Genome-wide analysis and transcriptional reprogrammings of MYB superfamily revealed positive insights into abiotic stress responses and anthocyanin accumulation in Carthamus tinctorius L.

2022 ◽  
Author(s):  
Yingqi Hong ◽  
Naveed Ahmad ◽  
Jianyi Zhang ◽  
Yanxi Lv ◽  
Xinyue Zhang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Carthamus Tinctorius ◽  
Anthocyanin Accumulation ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Analysis of Poplar SQUAMOSA-Promoter-Binding Protein (SBP) Family under Salt Stress

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 413
Author(s):  
Qing Guo ◽  
Li Li ◽  
Kai Zhao ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Growth And Development ◽  
Binding Protein ◽  
Gene Segment ◽  
Gene Expression Pattern ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein

SQUAMOSA promoter binding protein (SBP) is a kind of plant-specific transcription factor, which plays a crucial role in stress responses and plant growth and development by activating and inhibiting the transcription of multiple target genes. In this study, a total of 30 SBP genes were identified from Populus trichocarpa genome and randomly distributed on 16 chromosomes in poplar. According to phylogenetic analysis, the PtSBPs can be divided into six categories, and 14 out of the genes belong to VI. Furthermore, the SBP genes in VI were proved to have a targeting relationship with miR156. The homeopathic element analysis showed that the promoters of poplar SBP genes mainly contain the elements involved in growth and development, abiotic stress and hormone response. In addition, there existed 10 gene segment duplication events in the SBP gene duplication analysis. Furthermore, there were four poplar and Arabidopsis orthologous gene pairs among the poplar SBP members. What is more, poplar SBP gene family has diverse gene expression pattern under salt stress. As many as nine SBP members were responding to high salt stress and six members possibly participated in growth development and abiotic stress. Yeast two-hybrid experiments indicated that PtSBPs can form heterodimers to interact in the transcriptional regulatory networks. The genome-wide analysis of poplar SBP family will contribute to function characterization of SBP genes in woody plants.

scholarly journals Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

2020 ◽  
Author(s):  
Yue Liu ◽  
Nannan Liu ◽  
Xiong Deng ◽  
Dongmiao Liu ◽  
Mengfei Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Positive Selection ◽  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Acid Sites ◽  
Genome Wide Analysis ◽  
Dof Transcription Factor ◽  
Genome Wide

Abstract Background: DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results: Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions: The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

scholarly journals Genome-Wide Analysis of the Shi-Related Sequence Family and Functional Identification of GmSRS18 Involving in Drought and Salt Stresses in Soybean

2020 ◽  
Vol 21 (5) ◽  
pp. 1810
Author(s):  
Shu-Ping Zhao ◽  
Xin-Yuan Song ◽  
Lin-Lin Guo ◽  
Xiang-Zhan Zhang ◽  
Wei-Jun Zheng
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Functional Verification ◽  
Marker Genes ◽  
Functional Identification ◽  
Related Sequence ◽  
Genome Wide Analysis ◽  
Group I ◽  
Genome Wide

The plant-special SHI-RELATED SEQUENCE (SRS) family plays vital roles in various biological processes. However, the genome-wide analysis and abiotic stress-related functions of this family were less reported in soybean. In this work, 21 members of soybean SRS family were identified, which were divided into three groups (Group I, II, and III). The chromosome location and gene structure were analyzed, which indicated that the members in the same group may have similar functions. The analysis of stress-related cis-elements showed that the SRS family may be involved in abiotic stress signaling pathway. The analysis of expression patterns in various tissues demonstrated that SRS family may play crucial roles in special tissue-dependent regulatory networks. The data based on soybean RNA sequencing (RNA-seq) and quantitative Real-Time PCR (qRT-PCR) proved that SRS genes were induced by drought, NaCl, and exogenous abscisic acid (ABA). GmSRS18 significantly induced by drought and NaCl was selected for further functional verification. GmSRS18, encoding a cell nuclear protein, could negatively regulate drought and salt resistance in transgenic Arabidopsis. It can affect stress-related physiological index, including chlorophyll, proline, and relative electrolyte leakage. Additionally, it inhibited the expression levels of stress-related marker genes. Taken together, these results provide valuable information for understanding the classification of soybean SRS transcription factors and indicates that SRS plays important roles in abiotic stress responses.

Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses

2018 ◽  
Vol 45 (6) ◽  
pp. 2653-2669 ◽  
Author(s):  
Adwaita Prasad Parida ◽  
Utkarsh Raghuvanshi ◽  
Amit Pareek ◽  
Vijendra Singh ◽  
Rahul Kumar ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Fruit Development ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Genes Encoding

scholarly journals Genome-Wide Analysis of DEAD-box RNA Helicase Family in Wheat (Triticum aestivum) and Functional Identification of TaDEAD-box57 in Abiotic Stress Responses

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing-Na Ru ◽  
Ze-Hao Hou ◽  
Lei Zheng ◽  
Qi Zhao ◽  
Feng-Zhi Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Survival Rates ◽  
Rna Helicase ◽  
Genome Wide Analysis ◽  
Dead Box ◽  
Genome Wide ◽  
Transgenic Lines

DEAD-box RNA helicases constitute the largest subfamily of RNA helicase superfamily 2 (SF2), and play crucial roles in plant growth, development, and abiotic stress responses. Wheat is one of the most important cereal crops in worldwide, and abiotic stresses greatly restrict its production. So far, the DEAD-box RNA helicase family has yet to be characterized in wheat. Here, we performed a comprehensive genome-wide analysis of the DEAD-box RNA helicase family in wheat, including phylogenetic relationships, chromosomal distribution, duplication events, and protein motifs. A total of 141 TaDEAD-box genes were identified and found to be unevenly distributed across all 21 chromosomes. Whole genome/segmental duplication was identified as the likely main driving factor for expansion of the TaDEAD-box family. Expression patterns of the 141 TaDEAD-box genes were compared across different tissues and under abiotic stresses to identify genes to be important in growth or stress responses. TaDEAD-box57-3B was significantly up-regulated under multiple abiotic stresses, and was therefore selected for further analysis. TaDEAD-box57-3B was localized to the cytoplasm and plasma membrane. Ectopic expression of TaDEAD-box57-3B in Arabidopsis improved tolerance to drought and salt stress as measured by germination rates, root lengths, fresh weights, and survival rates. Transgenic lines also showed higher levels of proline and chlorophyll and lower levels of malonaldehyde (MDA) than WT plants in response to drought or salt stress. In response to cold stress, the transgenic lines showed significantly better growth and higher survival rates than WT plants. These results indicate that TaDEAD-box57-3B may increase tolerance to drought, salt, and cold stress in transgenic plants through regulating the degree of membrane lipid peroxidation. This study provides new insights for understanding evolution and function in the TaDEAD-box gene family.

scholarly journals Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

2019 ◽  
Author(s):  
Yue Liu ◽  
Nannan Liu ◽  
Xiong Deng ◽  
Dongmiao Liu ◽  
Mengfei Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Positive Selection ◽  
Gene Family ◽  
Stress Responses ◽  
Functional Divergence ◽  
Acid Sites ◽  
Genome Wide Analysis ◽  
Dof Transcription Factor ◽  
Genome Wide

Abstract Background DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and RT-qPCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

scholarly journals Genome-wide investigation of Hydroxycinnamoyl CoA: Shikimate Hydroxycinnamoyl Transferase (HCT) gene family in Carthamus tinctorius L.

2021 ◽  
Vol 49 (3) ◽  
pp. 12489
Author(s):  
Sun FAN ◽  
Naveed AHMAD ◽  
Jin LIBO ◽  
Zhang XINYUE ◽  
Ma XINTONG ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Carthamus Tinctorius ◽  
Plant Growth And Development ◽  
Monolignol Biosynthesis ◽  
Genome Wide ◽  
Wide Range

Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) is mainly associated with monolignol biosynthesis, a central precursor to producing guaiacyl and syringyl lignins in plants. However, the explicit regulatory mechanism of HCT-mediated monolignol biosynthesis in plants still remained unclear. Here, the genome-wide analysis of the HCT gene family in Carthamus tinctorius as a target for understanding growth, development, and stress-responsive mechanisms was investigated. A total of 82 CtHCT genes were identified and characterized. Most of the CtHCTs proteins demonstrated the presence of two common conserved domains, including HXXXD and DFGWG. In addition, the conserved structure of protein motifs, PPI network, cis-regulatory units, and gene structure analysis demonstrated several genetic determinants reflecting the wide range of functional diversity of CtHCT-encoding genes. The observed expression analysis of CtHCT genes in different flowering stages under normal conditions partially highlighted their putative roles in plant growth and development pathways. Moreover, CtHCT genes appeared to be associated with abiotic stress responses as validated by the expression profiling in various flowering phases under light irradiation and MeJA treatment. Altogether, these findings provide new insights into identifying crucial molecular targets associated with plant growth and development and present practical information for understanding abiotic stress-responsive mechanisms in plants.

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