scholarly journals Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12480
Author(s):  
Xiaowei Jia ◽  
Xuyang Si ◽  
Yangyang Jia ◽  
Hongyan Zhang ◽  
Shijun Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Gene Structure ◽  
Catalytic Domain ◽  
Diacylglycerol Kinase ◽  
Regulatory Elements ◽  
Amino Acid Sequences ◽  
Developmental Expression ◽  
Kinase Gene ◽  
Chinese Spring Wheat

The inositol phospholipid signaling system mediates plant growth, development, and responses to adverse conditions. Diacylglycerol kinase (DGK) is one of the key enzymes in the phosphoinositide-cycle (PI-cycle), which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGKs have not been reported in wheat. In this study, 24 DGK gene family members from the wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and an accessory domain. The analyses of phylogenetic and gene structure analyses revealed that each TaDGK gene could be grouped into clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation of functional domains, for example, of gene structure and amino acid sequences. Four coding sequences were then cloned from Chinese Spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification across wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated under salt and drought stresses, suggesting their possible roles in dealing with adverse environmental conditions. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. These results provide valuable information for understanding the putative functions of DGKs in wheat and support deeper functional analysis of this pivotal gene family. The 24 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat

2020 ◽  
Author(s):  
Xiaowei Jia ◽  
Xuyang Si ◽  
Yangyang Jia ◽  
Hongyan Zhang ◽  
Shijun Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Gene Structure ◽  
Hexaploid Wheat ◽  
Catalytic Domain ◽  
Diacylglycerol Kinase ◽  
Regulatory Elements ◽  
Amino Acid Sequences ◽  
Developmental Expression ◽  
Chinese Spring Wheat

Abstract Background The inositol phospholipid signaling system, which is based on the metabolism of phosphoinositide (PI), mediates plant growth, development, and responses to adversity. Diacylglycerol kinase (DGK) is one of the key enzymes in the PI-cycle, which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGK genes have not been reported in wheat. Results In this study, 20 DGK gene family members from the heterologous hexaploid wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and a accessory domain. The analyses of phylogenetic and gene structure revealed that each TaDGK gene could be grouped to clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation in functional domains, for example gene structure and amino acid sequences. By cloning, four coding sequences were ascertained from Chinese spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification in wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated express under salt and drought stresses, suggesting their possible roles in dealing with adversity environment. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. Conclusions These results provide valuable information for understanding the putative functions of DGK genes in wheat, and conduce to ulterior functional analysis of this pivotal gene family. The 20 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

scholarly journals Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L.

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 400 ◽  
Author(s):  
Intikhab Alam ◽  
Dong-Li Cui ◽  
Khadija Batool ◽  
Yan-Qing Yang ◽  
Yun-Hai Lu
Keyword(s):  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Expression Analysis ◽  
Gene Structure ◽  
Purifying Selection ◽  
Brassica Species ◽  
Promoter Sequence ◽  
Regulatory Elements ◽  
Hect Domain ◽  
E3 Ligases

The HECT-domain protein family is one of the most important classes of E3 ligases. While the roles of this family in human diseases have been intensively studied, the information for plant HECTs is limited. In the present study, we performed the identification of HECT genes in Brassica rapa and Brassica oleracea, followed by analysis of phylogeny, gene structure, additional domains, putative cis-regulatory elements, chromosomal location, synteny, and expression. Ten and 13 HECT genes were respectively identified in B. rapa and B. oleracea and then resolved into seven groups along with their Arabidopsis orthologs by phylogenetic analysis. This classification is well supported by analyses of gene structure, motif composition within the HECT domain and additional protein domains. Ka/Ks ratio analysis showed that these HECT genes primarily underwent purifying selection with varied selection pressures resulting in different rates of evolution. RNA-Seq data analysis showed that the overwhelming majority of them were constitutively expressed in all tested tissues. qRT-PCR based expression analysis of the 10 B. rapa HECT genes under salt and drought stress conditions showed that all of them were responsive to the two stress treatments, which was consistent with their promoter sequence analysis revealing the presence of an important number of phytohormone-responsive and stress-related cis-regulatory elements. Our study provides useful information and lays the foundation for further functional determination of each HECT gene across the Brassica species.

Gene structure, evolution and expression analysis of the P-ATPase gene family in Chinese pear (Pyrus bretschneideri)

2020 ◽  
Vol 88 ◽  
pp. 107346
Author(s):  
Muhammad Aamir Manzoor ◽  
Xi Cheng ◽  
Guohui Li ◽  
Xueqiang Su ◽  
Muhammad Abdullah ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Gene Structure ◽  
Structure Evolution ◽  
Atpase Gene

Comprehensive genomic analysis and expression profiling of diacylglycerol kinase gene family in Malus prunifolia (Willd.) Borkh

Gene ◽  
2015 ◽  
Vol 561 (2) ◽  
pp. 225-234 ◽  
Author(s):  
Yali Li ◽  
Yanxiao Tan ◽  
Yun Shao ◽  
Mingjun Li ◽  
Fengwang Ma
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Genomic Analysis ◽  
Diacylglycerol Kinase ◽  
Kinase Gene ◽  
Malus Prunifolia

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 ◽  
Yue Chen ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
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 (Cs LecRLK) 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 LecRLK s might play in the life cycle of cucumber.

scholarly journals Genome-Wide Identification, Characterization and Expression Analysis of Non-Arginine Aspartate Receptor like kinase gene family under Colletotrichum truncatum stress conditions in Hot pepper

2020 ◽  
Author(s):  
R Srideepthi ◽  
MSR Krishna ◽  
P Suneetha ◽  
R Sai Krishna ◽  
S Karthikeyan
Keyword(s):  
Disease Resistance ◽  
Gene Family ◽  
Expression Profiles ◽  
Regulatory Elements ◽  
Hot Pepper ◽  
Colletotrichum Truncatum ◽  
Kinase Gene ◽  
Improvement Programs ◽  
Arginine Aspartate ◽  
Six Genes

AbstractReceptor Like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Non arginine aspartate (non-RD) an important class of RLKs plays a vital role in disease resistance and apoptosis in plants. In present investigation, a comprehensive Insilco analysis for non-RD Kinase gene family including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, gene duplication analysis, promoter analysis and transcript expression profiles were elucidated. In this study twenty six genes were observed on nine out of twelve chromosomes. All these genes were clustered into seven subfamilies under large monophyletic group termed as Interleukin-1 Receptor-Associated Kinase (IRAK) family. Structural diversity in genomic structure among non-RD kinase gene family were identified and presence of pathogen induced cis regulatory elements like STRE, MYC, MYB,W box were found. Expression profiles of genes involved in providing resistance to anthracnose pathogen Colletotrichum truncatum in hot pepper were analyzed at different infective stages in both resistant and susceptible genotypes. Among twenty six genes, CaRLK1 gene belonging to LRRXII subfamily was up regulated under severe stress after infection in resistant genotype PBC-80. This integrative approach has helped us to identify candidate genes involved in disease resistance which would be helpful in future crop improvement programs.

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 Genome-wide identification and characterization of ABA receptor PYL gene family in rice

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Shashank Kumar Yadav ◽  
Vinjamuri Venkata Santosh Kumar ◽  
Rakesh Kumar Verma ◽  
Pragya Yadav ◽  
Ankit Saroha ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Expression Profiles ◽  
Foxtail Millet ◽  
Evolutionary Relationship ◽  
Regulatory Elements ◽  
Fine Tuning ◽  
Aba Receptor

Abstract Background Abscisic acid (ABA), a key phytohormone that controls plant growth and stress responses, is sensed by the pyrabactin resistance 1(PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family of proteins. Comprehensive information on evolution and function of PYL gene family in rice (Oryza sativa) needs further investigation. This study made detailed analysis on evolutionary relationship between PYL family members, collinearity, synteny, gene structure, protein motifs, cis-regulatory elements (CREs), SNP variations, miRNAs targeting PYLs and expression profiles in different tissues and stress responses. Results Based on sequence homology with Arabidopsis PYL proteins, we identified a total of 13 PYLs in rice (BOP clade) and maize (PACCMAD clade), while other members of BOP (wheat – each diploid genome, barley and Brachypodium) and PACCMAD (sorghum and foxtail millet) have 8-9 PYLs. The phylogenetic analysis divided PYLs into three subfamilies that are structurally and functionally conserved across species. Gene structure and motif analysis of OsPYLs revealed that members of each subfamily have similar gene and motif structure. Segmental duplication appears be the driving force for the expansion of PYLs, and the majority of the PYLs underwent evolution under purifying selection in rice. 32 unique potential miRNAs that might target PYLs were identified in rice. Thus, the predicted regulation of PYLs through miRNAs in rice is more elaborate as compared with B. napus. Further, the miRNAs identified to in this study were also regulated by stresses, which adds additional layer of regulation of PYLs. The frequency of SAPs identified was higher in indica cultivars and were predominantly located in START domain that participate in ABA binding. The promoters of most of the OsPYLs have cis-regulatory elements involved in imparting abiotic stress responsive expression. In silico and q-RT-PCR expression analyses of PYL genes revealed multifaceted role of ABARs in shaping plant development as well as abiotic stress responses. Conclusion The predicted miRNA mediated regulation of OsPYLs and stress regulated expression of all OsPYLs, at least, under one stress, lays foundation for further validation and fine tuning ABA receptors for stress tolerance without yield penalty in rice.

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