Gene structure and expression analysis of the drought- and abscisic acid-responsive CDeT11-24 gene family from the resurrection plant Craterostigma plantagineum Hochst

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

Download Full-text

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

PeerJ ◽

10.7717/peerj.12480 ◽

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.

Download Full-text

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

10.21203/rs.3.rs-49275/v1 ◽

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.

Download Full-text

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

BMC Plant Biology ◽

10.1186/s12870-020-02576-0 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Ting Zhu ◽

Yue Liu ◽

Liting Ma ◽

Xiaoying Wang ◽

Dazhong Zhang ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Gene Structure ◽

Expression Patterns ◽

Wheat Yield ◽

Chromosomal Distribution ◽

Positive Role ◽

Qrt Pcr ◽

Genome Wide ◽

Duplication Events

Abstract Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

Download Full-text