scholarly journals Genome-wide identification, evolution, and expression of the SNARE gene family in wheat resistance to powdery mildew

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10788
Author(s):  
Guanghao Wang ◽  
Deyu Long ◽  
Fagang Yu ◽  
Hong Zhang ◽  
Chunhuan Chen ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Protein Function ◽  
Expression Patterns ◽  
Wheat Variety ◽  
Eukaryotic Cell ◽  
Snare Proteins ◽  
Phylogenetic Tree Analysis ◽  
Cis Acting ◽  
Genome Wide ◽  
Transport Vesicle

SNARE proteins mediate eukaryotic cell membrane/transport vesicle fusion and act in plant resistance to fungi. Herein, 173 SNARE proteins were identified in wheat and divided into 5 subfamilies and 21 classes. The number of the SYP1 class type was largest in TaSNAREs. Phylogenetic tree analysis revealed that most of the SNAREs were distributed in 21 classes. Analysis of the genetic structure revealed large differences among the 21 classes, and the structures in the same group were similar, except across individual genes. Excluding the first homoeologous group, the number in the other homoeologous groups was similar. The 2,000 bp promoter region of the TaSNARE genes were analyzed, and many W-box, MYB and disease-related cis-acting elements were identified. The qRT-PCR-based analysis of the SNARE genes revealed similar expression patterns of the same subfamily in one wheat variety. The expression patterns of the same gene in resistant/sensitive varieties largely differed at 6 h after infection, suggesting that SNARE proteins play an important role in early pathogen infection. Here, the identification and expression analysis of SNARE proteins provide a theoretical basis for studies of SNARE protein function and wheat resistance to powdery mildew.

scholarly journals Genome-wide identification of SNARE gene in plant and expression pattern of TaSNARE in wheat

2019 ◽  
Author(s):  
Guanghao Wang ◽  
Deyu Long ◽  
Fagang Yu ◽  
Hong Zhang ◽  
Chunhuan Chen ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Expression Patterns ◽  
Eukaryotic Cell ◽  
Snare Proteins ◽  
Snare Protein ◽  
Group 14 ◽  
Wheat Varieties ◽  
Cis Acting ◽  
Protein Receptor ◽  
Genome Wide

SNARE (Soluble N - ethylmaleimide - sensitive - factor attachment protein receptor) proteins are mainly mediated eukaryotic cell membrane fusion of vesicles transportation, also play an important role in plant resistance to fungal infection. In this study, 1342 SNARE proteins were identified in 18 plants. According to the reported research, it was splited into 5 subfamilies (Qa, Qb, Qc, Qb+Qc and R) and 21 classes. The number of SYP1 small classes in Qa is the largest (227), and Qb+Qc is the smallest (67). Secondly, through the analysis of phylogenetic trees, it was shown that the most SNAREs of 18 plants were distributed in 21 classes. Further analysis of the genetic structure showed that there was a large difference of 21 classes, and the structure of the same group was similar except for individual genes. In wheat, 173 SNARE proteins were identified, except for the first homologous group (14), and the number of others homologous groups were similar. The 2000bp promoter region upstream of wheat SNARE gene was analyzed, and a large number of W-box, MYB and disease-related cis-acting elements were found. The qRT-PCR results of the SNARE gene showed that the expression patterns of the same subfamily were similar in one wheat varieties. The expression patterns of the same gene in resistant/sensitive varieties were largely different at 6h after infection. This results might indicate that early stages of the SNARE protein in pathogen infection play an important role. In this study, the identification and expression analysis of the SNARE protein provides a theoretical basis for future studies on the function of the SNARE protein and wheat resistance to powdery mildew.

scholarly journals Genome-wide identification of SNARE gene in plant and expression pattern of TaSNARE in wheat

2019 ◽  
Author(s):  
Guanghao Wang ◽  
Deyu Long ◽  
Fagang Yu ◽  
Hong Zhang ◽  
Chunhuan Chen ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Expression Patterns ◽  
Eukaryotic Cell ◽  
Snare Proteins ◽  
Snare Protein ◽  
Group 14 ◽  
Wheat Varieties ◽  
Cis Acting ◽  
Protein Receptor ◽  
Genome Wide

SNARE (Soluble N - ethylmaleimide - sensitive - factor attachment protein receptor) proteins are mainly mediated eukaryotic cell membrane fusion of vesicles transportation, also play an important role in plant resistance to fungal infection. In this study, 1342 SNARE proteins were identified in 18 plants. According to the reported research, it was splited into 5 subfamilies (Qa, Qb, Qc, Qb+Qc and R) and 21 classes. The number of SYP1 small classes in Qa is the largest (227), and Qb+Qc is the smallest (67). Secondly, through the analysis of phylogenetic trees, it was shown that the most SNAREs of 18 plants were distributed in 21 classes. Further analysis of the genetic structure showed that there was a large difference of 21 classes, and the structure of the same group was similar except for individual genes. In wheat, 173 SNARE proteins were identified, except for the first homologous group (14), and the number of others homologous groups were similar. The 2000bp promoter region upstream of wheat SNARE gene was analyzed, and a large number of W-box, MYB and disease-related cis-acting elements were found. The qRT-PCR results of the SNARE gene showed that the expression patterns of the same subfamily were similar in one wheat varieties. The expression patterns of the same gene in resistant/sensitive varieties were largely different at 6h after infection. This results might indicate that early stages of the SNARE protein in pathogen infection play an important role. In this study, the identification and expression analysis of the SNARE protein provides a theoretical basis for future studies on the function of the SNARE protein and wheat resistance to powdery mildew.

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 Coping with Polychlorinated Biphenyl (PCB) Toxicity: Physiological and Genome-Wide Responses of Burkholderia xenovorans LB400 to PCB-Mediated Stress

2006 ◽  
Vol 72 (10) ◽  
pp. 6607-6614 ◽  
Author(s):  
J. Jacob Parnell ◽  
Joonhong Park ◽  
Vincent Denef ◽  
Tamara Tsoi ◽  
Syed Hashsham ◽  
...  
Keyword(s):  
Protein Function ◽  
Polychlorinated Biphenyl ◽  
Membrane Separation ◽  
Expression Patterns ◽  
Burkholderia Xenovorans ◽  
Inhibition Of Growth ◽  
Burkholderia Xenovorans Lb400 ◽  
Genome Wide ◽  
Differential Gene ◽  
Genome Wide Expression

ABSTRACT The biodegradation of polychlorinated biphenyls (PCBs) relies on the ability of aerobic microorganisms such as Burkholderia xenovorans sp. LB400 to tolerate two potential modes of toxicity presented by PCB degradation: passive toxicity, as hydrophobic PCBs potentially disrupt membrane and protein function, and degradation-dependent toxicity from intermediates of incomplete degradation. We monitored the physiological characteristics and genome-wide expression patterns of LB400 in response to the presence of Aroclor 1242 (500 ppm) under low expression of the structural biphenyl pathway (succinate and benzoate growth) and under induction by biphenyl. We found no inhibition of growth or change in fatty acid profile due to PCBs under nondegrading conditions. Moreover, we observed no differential gene expression due to PCBs themselves. However, PCBs did have a slight effect on the biosurface area of LB400 cells and caused slight membrane separation. Upon activation of the biphenyl pathway, we found growth inhibition from PCBs beginning after exponential-phase growth suggestive of the accumulation of toxic compounds. Genome-wide expression profiling revealed 47 differentially expressed genes (0.56% of all genes) under these conditions. The biphenyl and catechol pathways were induced as expected, but the quinoprotein methanol metabolic pathway and a putative chloroacetaldehyde dehydrogenase were also highly expressed. As the latter protein is essential to conversion of toxic metabolites in dichloroethane degradation, it may play a similar role in the degradation of chlorinated aliphatic compounds resulting from PCB degradation.

scholarly journals Genome-wide characterization of SPL gene family in Codonopsis pilosula reveals the novel roles of CpSPL2 and CpSPL10 in promoting the accumulation of secondary metabolites and growth of C. pilosula hairy root

2020 ◽  
Author(s):  
Jing Yang ◽  
Zhonglong Guo ◽  
Yao Cao ◽  
Rui Chen ◽  
Wentao Wang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Hairy Root ◽  
Expression Patterns ◽  
Light Stress ◽  
The Novel ◽  
Promoter Regions ◽  
Cis Acting ◽  
Codonopsis Pilosula ◽  
Genome Data ◽  
Genome Wide

Abstract Background SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors play critical roles in regulating diverse aspects of plant growth and development, including vegetative phase change, plant architecture, anthocyanin accumulation, lateral root growth, etc. Codonopsis pilosula is a famous medicinal plant and its dried root, named Dangshen, is one of the most widely used traditional Chinese medicine. However, little information about SPL genes in this species has been reported. Results In the present study, 15 SPL genes were identified based on the genome data of Codonopsis pilosula. Ten of the 15 CpSPLs were predicted to be the targets of miR156. Phylogenetic analysis clustered CpSPLs into seven groups (G1-G7) along with 16 SPLs from Arabidopsis thaliana. CpSPLs in the same group share similar gene structure and conserved motif composition. Cis-acting elements responding to light, stress, and phytohormone widely exist in their promoter regions. Our qRT-PCR results indicated that 15 CpSPLs were differentially expressed in different tissues (root, stem, leaf, flower, and calyx), different developmental periods (1, 2 and 3 months after germination), and various conditions (NaCl, MeJA and ABA treatment). Compared with the control, overexpression of CpSPL2 or CpSPL10 significantly promoted not only the growth of hairy roots, but also the accumulation of total saponins and lobetyolin. Conclusions The SPL genes in the C. pilosula genome were identified and their expression patterns were analyzed. The novel roles of CpSPL2 and CpSPL10 in promoting the accumulation of secondary metabolites and growth of C. pilosula hairy root were revealed. Our results established a foundation for further investigation of CpSPLs and provided novel insights into their biological functions.

scholarly journals Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

2021 ◽  
Vol 22 (24) ◽  
pp. 13568
Author(s):  
Zhengfu Yang ◽  
Hongmiao Jin ◽  
Junhao Chen ◽  
Caiyun Li ◽  
Jiani Wang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Expression Patterns ◽  
Carya Illinoinensis ◽  
Expression Levels ◽  
Cis Acting ◽  
Similar Expression ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Ethylene Responsive Factor

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

Genome-Wide Identification and Characterization of the FAR1/FHY3 Family in Populus trichocarpa Torr. & Gray and Expression Analysis in Light Response

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1385
Author(s):  
Jiujun Du ◽  
Lei Zhang ◽  
Xiaolan Ge ◽  
Xiaodong Xiang ◽  
Demei Cao ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Higher Plants ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Light Response ◽  
Cis Acting ◽  
Poplar Genome ◽  
Genome Wide ◽  
Identification And Characterization

Light is an important environmental factor for plant growth, and in higher plants, phytochrome A (phyA) is the predominant far-red photoreceptor, involved in various photoresponses. The FAR1/FHY3 transcription factor family, derived from transposases, is able to regulate plant development in response to multiple photosensitizers phytochrome. In total, 51 PtrFRSs were identified in the poplar genome, and were divided into 4 subfamilies. Among them, 47 PtrFRSs are located on 17 chromosomes. Upstream cis-acting elements of the PtrFRS genes were classified into three categories: growth and metabolism, stress and hormone, and the hormone and stress categories contained most of the cis-acting elements. Analysis of the regulatory networks and expression patterns showed that most PtrFRSs responded to changes in light intensity and were involved in the regulation of phytochromes. In this study, 51 PtrFRSs were identified and comprehensively bioinformatically analyzed, and preliminary functional analysis and prediction of PtrFRSs was carried out.

scholarly journals Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1134
Author(s):  
Shichao Liu ◽  
Ruibin Sun ◽  
Xiaojian Zhang ◽  
Zili Feng ◽  
Feng Wei ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Biotic And Abiotic Stresses ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
Duplication Events ◽  
Polyethylene Glycol 6000 ◽  
Similar Gene

The 12-oxo-phytodienoic acid reductases (OPRs) have been proven to play a major role in plant development and growth. Although the classification and functions of OPRs have been well understood in Arabidopsis, tomato, rice, maize, and wheat, the information of OPR genes in cotton genome and their responses to biotic and abiotic stresses have not been reported. In this study, we found 10 and 9 OPR genes in Gossypium hirsutum and Gossypium barbadense, respectively. They were classified into three groups, based on the similar gene structure and conserved protein motifs. These OPR genes just located on chromosome 01, chromosome 05, and chromosome 06. In addition, the whole genome duplication (WGD) or segmental duplication events contributed to the evolution of the OPR gene family. The analyses of cis-acting regulatory elements of GhOPRs showed that the functions of OPR genes in cotton might be related to growth, development, hormone, and stresses. Expression patterns showed that GhOPRs were upregulated under salt treatment and repressed by polyethylene glycol 6000 (PEG6000). The expression patterns of GhOPRs were different in leaf, root, and stem under V. dahliae infection. GhOPR9 showed a higher expression level than other OPR genes in cotton root. The virus-induced gene silencing (VIGS) analysis suggested that knockdown of GhOPR9 could increase the susceptibility of cotton to V. dahliae infection. Furthermore, GhOPR9 also modulated the expressions of jasmonic acid (JA) pathway-regulated genes under the V. dahliae infection. Overall, our results provided the evolution and potential functions of the OPR genes in cotton. These findings suggested that GhOPR9 might play an important role in cotton resistance to V. dahliae.

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.

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