scholarly journals Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Tissue Specificity ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background Xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in cell wall reconstruction and stress resistance in plants. However, the detailed characteristics of XTH family genes and their expression pattern under salt stress have not been reported in poplar. Results In this study, a total of 43 PtrXTH genes were identified from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoters of the PtrXTH genes contain mutiple cis-acting elements related to growth and development and stress responses. Collinearity analysis revealed that the XTH genes from poplar has an evolutionary relationship with other six species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Based on RNA-Seq analysis, the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, there are11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress. In addition, the accuracy of RNA-Seq results was verified by RT-qPCR. Conclusion All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study will lay a theoretical foundation for further study on molecular function of XTH genes in poplar.

scholarly journals Genome-wide Identification and Expression Analysis of the Eyloglucan Endotransglucosylase/hydrolase Gene Family in Poplar

2021 ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Promoter Regions ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background: Xyloglucan endotransglucosylase/hydrolase (XTH) plays an important role in the process of plant cell wall reconstruction, and also involved in plants stress resistance. However, its characteristics of XTH family genes have not been reported in poplar. Results: In this study, we found 43 PtrXTH genes from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoter regions of the PtrXTH genes contain many cis-acting elements related to growth and development and adverse stresses responses. Collinearity analysis revealed that the XTH family from poplarhave an evolutionary relationship with other five species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Through RNA-Seq analysis, we found that the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, we found 11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress, and verified the accuracy of RNA-Seq analysis by RT-qPCR.Conclusion: All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study laid a theoretical foundation for further study on the functions of XTH genes in poplar.

scholarly journals Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

2021 ◽  
Author(s):  
Zhen Tian ◽  
Xiaodong Qin ◽  
Hui Wang ◽  
Ji Li ◽  
Jinfeng Chen
Keyword(s):  
Floral Induction ◽  
Structural Characteristics ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Biological Functions ◽  
Promoter Regions ◽  
Cucumis Sativus L ◽  
Cis Acting ◽  
Genome Wide ◽  
Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

scholarly journals Global identification and analysis of microRNAs involved in salt stress responses in two alfalfa (Medicago sativa ‘Millennium’) lines

2020 ◽  
Vol 100 (4) ◽  
pp. 445-455
Author(s):  
Jin Ma ◽  
Yichun Wang ◽  
Jiayun Li
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Salt Stress Response ◽  
Differentially Expressed Mirnas ◽  
Relative Water ◽  
Global Identification ◽  
Relative Electrical Conductivity

Alfalfa is an important economic crop; a mutant (M) strain was identified during planting and production. M plants consistently had better relative water content and relative electrical conductivity under higher salt conditions compared with the wild type (WT) plants, suggesting that M plants have higher tolerance for salt. To understand the microRNAs (miRNAs) involved in salt stress response in alfalfa, 128 miRNAs were identified from the WT and M alfalfa plants under normal and saline conditions. Of the 128 miRNAs, 29 and 23 differentially expressed miRNAs were identified in the M vs. WT control (M-CK vs. WT-CK) and salt-stressed M vs. WT (M-salt vs. WT-salt) comparison, respectively. These miRNAs responded to salt stress and showed different expression patterns after salt treatment. Their potential target genes were predicted and further analysed by GO classification and KEGG pathway analysis, where the majority of target genes were associated with plant growth and development, and exhibited significant changes in WT and M plants. In addition, compared with the WT plants, miR172-CNGC, miR319-CAX2, miR408-NHX and miR2590-CHX14/15 showed significant upregulation in M alfalfa plants, suggesting that M plants have higher ion transport levels. The differential expression profiles of miRNAs and putative target genes were further validated by quantitative real-time polymerase chain reaction. It is speculated that these miRNAs are involved in the increased salt tolerance of the M alfalfa plants.

scholarly journals Differential Regulation of NAPDH Oxidases in Salt-Tolerant Eutrema salsugineum and Salt-Sensitive Arabidopsis thaliana

2021 ◽  
Vol 22 (19) ◽  
pp. 10341
Author(s):  
Maria Pilarska ◽  
Dorothea Bartels ◽  
Ewa Niewiadomska
Keyword(s):  
Arabidopsis Thaliana ◽  
Salt Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Cis Acting ◽  
Promoter Sequences ◽  
Eutrema Salsugineum ◽  
Gene Expression Analyses ◽  
Hormone Responses ◽  
In Silico Analyses

Reactive oxygen species (ROS) signalling is crucial in modulating stress responses in plants, and NADPH oxidases (NOXs) are an important component of signal transduction under salt stress. The goal of this research was to investigate whether the regulation of NOX-dependent signalling during mild and severe salinity differs between the halophyte Eutrema salsugineum and the glycophyte Arabidopsis thaliana. Gene expression analyses showed that salt-induced expression patterns of two NOX genes, RBOHD and RBOHF, varied between the halophyte and the glycophyte. Five days of salinity stimulated the expression of both genes in E. salsugineum leaves, while their expression in A. thaliana decreased. This was not accompanied by changes in the total NOX activity in E. salsugineum, while the activity in A. thaliana was reduced. The expression of the RBOHD and RBOHF genes in E. salsugineum leaves was induced by abscisic acid (ABA) and ethephon spraying. The in silico analyses of promoter sequences of RBOHD and RBOHF revealed multiple cis-acting elements related to hormone responses, and their distribution varied between E. salsugineum and A. thaliana. Our results indicate that, in the halophyte E. salsugineum, the maintenance of the basal activity of NOXs in leaves plays a role during acclimation responses to salt stress. The different expression patterns of the RBOHD and RBOHF genes under salinity in E. salsugineum and A. thaliana point to a modified regulation of these genes in the halophyte, possibly through ABA- and/or ethylene-dependent pathways.

scholarly journals Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10934
Author(s):  
Ruihua Wang ◽  
Taili Han ◽  
Jifeng Sun ◽  
Ligong Xu ◽  
Jingjing Fan ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Rapa ◽  
Expression Patterns ◽  
Structural Evolution ◽  
Amino Acid Residues ◽  
Rna Seq ◽  
Cis Acting ◽  
Genome Wide ◽  
Genome Triplication

Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.

scholarly journals Characterization of MATE Gene Family And Its Role In Drought, Heat, And Salt Tolerance In Wheat (Triticum Aestivum L.)

2021 ◽  
Author(s):  
Joseph Noble Amoah ◽  
Yong Weon Seo
Keyword(s):  
Salt Stress ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Stress Conditions ◽  
Crop Species ◽  
Expression Levels ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome

Abstract To explore the response of multidrug and toxic compound extrusion (MATE) proteins to drought, heat, and salt stress in wheat, a genome-wide identification and expression study was performed. 20 MATE genes located on 4 of the 12 chromosomes were identified and categorized into four (I-1V) subfamilies, based on phylogenetic analysis. Wheat MATE family expansion was primarily driven by whole-genome duplication (WGD) and tandem events. In the same subfamily, gene exon-intron structures and motif composition are more similar. TaMATE genes had cis-acting elements that were implicated in stress and defense response. Tae-miR5175e was identified as the highly expressed miRNA that targets TaMATEs by miRNA prediction. When compared to controls, the relative expression patterns of seven TaMATE genes were substantially elevated during drought stress. TaMATE2, 10, 13, and 14 expression levels considerably elevated after 15 days (d) of heat stress, whereas TaMATE2, 14, 18, and 20 expression levels were highly upregulated following 15 d of salt stress treatment, indicating the crucial role of TaMATEs under these abiotic stress conditions. Furthermore, drought, heat, and salt stress decreased wheat water content, but increased malondialdehyde (MDA), electrolyte leakage (EL), and proline content, whereas the expression of the 7 putative MATE genes was correlated with physio-biochemical indicators of these stress conditions. The findings contribute to a better understanding of the complexities of MATEs and present a theoretical base for future MATE gene discovery and application in wheat and other crop species.

Combined RNA-seq, small RNA and degradome sequencing approaches insights into salt-stress responses in Beta vulgaris

2019 ◽  
Author(s):  
Junliang Li ◽  
Jie Cui ◽  
Dayou Cheng ◽  
Cuihong Dai ◽  
Tianjiao Liu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Beta Vulgaris ◽  
Small Rna ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Salt Stress Response ◽  
Degradome Sequencing ◽  
A Genome

Abstract Background Salinity is one of the most serious threat to agriculture worldwide. Sugar beet is an important sugar-yielding crop and has a certain tolerance to salt. While a genome-wide analysis of genes involved in salt-stress remains largely unknown in B. vulgaris. Results Three high-throughput sequencing approaches, namely, RNA-seq, small RNA and degradome sequencing were used to exploring the molecular basis of salt-resistance in beta vulgaris. A total of 12 230 differentially expressed genes were identified, which were mainly related to transcription factors, protein kinases, and enzymes. The small RNA sequencing resulted in the identification of 476 miRNAs included 219 known and 257 novel miRNAs, of which 130 were differentially expressed under salt-stress. A total of 2534 targets were predicted for 317 miRNAs by bioinformatics and degradome sequencing. Functional analysis of these targets suggested that miRNA-mediated post-transcriptional regulation plays a crucial role in transcriptional reprogramming under stress. The combination analysis of multi-omics revealed 209 negative correlation mRNA-miRNA pairs. All these data were used to construct a hypothetical regulatory network of beta vulgaris in response to salt stress. Conclusion These components and the preliminary network provides better insights into the molecular mechanism of salt-stress response, and also offers candidate genes for beet improvement.

scholarly journals Calcium-Dependent Protein Kinase Genes in Glycyrrhiza Uralensis Appear to be Involved in Promoting the Biosynthesis of Glycyrrhizic Acid and Flavonoids under Salt Stress

Molecules ◽  
2019 ◽  
Vol 24 (9) ◽  
pp. 1837 ◽  
Author(s):  
Xuechen Tong ◽  
Aiping Cao ◽  
Fei Wang ◽  
Xifeng Chen ◽  
Shuangquan Xie ◽  
...  
Keyword(s):  
Salt Stress ◽  
Glycyrrhizic Acid ◽  
Expression Patterns ◽  
Glycyrrhiza Uralensis ◽  
Calcium Signal ◽  
Cis Acting ◽  
Calcium Dependent ◽  
Genome Wide ◽  
A Genome ◽  
Dependent Protein

As calcium signal sensors, calcium-dependent protein kinases (CPKs) play vital roles in stimulating the production of secondary metabolites to participate in plant development and response to environmental stress. However, investigations of the Glycyrrhiza uralensis CPK family genes and their multiple functions are rarely reported. In this study, a total of 23 GuCPK genes in G. uralensis were identified, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, and promoter cis-acting elements were analyzed. Ten GuCPKs showed root-specific preferential expressions, and GuCPKs indicated different expression patterns under treatments of CaCl2 and NaCl. In addition, under 2.5 mM of CaCl2 and 30 mM of NaCl treatments, the diverse, induced expression of GuCPKs and significant accumulations of glycyrrhizic acid and flavonoids suggested the possible important function of GuCPKs in regulating the production of glycyrrhizic acid and flavonoids. Our results provide a genome-wide characterization of CPK family genes in G. uralensis, and serve as a foundation for understanding the potential function and regulatory mechanism of GuCPKs in promoting the biosynthesis of glycyrrhizic acid and flavonoids under salt stress.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

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