthesis. 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. These results form the basis of further experiments to validate and engineer the regulatory network of Nannochloropsis spp. for enhanced biofuel production.


Jianqiang Hu, Dongmei Wang, Jing Li, Gongchao Jing, Kang Ning, Jian Xu (2014) “Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae NannochloropsisScientific Reports, , 4 : 5454 | DOI: 10.1038/srep05454