scholarly journals Genome-Wide Characterization, Evolution, and Expression Profiling of VQ Gene Family in Response to Phytohormone Treatments and Abiotic Stress in Eucalyptus grandis

2019 ◽  
Vol 20 (7) ◽  
pp. 1765 ◽  
Author(s):  
Huifang Yan ◽  
Yujiao Wang ◽  
Bing Hu ◽  
Zhenfei Qiu ◽  
Bingshan Zeng ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Breeding ◽  
Eucalyptus Grandis ◽  
Pcr Analysis ◽  
Quantitative Real Time Pcr ◽  
Motif Analysis ◽  
Comprehensive Overview ◽  
Abiotic Stressors ◽  
Genome Wide ◽  
Gene Expression Analyses

VQ genes play important roles in plant development, growth, and stress responses. However, little information regarding the functions of VQ genes is available for Eucalyptus grandis. In our study, genome-wide characterization and identification of VQ genes were performed in E. grandis. Results showed that 27 VQ genes, which divided into seven sub-families (I–VII), were found, and all but two VQ genes showed no intron by gene structure and conserved motif analysis. To further identify the function of EgrVQ proteins, gene expression analyses were also developed under hormone treatments (brassinosteroids, methyl jasmonate, salicylic acid, and abscisic acid) and abiotic conditions (salt stress, cold 4 °C, and heat 42 °C). The results of a quantitative real-time PCR analysis indicated that the EgrVQs were variously expressed under different hormone treatments and abiotic stressors. Our study provides a comprehensive overview of VQ genes in E. grandis, which will be beneficial in the molecular breeding of E. grandis to promote its resistance to abiotic stressors; the results also provide a basis from which to conduct further investigation into the functions of VQ genes in E. grandis.

scholarly journals Genome-Wide Identification and Transcriptional Expression Analysis of Cucumber Superoxide Dismutase (SOD) Family in Response to Various Abiotic Stresses

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Yong Zhou ◽  
Lifang Hu ◽  
Hao Wu ◽  
Lunwei Jiang ◽  
Shiqiang Liu
Keyword(s):  
Superoxide Dismutase ◽  
Expression Analysis ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Promoter Sequence ◽  
Pcr Analysis ◽  
Motif Analysis ◽  
Genome Wide ◽  
Potential Applications ◽  
Almost All

Superoxide dismutase (SOD) proteins are widely present in the plant kingdom and play important roles in different biological processes. However, little is known about the SOD genes in cucumber. In this study, night SOD genes were identified from cucumber (Cucumis sativus) using bioinformatics-based methods, including 5 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Phylogenetic analyses with SODs from cucumber and several other species revealed that these SOD proteins can be traced back to two ancestral SODs before the divergence of monocot and dicot plants. Many cis-elements related to stress responses and plant hormones were found in the promoter sequence of each CsSOD gene. Gene expression analysis revealed that most of the CsSOD genes are expressed in almost all the tested tissues. qRT-PCR analysis of 8 selected CsSOD genes showed that these genes could respond to heat, cold, osmotic, and salt stresses. Our results provide a basis for further functional research on SOD gene family in cucumber and facilitate their potential applications in the genetic improvement of cucumber.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8471 ◽  
Author(s):  
Lei Ling ◽  
Yue Qu ◽  
Jintao Zhu ◽  
Dan Wang ◽  
Changhong Guo
Keyword(s):  
Cicer Arietinum ◽  
Medicago Truncatula ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Biotic And Abiotic Stress ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Specific Proteins ◽  
Solid Foundation ◽  
In Silico Analyses

Valine-glutamine (VQ) proteins are plant-specific proteins that play crucial roles in plant development as well as biotic and abiotic stress responses. VQ genes have been identified in various plants; however, there are no systematic reports in Cicer arietinum or Medicago truncatula. Herein, we identified 19 and 32 VQ genes in C. arietinum and M. truncatula, respectively. A total of these VQ genes were divided into eight groups (I–VIII) based on phylogenetic analysis. Gene structure analyses and motif patterns revealed that these VQ genes might have originated from a common ancestor. In silico analyses demonstrated that these VQ genes were expressed in different tissues. qRT-PCR analysis indicated that the VQ genes were differentially regulated during multiple abiotic stresses. This report presents the first systematic analysis of VQ genes from C. arietinum and M. truncatula and provides a solid foundation for further research of the specific functions of VQ proteins.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

2019 ◽  
Author(s):  
Yongbin Wang ◽  
Zhenfeng Jiang ◽  
Zhenxiang Li ◽  
Yuanling Zhao ◽  
Weiwei Tan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Domain ◽  
Genome Wide ◽  
Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

scholarly journals Genome-wide analysis of BURP genes and identification of a BURP-V gene RcBURP4 in Rosachienesis

2021 ◽  
Author(s):  
Lufeng Fu ◽  
Zhujun Zhang ◽  
Hai Wang ◽  
Xiaojuan Zhao ◽  
Lin Su ◽  
...  
Keyword(s):  
Stress Responses ◽  
Light Response ◽  
Regulatory Elements ◽  
Vital Role ◽  
Severe Drought ◽  
Comprehensive Overview ◽  
Genome Database ◽  
Genome Wide ◽  
Bioinformatic Approaches ◽  
The Rose

Abstract BURP proteins are unique to plants and may contribute greatly to growth, development, and stress responses of plants. Despite the vital role of BURP proteins, little is known about these proteins in rose (Rosa spp.). In the present study, nine genes belonging to the BURP family in R. chienesis were identified by using multiple bioinformatic approaches against the rose genome database. The nine RcBURPs, with diverse structures, were located on all chromosomes of the rose genome, except for Chr2 and Chr3. Phylogenic analysis revealed that these RcBURPs can be classified into eight subfamilies, including BNM2-like, PG1β-like, USP-like, RD22-like, BURP-V, BURP-VI, BURP-VII, and BURP-VIII. Conserved motif and exon-intron analyses indicated a conserved pattern within the same subfamily. The presumed cis-regulatory elements (CREs) within the promoter region of each RcBURP were analyzed and the results showed that all RcBURPs contained different types of CREs, including abiotic stress-, light response-, phytohormones response-, and plant growth and development-related CREs. Transcriptomic analysis revealed that a BURP-V member, RcBURP4, was induced in rose leaves and roots under mild and severe drought treatments. We then overexpressed RcBURP4 in Arabidopsis and examined its role under abscisic acid (ABA), NaCl, polyethylene glycol (PEG), and drought treatments. Furthermore, RcBURP4-silenced rose plants exhibited decreased tolerance to dehydration. The results obtained from this study provide the first comprehensive overview of RcBURPs and highlight the importance of RcBURP4 in rose plant.

scholarly journals Genome-wide analysis and expression characteristics of small auxin-up RNA (SAUR) genes in moso bamboo (Phyllostachys edulis)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 325-336 ◽  
Author(s):  
Qingsong Bai ◽  
Dan Hou ◽  
Long Li ◽  
Zhanchao Cheng ◽  
Wei Ge ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Shoot Growth ◽  
Subcellular Location ◽  
Moso Bamboo ◽  
Pcr Analysis ◽  
Phyllostachys Edulis ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
Gene Structures

Moso bamboo (Phyllostachys edulis) is well known for its rapid shoot growth. Auxin exerts pleiotropic effects on plant growth. The small auxin-up RNA (SAUR) genes are early auxin-responsive genes involved in plant growth. In total, 38 SAUR genes were identified in P. edulis (PheSAUR). A comprehensive overview of the PheSAUR gene family is presented, including the gene structures, phylogeny, and subcellular location predictions. A transcriptome analysis indicated that 37 (except PheSAUR18) of the PheSAUR genes were expressed during shoot growth process and that the PheSAUR genes were differentially expressed. Furthermore, quantitative real-time PCR analysis indicated that all of the PheSAUR genes could be induced in different tissues of seedlings and that 37 (except PheSAUR41) of the PheSAUR genes were up-regulated after indole-3-acetic acid (IAA) treatment. These results reveal a comprehensive overview of the PheSAUR gene family and may pave the way for deciphering their functions during bamboo development.

scholarly journals Genome-Wide Analysis of BURP Genes and Identification of a BURP-V Gene RcBURP4 in Rosa Chienesis

2021 ◽  
Author(s):  
Lufeng Fu ◽  
Zhujun Zhang ◽  
Hai Wang ◽  
Xiaojuan Zhao ◽  
Lin Su ◽  
...  
Keyword(s):  
Stress Responses ◽  
Light Response ◽  
Regulatory Elements ◽  
Vital Role ◽  
Severe Drought ◽  
Comprehensive Overview ◽  
Genome Database ◽  
Genome Wide ◽  
Leaves And Roots ◽  
The Rose

Abstract BURP proteins are unique to plants and may contribute greatly to growth, development, and stress responses of plants. Despite the vital role of BURP proteins, little is known about these proteins in rose (Rosa spp.). In the present study, nine genes belonging to the BURP family in R. chienesis were identified by using multiple bioinformatic approaches against the rose genome database. The nine RcBURPs, with diverse structures, were located on all chromosomes of the rose genome, except for Chr2 and Chr3. Phylogenic analysis revealed that these RcBURPs can be classified into eight subfamilies, including BNM2-like, PG1β-like, USP-like, RD22-like, BURP-V, BURP-VI, BURP-VII, and BURP-VIII. Conserved motif and exon-intron analyses indicated a conserved pattern within the same subfamily. The presumed cis-regulatory elements (CREs) within the promoter region of each RcBURP were analyzed and the results showed that all RcBURPs contained different types of CREs, including abiotic stress-, light response-, phytohormones response-, and plant growth and development-related CREs. Transcriptomic analysis revealed that a BURP-V member, RcBURP4, was induced in rose leaves and roots under mild and severe drought treatments. We then overexpressed RcBURP4 in Arabidopsis and examined its role under abscisic acid (ABA), NaCl, polyethylene glycol (PEG), and drought treatments. Nine stress-responsive genes expression were changed in RcBURP4-overexpressing leaves and roots. Furthermore, RcBURP4-silenced rose plants exhibited decreased tolerance to dehydration. The results obtained from this study provide the first comprehensive overview of RcBURPs and highlight the importance of RcBURP4 in rose plant.

scholarly journals Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11647
Author(s):  
Nida Mushtaq ◽  
Faiza Munir ◽  
Alvina Gul ◽  
Rabia Amir ◽  
Rehan Zafar Paracha
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Stress Responses ◽  
Functional Characterization ◽  
Domain Architecture ◽  
Plant Tolerance ◽  
Motif Analysis ◽  
Genome Wide ◽  
Responsive Element ◽  
Dreb Gene

Background The dehydration responsive element-binding (DREB) gene family plays a crucial role as transcription regulators and enhances plant tolerance to abiotic stresses. Although the DREB gene family has been identified and characterized in many plants, knowledge about it in Solanum tuberosum (Potato) is limited. Results In the present study, StDREB gene family was comprehensively analyzed using bioinformatics approaches. We identified 66 StDREB genes through genome wide screening of the Potato genome based on the AP2 domain architecture and amino acid conservation analysis (Valine at position 14th). Phylogenetic analysis divided them into six distinct subgroups (A1–A6). The categorization of StDREB genes into six subgroups was further supported by gene structure and conserved motif analysis. Potato DREB genes were found to be distributed unevenly across 12 chromosomes. Gene duplication proved that StDREB genes experienced tandem and segmental duplication events which led to the expansion of the gene family. The Ka/Ks ratios of the orthologous pairs also demonstrated the StDREB genes were under strong purification selection in the course of evolution. Interspecies synteny analysis revealed 45 and 36 StDREB genes were orthologous to Arabidopsis and Solanum lycopersicum, respectively. Moreover, subcellular localization indicated that StDREB genes were predominantly located within the nucleus and the StDREB family’s major function was DNA binding according to gene ontology (GO) annotation. Conclusions This study provides a comprehensive and systematic understanding of precise molecular mechanism and functional characterization of StDREB genes in abiotic stress responses and will lead to improvement in Solanum tuberosum.

scholarly journals Genome-wide characterization and expression profiling analysis of the xyloglucan endotransglycosylase/hydrolase gene family in Brachypodium distachyon

2020 ◽  
Author(s):  
Hongyan Shen ◽  
Qiuping Tan ◽  
Wei Xiao ◽  
Wenpeng Deng ◽  
Xiaoyan Yu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Expression Patterns ◽  
Growth Stages ◽  
Xyloglucan Endotransglycosylase ◽  
Motif Analysis ◽  
Group I ◽  
Genome Wide

Abstract Background: Xyloglucan endotransglucosylase/hydrolases (XTHs) are a class of cell wall-associated enzymes involved in the construction and remodeling of cellulose/xyloglucan crosslinks. However, knowledge of this gene family in the model monocot Brachypodium distachyon is limited. Results: A total of 29 BdXTH genes were identified from the reference genome, and these were further divided into three main groups (Group I/II, Group III, and the Ancestral Group) through comparative phylogenetic analysis. Gene structure and protein motif analysis indicate that closely clustered BdXTH genes are relatively conserved within each group. A highly conserved amino acid domain (DEIDFEFLG) responsible for catalytic activity was identified in all BdXTH proteins. We detected three pairs of segmentally duplicated BdXTH genes and five groups of tandemly duplicated BdXTH genes, which have played important roles in the expansion of the BdXTH gene family. Cis -elements related to hormones, growth, and abiotic stress responses were identified in the promoters of each BdXTH gene. Most BdXTH genes have distinct expression patterns in different tissues and growth stages. Furthermore, when roots were treated with two abiotic stresses (salinity and drought) and four plant hormones (IAA, auxin; GA3, gibberellin; ABA, abscisic acid and BR, brassinolide), the expression levels of many BdXTH genes changed significantly, suggesting possible roles in response to various environmental stimuli and plant hormones. Conclusion: In this study, we performed genome-wide identification, characterization, and expression pattern analysis of the XTH gene family in Brachypodium, which provide valuable information for further elucidation of the biological functions of BdXTH genes in the model grass B. distachyon.

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
Yue Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background: Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber (Cucumis sativus L.). Results: In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (CsLecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion: This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLKs might play in the life cycle of cucumber.

scholarly journals Mulberry EIL3 confers salt and drought tolerances and modulates ethylene biosynthetic gene expression

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6391 ◽  
Author(s):  
Changying Liu ◽  
Jun Li ◽  
Panpan Zhu ◽  
Jian Yu ◽  
Jiamin Hou ◽  
...  
Keyword(s):  
Stress Responses ◽  
Abiotic Stresses ◽  
Woody Plant ◽  
Pcr Analysis ◽  
Biosynthetic Gene ◽  
Quantitative Real Time Pcr ◽  
Biosynthetic Genes ◽  
Gene Encoding ◽  
Salt And Drought Stresses ◽  
Plant Abiotic Stress

Ethylene regulates plant abiotic stress responses and tolerances, and ethylene-insensitive3 (EIN3)/EIN3-like (EIL) proteins are the key components of ethylene signal transduction. Although the functions of EIN3/EIL proteins in response to abiotic stresses have been investigated in model plants, little is known in non-model plants, including mulberry (Morus L.), which is an economically important perennial woody plant. We functionally characterized a gene encoding an EIN3-like protein from mulberry, designated as MnEIL3. A quantitative real-time PCR analysis demonstrated that the expression of MnEIL3 could be induced in roots and shoot by salt and drought stresses. Arabidopsis overexpressing MnEIL3 exhibited an enhanced tolerance to salt and drought stresses. MnEIL3 overexpression in Arabidopsis significantly upregulated the transcript abundances of ethylene biosynthetic genes. Furthermore, MnEIL3 enhanced the activities of the MnACO1 and MnACS1 promoters, which respond to salt and drought stresses. Thus, MnEIL3 may play important roles in tolerance to abiotic stresses and the expression of ethylene biosynthetic genes.

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