scholarly journals Genome-Wide Identification and Analysis of SRO Gene Family in Chinese Cabbage (Brassica rapa L.)

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1235
Author(s):  
Yali Qiao ◽  
Xueqin Gao ◽  
Zeci Liu ◽  
Yue Wu ◽  
Linli Hu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
High Temperature ◽  
Low Temperature ◽  
Gene Family ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Abiotic Stresses ◽  
Expression Levels ◽  
Relative Expression ◽  
Small Proteins

Similar to radical-induced cell death 1 (SROs) is a family of small proteins unique to plants. SRO transcription factors play an important role in plants’ response to biotic and abiotic stresses. In this study, we identified 12 BrSRO genes in Chinese cabbage (Brassica rapa L.). Among them, a comprehensive overview of the SRO gene family is presented, including physical and chemical characteristics, chromosome locations, phylogenetic analysis, gene structures, motif analysis, and cis-element analyses. The number of amino acids of BrSRO genes is between 77–779 aa, isoelectric point changed from 6.02 to 9.6. Of the 12 BrSRO genes, 11 were randomly distributed along the 7 chromosomes, while BrSRO12 was located along unassigned scaffolds. Phylogenetic analysis indicated that the SRO proteins from six species, including Arabidopsis, banana, rice, Solanum lycopersicum, Zea mays, and Chinese cabbage were divided into eleven groups. The exon-rich BrSRO6 and BrSRO12 containing 15 exons were clustered to group K. All 12 genes have motif 2, which indicate that motif 2 is a relatively conservative motif. There are many hormone and stress response elements in BrSRO genes. The relative expression levels of 12 BrSRO genes under high temperature, drought, salt, and low temperature conditions were analyzed by real-time fluorescence quantitative PCR. The results indicated the relative expression level of BrSRO8 was significantly up-regulated when plants were exposed to high temperature. The relative expression levels of BrSRO1, 3, 7, 8, and 9 were higher under low temperature treatment. The up-regulated genes response to drought and salt stresses were BrSRO1, 5, 9 and BrSRO1, 8, respectively. These results indicated that these genes have certain responses to different abiotic stresses. This work has provided a foundation for further functional analyses of SRO genes in Chinese cabbage.

scholarly journals Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fan Liu ◽  
Hua Li ◽  
Junwei Wu ◽  
Bin Wang ◽  
Na Tian ◽  
...  
Keyword(s):  
High Temperature ◽  
Low Temperature ◽  
Pcr Analysis ◽  
Type I ◽  
Segmental Duplications ◽  
Expression Levels ◽  
Genome Wide ◽  
Encoded Proteins ◽  
Gene Structures ◽  
Lipoxygenase Gene Family

AbstractThe LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.

scholarly journals Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

2021 ◽  
Author(s):  
Li Ma ◽  
Jing Bai ◽  
Jia Xu ◽  
Weiliang Qi ◽  
Haiyun Li ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Brassica Rapa ◽  
Cold Resistance ◽  
Resistance Mechanism ◽  
Northern China ◽  
Low Temperature Stress ◽  
Oilseed Crop ◽  
Cold Response

Abstract Winter Brassica rapa is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. APX plays important roles in response of this plant to abiotic stress and in scavenging free radicals. In this study, 59 DEPs were isolated and identified from winter B. rapa and B. napus using bidirectional electrophoresis, and APX was found to be differentially expressed in these two species. Therefore, the roles of APX proteins in the cold response and superoxide metabolism pathways in both rapeseed species were further investigated. And comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profile in APX gene family. Most of the BrAPX genes were specifically expressed under low temperature stress and behaved significantly differently in cold-tolerant and cold-sensitive varieties. qPCR was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress, and these candidate genes and proteins may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

scholarly journals A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress

2020 ◽  
Author(s):  
Peisen Su ◽  
Jun Yan ◽  
Wen Li ◽  
Liang Wang ◽  
Jinxiao Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Evolutionary Model ◽  
Transgenic Wheat ◽  
Class Iii ◽  
Expression Levels ◽  
Peroxidase Gene ◽  
Stress Related Genes ◽  
Class Iii Peroxidase

Abstract Background: Salt and drought are the main abiotic stresses that restrict yield of crops. It is reported that peroxidases (PRXs) are involved in various abiotic stress responses. However, few wheat PRXs are characterized in the mechanism of abiotic stresses. Results: In this study, a novel wheat peroxidase (PRX) gene named TaPRX-2A, a member of wheat class III peroxidase gene family, was cloned and characterized in salt stress response. Based on the identification and evolutionary analysis of class III PRXs in 12 plants, we proposed an evolutionary model that TaPRX-2A might have experienced some exon fusion events during evolution. We also detected the positive selection of PRX domain in 13 PRXs involving our evolutionary model, and found 2 or 6 positively selected sites during TaPRX-2A evolution. The results of expression pattern showed that TaPRX-2A exhibited relatively higher expression levels in root tissue compared with that of leaf and stem tissues by using qRT-PCR. This TaPRX-2A was also induced by some stresses and hormone treatments including PEG6000, NaCl, hydrogen peroxide (H 2 O 2 ), salicylic acid (SA), methyljasmonic acid (MeJA) and abscisic acid (ABA). Transgenic wheat plants with overexpression of TaPRX-2A showed higher tolerance to salt stress than wild type (WT) plants. Confocal microscopy revealed that TaPRX-2A :eGFP was mainly localized in nuclei. The survival rate, relative water content and shoot length were higher in TaPRX-2A -overexpressing wheat than WT. However, root lengths were no significant difference between transgenic wheat and WT. The activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were enhanced in TaPRX-2A -overexpressing wheat than WT, resulting in the reduction of reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content. We also measured the expression levels of downstream stress-related genes ( RD22 , TLP4 , ABAI , GLP4 , GST22 , FeSOD, CuSOD, and CAT ). The results showed that RD22 , TLP4 , ABAI , GST22 , FeSOD, and CAT exhibited higher expression in TaPRX-2A -overexpressing lines than in WT under salt stress. Conclusions: The results show that TaPRX-2A plays a positive factor in response to salt stress by scavenging ROS and regulating stress-related genes.

Genome-wide Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

2020 ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Motif Analysis ◽  
Functional Homology ◽  
Exogenous Compounds

Abstract Background: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice.Results: In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. In addition, physical and chemical properties of the encoded proteins, subcellular localization, chromosome localization, stress-related cis-elements in abiotic stresses were determined, and a phylogenetic analysis and conserved motif analysis were performed. The rice MATE family can be divided into four subfamilies. It is speculated that members of the rice MATE family have many potential functions, such as the transport and accumulation of flavonoids and alkaloids, the extrusion of plant or exogenous compounds, the regulation of disease resistance and the response to abiotic stress, based on the proteins and cis-acting elements with known functions in the same subfamily. Analysis of gene expression showed that most of the genes were constitutively expressed. Furthermore, eight MATE genes were chosen for qRT-PCR-based analysis and showed differential expression patterns in response to salt and drought stress. Conclusions: Phylogenetic analysis, element prediction, expression data and homology with other species provided strong evidence for functional homology of MATE gene in rice. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Litchi Flowering is Regulated by Expression of Short Vegetative Phase Genes

2018 ◽  
Vol 143 (2) ◽  
pp. 101-109
Author(s):  
Jiaqi Hu ◽  
Hye-Ji Kim ◽  
Houbin Chen ◽  
Biyan Zhou
Keyword(s):  
Low Temperature ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Molecular Characteristics ◽  
Vegetative Phase ◽  
Expression Levels ◽  
Relative Expression ◽  
Short Vegetative Phase ◽  
Relative Expression Level

Short vegetative phase (SVP), a MADS-domain transcription factor, was shown to act as a repressor of flowering in arabidopsis (Arabidopsis thaliana). Although the role of SVPs in flowering is well characterized in the model plant arabidopsis, little is known in evergreen woody litchi (Litchi chinensis). In this study, three litchi SVP homologs (LcSVP1, LcSVP2, and LcSVP3) were cloned, and the bioinformatic analysis of the LcSVPs was carried out to identify their molecular characteristics. Their expression patterns in the apical meristem (AM) during the transition from vegetative to reproductive phase were studied under natural flowering inductive conditions. Also, brassinosteroid (BR) treatment under low temperature conditions was performed to elucidate the role of LcSVPs in the BR-regulated flowering. The results showed that LcSVPs belonged to the MADS superfamily. LcSVP relative expression levels in AMs of the early- and late-flowering cultivars showed decreasing trends with the transition from vegetative to reproductive growth. Under low temperature condition, relative expression levels of LcSVP1, LcSVP2, and LcSVP3 in AMs or panicle primordia showed decreasing trends, whereas those in the AMs of the BR-treated trees remained at relatively high levels. Relative expression analysis of the litchi homolog, flowering locus t 1 (LcFT1), showed that the BR-treated leaves had lower relative expression level than nontreated control leaves. The findings suggest that LcSVPs act as repressors involved in flowering in natural conditions and the BR-regulated flowering.

scholarly journals Insights into the Superoxide Dismutase Gene Family and Its Roles in Dendrobium catenatum under Abiotic Stresses

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1452
Author(s):  
Hui Huang ◽  
Hui Wang ◽  
Yan Tong ◽  
Yuhua Wang
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Light Response ◽  
Vital Role ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Expression Levels

Dendrobium catenatum is a member of epiphytic orchids with extensive range of pharmacological properties and ornamental values. Superoxide dismutase (SOD), a key member of antioxidant system, plays a vital role in protecting plants against oxidative damage caused by various biotic and abiotic stresses. So far, little is known about the SOD gene family in D. catenatum. In this study, eight SOD genes, including four Cu/ZnSODs, three FeSODs and one MnSOD, were identified in D. catenatum genome. Phylogenetic analyses of SOD proteins in D. catenatum and several other species revealed that these SOD proteins can be assigned to three subfamilies based on their metal co-factors. Moreover, the similarities in conserved motifs and gene structures in the same subfamily corroborated their classification and inferred evolutionary relationships. There were many hormone and stress response elements in DcaSODs, of which light responsiveness elements was the largest group. All DcaSODs displayed tissue-specific expression patterns and exhibited abundant expression levels in flower and leaf. According to public RNA-seq data and qRT-PCR analysis showed that the almost DcaSODs, except for DcaFSD2, were highly expressed under cold and drought treatments. Under heat, light, and salt stresses, DcaCSD1, DcaCSD2, DcaCSD3 were always significantly up-regulated, which may play a vital role in coping with various stresses. The expression levels of DcaFSD1 and DcaFSD2 were promoted by high light, suggesting their important roles in light response. These findings provided valuable information for further research on DcaSODs in D. catenatum.

scholarly journals Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis)

Genomics ◽  
2014 ◽  
Vol 103 (1) ◽  
pp. 135-146 ◽  
Author(s):  
Xiao-Ming Song ◽  
Tong-Kun Liu ◽  
Wei-Ke Duan ◽  
Qing-Hua Ma ◽  
Jun Ren ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gras Gene

scholarly journals Genome-wide identification and expression analysis of the glutathione S-transferase (GST) family under different developmental tissues and abiotic stresses in Chinese cabbage (Brassica rapa ssp. pekinensis)

2018 ◽  
Author(s):  
Jiangtao Du ◽  
Jie Ren ◽  
Xueling Ye ◽  
Ailin Hou ◽  
Wei Fu ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Abiotic Stresses ◽  
Environmental Changes ◽  
Cadmium Stress ◽  
Stress Conditions ◽  
Glutathione S Transferase ◽  
Genome Wide ◽  
High And Low Temperatures ◽  
Gst Family

The glutathione-S-transferase (GST) family of proteins is ancient and versatile, and plays an important role in combating exogenous pathogens, endogenous toxicants, and various abiotic stresses. Although the GST family has been studied in many crops, few studies have been reported in Chinese cabbage (Brassica rapa ssp. Pekinensis). In the present work, genome-wide analysis of the GST family in Chinese cabbage was carried out, and the expression and functions of genes under different conditions were investigated. A total of 88 GST genes were identified and divided into seven subfamilies according to their evolutionary relationships. Tandem duplication of genes was revealed as the main mechanism of expansion in this family. Transcriptome analysis under high and low temperatures and abiotic stress conditions revealed that most GST genes respond to environmental changes to varying degrees, particularly under herbicide and cadmium stress conditions. Our findings provide a basis for analysing the functions of GST family members in Chinese cabbage, especially in response to various abiotic stresses.

scholarly journals A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress

2020 ◽  
Author(s):  
Peisen Su ◽  
Jun Yan ◽  
Wen Li ◽  
Liang Wang ◽  
Jinxiao Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Evolutionary Model ◽  
Evolutionary Analysis ◽  
Class Iii ◽  
Expression Levels ◽  
Stress Related Genes

Abstract Background: Salt and drought are the main abiotic stresses that restrict the yield of crops. Peroxidases (PRXs) are involved in various abiotic stress responses. Furthermore, only few wheat PRXs have been characterized in the mechanism of the abiotic stress response.Results: In this study, a novel wheat peroxidase (PRX) gene named TaPRX-2A, a member of wheat class III PRX gene family, was cloned and its response to salt stress was characterized. Based on the identification and evolutionary analysis of class III PRXs in 12 plants, we proposed an evolutionary model for TaPRX-2A, suggesting that occurrence of some exon fusion events during evolution. We also detected the positive selection of PRX domain in 13 PRXs involving our evolutionary model, and found 2 or 6 positively selected sites during TaPRX-2A evolution. Quantitative reverse transcription–polymerase chain reaction (qRT–PCR) results showed that TaPRX-2A exhibited relatively higher expression levels in root tissue than those exhibited in leaf and stem tissues. TaPRX-2A expression was also induced by abiotic stresses and hormone treatments such as polyethylene glycol 6000, NaCl, hydrogen peroxide (H2O2), salicylic acid (SA), methyljasmonic acid (MeJA) and abscisic acid (ABA). Transgenic wheat plants with overexpression of TaPRX-2A showed higher tolerance to salt stress than wild-type (WT) plants. Confocal microscopy revealed that TaPRX-2A-eGFP was mainly localized in cell nuclei. Survival rate, relative water content, and shoot length were higher in TaPRX-2A-overexpressing wheat than in the WT wheat, whereas root length was not significantly different. The activities of s superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were enhanced in TaPRX-2A-overexpressing wheat compared with those in the WT wheat, resulting in the reduction of reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content. The expression levels of downstream stress-related genes showed that RD22, TLP4, ABAI, GST22, FeSOD, and CAT exhibited higher expressions in TaPRX-2A-overexpressing wheat than in WT under salt stress.Conclusions: The results show that TaPRX-2A plays a positive role in the response to salt stress by scavenging ROS and regulating stress-related genes.

scholarly journals Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11176
Author(s):  
Han Wang ◽  
Zong-Huan Ma ◽  
Juan Mao ◽  
Bai-Hong Chen
Keyword(s):  
Vitis Vinifera ◽  
Gene Family ◽  
Function Analysis ◽  
Family Members ◽  
Shielding Effect ◽  
Future Research ◽  
Vitis Vinifera L ◽  
Protein Subunit ◽  
Expression Levels ◽  
Relative Expression

EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H2O2) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.

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