scholarly journals Transcriptome analysis of newly classified bZIP transcription factors of Brassica rapa in cold stress response

Genomics ◽  
2014 ◽  
Vol 104 (3) ◽  
pp. 194-202 ◽  
Author(s):  
Indeok Hwang ◽  
Hee-Jeong Jung ◽  
Jong-In Park ◽  
Tae-Jin Yang ◽  
Ill-Sup Nou
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Cold Stress ◽  
Brassica Rapa ◽  
Transcriptome Analysis ◽  
Bzip Transcription Factors

scholarly journals Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1867
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Jiatong Wei ◽  
Kewei Cai ◽  
Hongzhi Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Cold Stress ◽  
Gene Family ◽  
Gene Families ◽  
Regulatory Function ◽  
Wrky Gene ◽  
Wrky Transcription Factors ◽  
Biotic Stresses ◽  
Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

scholarly journals Genome-Wide Identification and Characterization of bZIP Transcription Factors inBrassica oleraceaunder Cold Stress

2016 ◽  
Vol 2016 ◽  
pp. 1-18 ◽  
Author(s):  
Indeok Hwang ◽  
Ranjith Kumar Manoharan ◽  
Jong-Goo Kang ◽  
Mi-Young Chung ◽  
Young-Wook Kim ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Cold Stress ◽  
Stress Responses ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Amino Acid Sequence Similarity ◽  
Sequencing Data ◽  
Cold Response ◽  
Bzip Transcription Factors

Cabbages (Brassica oleraceaL.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsiveBolbZIPgenes were screened in inbred lines,BN106andBN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes,Bol008071,Bol033132, andBol042729, was significantly increased inBN107under cold conditions and was unchanged inBN106. The upregulation of these genes inBN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes,Bol033132has 97% sequence similarity toBra020735, which was identified in a screen for cold-related genes inB. rapaand a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses.

Citrus sinensis CBF1 Functions in Cold Tolerance by Modulating Putrescine Biosynthesis Through Regulation of ARGININE DECARBOXYLASE

2021 ◽  
Author(s):  
Jie Song ◽  
Hao Wu ◽  
Feng He ◽  
Jing Qu ◽  
Yue Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Transgenic Plants ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Arginine Decarboxylase ◽  
Wild Type ◽  
Shed Light

Abstract C-repeat (CRT) binding factors (CBFs) are well known to act as crucial transcription factors that function in cold stress response. Arginine decarboxylase (ADC)-mediated putrescine biosynthesis has been reported to be activated in plants exposed to cold conditions, but it remains elusive whether CBFs can regulate ADC expression and putrescine accumulation. In this study, we show that cold up-regulated ADC gene (CsADC) and elevation of endogenous putrescine content in sweet orange (Citrus sinensis). Promoter of CsADC contains two CRT sequences that are canonical elements recognized by CBFs. Sweet orange genome contains four CBFs (CsCBF1-4), in which CsCBF1 was significantly induced by cold. CsCBF1, located in the nucleus, was demonstrated to bind directly and specifically to the promoter of CsADC and acted as a transcriptional activator. Overexpression of CsCBF1 led to notable elevation of CsADC and putrescine level in sweet orange transgenic plants, along with remarkably enhanced cold tolerance, relative to the wild type (WT). However, pretreatment with D-arginine, an ADC inhibitor, caused prominent reduction of endogenous putrescine level in the overexpressing lines, accompanied by greatly compromised cold tolerance. Taken together, these results demonstrate that CBF1 of sweet orange directly regulates ADC expression and modulates putrescine synthesis for orchestrating the cold tolerance. Our findings shed light into the transcriptional regulation of putrescine accumulation through targeting the ADC gene in the presence of cold stress. Meanwhile, this study illustrates a new mechanism underlying the CBF-mediated cold stress response.

scholarly journals Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

2019 ◽  
Vol 20 (5) ◽  
pp. 1071 ◽  
Author(s):  
Li Ma ◽  
Jeffrey Coulter ◽  
Lijun Liu ◽  
Yuhong Zhao ◽  
Yu Chang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cold Stress ◽  
Brassica Rapa ◽  
Stress Responses ◽  
Ribosome Biogenesis ◽  
Physiological Activity ◽  
Growth Period ◽  
Ambient Air ◽  
Mapk Signaling ◽  
Winter Rapeseed

Low ambient air temperature limits the growth and selection of crops in cold regions, and cold tolerance is a survival strategy for overwintering plants in cold winters. Studies of differences in transcriptional levels of winter rapeseed (Brassica rapa L.) under cold stress can improve our understanding of transcript-mediated cold stress responses. In this study, two winter rapeseed varieties, Longyou-7 (cold-tolerant) and Lenox (cold-sensitive), were used to reveal morphological, physiological, and transcriptome levels after 24 h of cold stress, and 24 h at room temperature, to identify the mechanism of tolerance to cold stress. Compared to Lenox, Longyou-7 has a shorter growth period and greater belowground mass, and exhibits stronger physiological activity after cold stress. Subsequently, more complete genomic annotation was obtained by sequencing. A total of 10,251 and 10,972 differentially expressed genes (DEG) were identified in Longyou-7 and Lenox, respectively. Six terms closely related to cold stress were found by the Gene Ontology (GO) function annotation. Some of these terms had greater upregulated expression in Longyou-7, and the expression of these genes was verified by qRT-PCR. Most of these DEGs are involved in phenylpropanoid biosynthesis, plant hormone signal transduction, ribosome biogenesis, MAPK signaling pathway, basal transcription factors, and photosynthesis. Analysis of the genes involved in the peroxisome pathway revealed that Longyou-7 and Lenox may have different metabolic patterns. Some transcription factors may play an important role in winter rapeseed tolerance to cold stress, and Longyou-7 is slightly slower than Lenox. Our results provide a transcriptome database and candidate genes for further study of winter rapeseed cold stress.

scholarly journals Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Qi Yan ◽  
Fan Wu ◽  
Tiantian Ma ◽  
Xifang Zong ◽  
Qian Ma ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Response ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Basic Leucine Zipper ◽  
Phylogenetic Tree Analysis ◽  
Bzip Transcription Factors ◽  
Bzip Family

Abstract Background Transcription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However, no information is available for the bZIP family in Cleistogenes songorica, which is an important xerophytic and allotetraploid grass in desert grasslands. Results In this study, 86 CsbZIPs were identified in the allotetraploid C. songorica genome. For location analysis, CsbZIPs were distributed evenly across two subgenomes of C. songorica. Phylogenetic tree analysis among three species indicated that CsbZIPs were evolutionarily more closely related to OsbZIPs than AtbZIPs. Syntenic and phylogenetic analyses confirmed that the CsbZIPs were mainly expanded by whole-genome duplication events. Furthermore, it was determined that rice and C. songorica might have undergone purified selection during their long evolutionary history by calculating the Ks values and Ka/Ks ratios of orthologous gene pairs. By analysing the expression patterns of CsbZIPs in different tissues and under abiotic stresses, 21 CsbZIP genes were differentially expressed between chasmogamous (CH) and cleistogamous (CL) flowers, including two FLOWERING LOCUS D (FD) genes. In shoots and roots, 79.1 and 87.2% of the CsbZIP genes, respectively, displayed transcript changes under at least one stress treatment, such as heat, cold, drought and salt. Strikingly, 17 common CsbZIP genes showed differential expression under stress response and during CL flowering. Co-expression network, GO annotation and real-time quantitative reverse transcription PCR (qRT-PCR) analyses revealed a close relationship between CL flowering-associated genes and abiotic stress-related genes. Conclusions BZIP TFs were comprehensively analysed and identified in allotetraploid C. songorica. Our results provide insights into the evolutionary history of the bZIP family in C. songorica and provide abiotic stress-responsive and CL-associated candidate CsbZIP genes for potential applications in the genetic improvement of plants.

Dynamic transcriptome analysis reveals AP2/ERF transcription factors responsible for cold stress in rapeseed (Brassica napus L.)

2016 ◽  
Vol 291 (3) ◽  
pp. 1053-1067 ◽  
Author(s):  
Chunfang Du ◽  
Kaining Hu ◽  
Shuanshi Xian ◽  
Chunqing Liu ◽  
Jianchun Fan ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Brassica Napus ◽  
Cold Stress ◽  
Transcriptome Analysis ◽  
Brassica Napus L ◽  
Erf Transcription Factors

scholarly journals Transcriptome analysis and transcription factors responsive to drought stress in Hibiscus cannabinus

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8470
Author(s):  
Xia An ◽  
Guanrong Jin ◽  
Xiahong Luo ◽  
Changli Chen ◽  
Wenlue Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Transcriptome Analysis ◽  
Control Group ◽  
Response Mechanism ◽  
Control Groups ◽  
Stress Group ◽  
Significant Enrichment ◽  
And Control

Kenaf is an annual bast fiber crop. Drought stress influences the growth of kenaf stems and causes a marked decrease in fiber yield and quality. Research on the drought resistance of kenaf is therefore important, but limited information is available on the response mechanism of kenaf to drought stress. In this study, a transcriptome analysis of genes associated with the drought stress response in kenaf was performed. About 264,244,210 bp high-quality reads were obtained after strict quality inspection and data cleaning. Compared with the control group, 4,281 genes were differentially expressed in plants treated with drought stress for 7 d (the drought stress group). Compared with the control group, 605 genes showed differential expression in plants subjected to drought stress for 6 d and then watered for 1 d (the rewatering group). Compared with the rewatering group, 5,004 genes were differentially expressed in the drought stress group. In the comparisons between the drought stress and control groups, and between the drought stress and rewatering groups, the pathway that showed the most highly significant enrichment was plant hormone signal transduction. In the comparison between the rewatering and control groups, the pathways that showed the most highly significant enrichment were starch and sucrose metabolism. Eight transcription factors belonging to the AP2/ERF, MYB, NAC, and WRKY families (two transcription factors per family) detected in the leaf transcriptome were associated with the drought stress response. The identified transcription factors provide a basis for further investigation of the response mechanism of kenaf to drought stress.

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