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Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis
Hu, Jianqiang1,2; Wang, Dongmei1; Li, Jing1,2; Jing, Gongchao1; Ning, Kang1; Xu, Jian1
2014-06-26
Source PublicationSCIENTIFIC REPORTS
Volume4
AbstractNannochloropsis spp. 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. oceanica IMET1. 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. The degree of similarity in TF-family profiles is indicative of the phylogenetic relationship among the species, suggesting co-evolution of TF-family profiles and species. Furthermore, comparative analysis of six Nannochloropsis genomes revealed 68 "most-conserved" TFBS motifs, with 11 of which predicted to be related to lipid accumulation or photosynthesis. Mapping the IMET1 TFs and TFBS motifs to the reference plant TF-"TFBS motif" relationships in TRANSFAC enabled the prediction of 78 TF-"TFBS motif" interaction pairs, which consisted of 34 TFs (with 11 TFs potentially involved in the TAG biosynthesis pathway), 30 TFBS motifs and 2,368 regulatory connections between TFs and target genes. Our results form the basis of further experiments to validate and engineer the regulatory network of Nannochloropsis spp. for enhanced biofuel production.
SubtypeArticle
WOS HeadingsScience & Technology
DOI10.1038/srep05454
WOS KeywordREGULATORY ELEMENTS ; CHLAMYDOMONAS-REINHARDTII ; ESCHERICHIA-COLI ; GENE-REGULATION ; ARABIDOPSIS ; DATABASE ; DISCOVERY ; EVOLUTION ; SEQUENCE ; PREDICTION
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000337892000003
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qibebt.ac.cn/handle/337004/6304
Collection单细胞中心组群
Affiliation1.Chinese Acad Sci, Qingdao Inst BioEnergy & Bioproc Technol, Single Cell Ctr, CAS Key Lab Biofuels & Shandong Key Lab Energy Ge, Qingdao 266101, Shandong, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
Recommended Citation
GB/T 7714
Hu, Jianqiang,Wang, Dongmei,Li, Jing,et al. Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis[J]. SCIENTIFIC REPORTS,2014,4.
APA Hu, Jianqiang,Wang, Dongmei,Li, Jing,Jing, Gongchao,Ning, Kang,&Xu, Jian.(2014).Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis.SCIENTIFIC REPORTS,4.
MLA Hu, Jianqiang,et al."Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis".SCIENTIFIC REPORTS 4(2014).
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