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Identification of Dof transcription factors in ramie (Boehmeria nivea L. Gaud) and their expression in response to different nitrogen treatments.

ABSTRACT: 19 DNA binding with one finger (Dof) transcription factor genes were identified from genome and transcriptome data of ramie (Boehmeria nivea L. Gaud). Chemical character, subnuclear localization, motif analysis, phylogenetic analysis, and tissue-specific analysis were performed. To select BnDof genes participating in nitrogen metabolism, we analyzed the expression patterns of BnDof genes in different nitrogen conditions (N0, N4, N8, and N12) in different tissues. As a result, eight BnDof genes were identified. BnDof07 (stem) and BnDof14 (root) had higher expression levels in N0 and N4, and BnDof15 (stem and leaves) and BnDof18 (stem) both exhibited the highest expression level in N0, suggesting that these four genes may take part in nitrogen stress. In the leaves, BnDof01, BnDof06, BnDof09, and BnDof19 expression levels were higher in N8 and N12 but lower in N0 and N4. The present findings provide insights into nitrogen metabolism in ramie highlighting the need to investigate this aspect in further detail in future studies.

SUBMITTER: Xu X

PROVIDER: S-EPMC6251796 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Identification of Dof transcription factors in ramie (Boehmeria nivea L. Gaud) and their expression in response to different nitrogen treatments.

Xu Xiaomin X Li Fu F Wang Yanzhou Y Tang Shouwei S Dai Qiuzhong Q Zhu Siyuan S Liu Touming T

3 Biotech 20181123 12

19 DNA binding with one finger (Dof) transcription factor genes were identified from genome and transcriptome data of ramie (Boehmeria nivea L. Gaud). Chemical character, subnuclear localization, motif analysis, phylogenetic analysis, and tissue-specific analysis were performed. To select BnDof genes participating in nitrogen metabolism, we analyzed the expression patterns of BnDof genes in different nitrogen conditions (N0, N4, N8, and N12) in different tissues. As a ...[more]

PMID: 30498669

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Project description:BackgroundRamie fiber extracted from stem bark is one of the most important natural fibers. Drought is a main environment stress which severely inhibits the stem growth of ramie and leads to a decrease of the fiber yield. The drought stress-regulatory mechanism of ramie is poorly understood.ResultUsing Illumina sequencing, approximately 4.8 and 4.7 million (M) 21-nt cDNA tags were respectively sequenced in the cDNA libraries derived from the drought-stressed ramie (DS) and the control ramie under well water condition (CO). The tags generated from the two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in the two libraries revealed that there were 1516 potential drought stress-responsive genes, in which 24 genes function as transcription factor (TF). Among these 24 TFs, the unigene19721 encoding the DELLA protein which is a key negative regulator in gibberellins (GAs) signal pathway was probably markedly up-regulated under water stress for a increase of tag abundance in DS library, which is possibly responsible for the inhibition of the growth of drought-stressed ramie. In order to validate the change of expression of these potential stress-responsive TFs under water deficit condition, the unigene19721 and another eleven potential stress-responsive TFs were chosen for further expression analysis in well-watered and drought-stressed ramie by real-time quantitative PCR (qRT-PCR) and the result showed that all 12 TFs were authentically involved in the response of drought stress.ConclusionIn this study, twelve TFs involving in the response of drought stress were first found by Illumina tag-sequencing and qRT-PCR in ramie. The discovery of these drought stress-responsive TFs will be helpful for further understanding the drought stress-regulatory mechanism of ramie and improving the drought tolerance ability of ramie.

Project description:BACKGROUND:Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie. RESULTS:In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER. CONCLUSIONS:Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.

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Dataset Information

Identification of Dof transcription factors in ramie (Boehmeria nivea L. Gaud) and their expression in response to different nitrogen treatments.

Publications

Identification of Dof transcription factors in ramie (<i>Boehmeria nivea</i> L. Gaud) and their expression in response to different nitrogen treatments.

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