scholarly journals Identification, Classification, and Expression Analysis of the Triacylglycerol Lipase (TGL) Gene Family Related to Abiotic Stresses in Tomato

2021 ◽  
Vol 22 (3) ◽  
pp. 1387
Author(s):  
Qi Wang ◽  
Xin Xu ◽  
Xiaoyu Cao ◽  
Tixu Hu ◽  
Dongnan Xia ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Structural Characteristics ◽  
Limited Information ◽  
Triacylglycerol Lipase ◽  
Functional Studies ◽  
Solanum Lycopersicum L ◽  
Genome Wide

Triacylglycerol Lipases (TGLs) are the major enzymes involved in triacylglycerol catabolism. TGLs hydrolyze long-chain fatty acid triglycerides, which are involved in plant development and abiotic stress responses. Whereas most studies of TGLs have focused on seed oil metabolism and biofuel in plants, limited information is available regarding the genome-wide identification and characterization of the TGL gene family in tomato (Solanum lycopersicum L.). Based on the latest published tomato genome annotation ITAG4.0, 129 SlTGL genes were identified and classified into 5 categories according to their structural characteristics. Most SlTGL genes were distributed on 3 of 12 chromosomes. Segment duplication appeared to be the driving force underlying expansion of the TGL gene family in tomato. The promoter analysis revealed that the promoters of SlTGLs contained many stress responsiveness cis-elements, such as ARE, LTR, MBS, WRE3, and WUN-motifs. Expression of the majority of SlTGL genes was suppressed following exposure to chilling and heat, while it was induced under drought stress, such as SlTGLa9, SlTGLa6, SlTGLa25, SlTGLa26, and SlTGLa13. These results provide valuable insights into the roles of the SlTGL genes family and lay a foundation for further functional studies on the linkage between triacylglycerol catabolism and abiotic stress responses in tomato.

scholarly journals Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 23
Author(s):  
Antt Htet Wai ◽  
Muhammad Waseem ◽  
A B M Mahbub Morshed Khan ◽  
Ujjal Kumar Nath ◽  
Do Jin Lee ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Abiotic Stress Tolerance ◽  
Dependent Manner ◽  
Solanum Lycopersicum L ◽  
Genome Wide ◽  
Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

scholarly journals Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress

2020 ◽  
Author(s):  
Yanan Song ◽  
Hongli Cui ◽  
Ying Shi ◽  
Jinai Xue ◽  
Chunli Ji ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Stress Resistance ◽  
Segmental Duplication ◽  
Functional Characterization ◽  
High Stress ◽  
Camelina Sativa ◽  
Genome Wide ◽  
Large Expansion

Abstract Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina.Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress.Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.

scholarly journals Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

2018 ◽  
Author(s):  
Guodong Chen ◽  
Xiaolong Li ◽  
Xin qiao ◽  
Jiaming Li ◽  
Li Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Prunus Persica ◽  
Higher Plants ◽  
Chloride Transport ◽  
Structural Characteristics ◽  
Evolutionary Analysis ◽  
Anion Channels ◽  
Genome Wide ◽  
A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

scholarly journals Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting-1-Related Protein Kinase (SnRK) Genes in Triticum aestivum in Response to Abiotic Stress

2021 ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Structural Characteristics ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Plant Stress ◽  
Protein Motif ◽  
Genome Wide

The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.

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 identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanan Song ◽  
Hongli Cui ◽  
Ying Shi ◽  
Jinai Xue ◽  
Chunli Ji ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Stress Resistance ◽  
Segmental Duplication ◽  
Expression Profiles ◽  
High Stress ◽  
Camelina Sativa ◽  
Genome Wide ◽  
A Genome

Abstract Background WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas. Results A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress. Conclusions The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

Genome-wide identification and abiotic stress responses of DGK gene family in maize

2017 ◽  
Author(s):  
Yingnan Gu ◽  
Changjiang Zhao ◽  
Lin He ◽  
Bowei Yan ◽  
Jiejing Dong ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Genome Wide
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