scholarly journals Identification of WRKY gene family and characterization of cold stress-responsive WRKY genes in eggplant

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8777
Author(s):  
Yan Yang ◽  
Jun Liu ◽  
Xiaohui Zhou ◽  
Songyu Liu ◽  
Yong Zhuang
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Wrky Transcription Factor ◽  
Vital Role ◽  
Differentially Expressed ◽  
Virus Induced Gene Silencing ◽  
Motif Analysis ◽  
Genes Encoding ◽  
Wrky Proteins

Background WRKY proteins play a vital role in the plants response to different stresses, growth and development. Studies of WRKY proteins have been mainly focused on model plant Arabidopsis and a few other vegetable plants. However, the systematical study of eggplant WRKY transcription factor superfamily is scarce. Methods Bioinformatics has been used to identify and characterize the eggplant WRKY gene family. For the exploration of the differentially expressed WRKY genes, two cultivars with different cold-tolerance were used. Finally, we performed a virus-induced gene silencing (VIGS) experiment to verify the functions of SmWRKY26 and SmWRKY32. Results Fifty eight (58) genes encoding eggplant WRKY proteins were identified through searching the eggplant genome. Eggplant WRKY proteins could be classified into three groups or seven subgroups in accordance with other plants. WRKY variants were identified from the eggplant. Gene structure analysis showed that the number of intron in eggplant WRKY family was from 0 to 11, with an average of 4.4. Conserved motif analysis suggested that WRKY DNA-binding domain was conserved in eggplant WRKY proteins. Furthermore, RNA-seq data showed that WRKY genes were differentially expressed in eggplant response to cold stress. By using VIGS, the two differentially expressed genes-SmWRKY26 and SmWRKY32 were verified in response to cold stress. Discussions This study provides a foundation for further exploring the functions of WRKY proteins in eggplant response to stresses and eggplant genetic improvement in stresses.

scholarly journals Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analyses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8704 ◽  
Author(s):  
Hongju Jian ◽  
Ling Xie ◽  
Yanhua Wang ◽  
Yanru Cao ◽  
Mengyuan Wan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Cold Stress ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Regulatory Mechanisms ◽  
Primary Metabolites ◽  
Stress Treatment ◽  
Organic Acids And Sugars

The winter oilseed ecotype is more tolerant to low temperature than the spring ecotype. Transcriptome and metabolome analyses of leaf samples of five spring Brassica napus L. (B. napus) ecotype lines and five winter B. napus ecotype lines treated at 4 °C and 28 °C were performed. A total of 25,460 differentially expressed genes (DEGs) of the spring oilseed ecotype and 28,512 DEGs of the winter oilseed ecotype were identified after cold stress; there were 41 differentially expressed metabolites (DEMs) in the spring and 47 in the winter oilseed ecotypes. Moreover, more than 46.2% DEGs were commonly detected in both ecotypes, and the extent of the changes were much more pronounced in the winter than spring ecotype. By contrast, only six DEMs were detected in both the spring and winter oilseed ecotypes. Eighty-one DEMs mainly belonged to primary metabolites, including amino acids, organic acids and sugars. The large number of specific genes and metabolites emphasizes the complex regulatory mechanisms involved in the cold stress response in oilseed rape. Furthermore, these data suggest that lipid, ABA, secondary metabolism, signal transduction and transcription factors may play distinct roles in the spring and winter ecotypes in response to cold stress. Differences in gene expression and metabolite levels after cold stress treatment may have contributed to the cold tolerance of the different oilseed ecotypes.

scholarly journals Genome-Wide Identification and Expression Analysis of Tomato ADK Gene Family during Development and Stress

2021 ◽  
Vol 22 (14) ◽  
pp. 7708
Author(s):  
Lu Yang ◽  
Haohao Cao ◽  
Xiaoping Zhang ◽  
Liangxian Gui ◽  
Qiang Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Energy Homeostasis ◽  
Function Analysis ◽  
Evolutionary Relationship ◽  
Hormone Treatment ◽  
Specific Gene ◽  
Virus Induced Gene Silencing ◽  
Motif Analysis ◽  
Promoter Regions ◽  
Real Time Quantitative Pcr

Adenylate kinase (ADK) is widely distributed in organisms and plays an important role in cellular energy homeostasis. In plants, ADK has important functions in plant growth and development regulation as well as in adaptation to the environment. However, little information is available about the ADK genes in tomato (Solanum lycopersicum), an important economic crop. To investigate the characteristics and functions of ADK genes in tomato, a total of 11 ADK genes were identified and named according to their chromosomal locations. The ADK family in Arabidopsis, tomato, potato, and rice was divided into six groups, and motif analysis revealed that each SlADK protein contained five to eight conserved motifs. A total of 4 to 19 exons were identified in tomato ADK gene family members, and interestingly, most members possessed 4 exons. Several stress response elements were identified in the promoter regions of SlADKs. The 11 SlADKs were randomly distributed on 9 of the 12 tomato chromosomes. Three duplication events were observed between tomato chromosomes, and a high degree of conservation of synteny was demonstrated between tomato and potato. The online TomExpress platform prediction revealed that SlADKs were expressed in various tissues and organs, basically consistent with the data obtained from real-time quantitative PCR (qPCR). The qPCR verification was also performed to determine the expression level of SlADKs and demonstrated that the genes responded to multiple abiotic stresses, such as drought, salt, and cold. Besides, the qPCR results showed that SlADK transcription was responsive to most of the applied hormone treatment. For correlation network analysis under 44 global conditions, the results showed that the number of 17, 3, 4, and 6 coexpressed genes matched with SlADK5, 8, 9, and 11, respectively. For specific gene function analysis, expression of SlADK10 was inhibited using virus-induced gene silencing (VIGS). Compared to wild-type plants, plants with silenced SlADK10 gene had poor drought resistance, indicating SlADK10 regulated drought tolerance of tomato positively. In summary, the information provided in the present study will be helpful to understand the evolutionary relationship and their roles of tomato ADK gene family in further research.

Characterization of five subgroups of the sieve element occlusion gene family in Glycine max reveals genes encoding non-forisome P-proteins, forisomes and forisome tails

2014 ◽  
Vol 86 (1-2) ◽  
pp. 51-67 ◽  
Author(s):  
Sascia Zielonka ◽  
Antonia M. Ernst ◽  
Susan Hawat ◽  
Richard M. Twyman ◽  
Dirk Prüfer ◽  
...  
Keyword(s):  
Glycine Max ◽  
Gene Family ◽  
Sieve Element ◽  
Genes Encoding ◽  
P Proteins

scholarly journals Genome-Wide Identification, Characterization and Expression Profiling of Aluminum-Activated Malate Transporters in Eriobotrya japonica Lindl.

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 441
Author(s):  
Muhammad Moaaz Ali ◽  
Shariq Mahmood Alam ◽  
Raheel Anwar ◽  
Sajid Ali ◽  
Meng Shi ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Purifying Selection ◽  
Vital Role ◽  
Eriobotrya Japonica ◽  
Motif Analysis ◽  
Aluminum Stress ◽  
Genome Wide ◽  
Syntenic Analysis

Aluminum-activated malate transporters (ALMTs) have multiple potential roles in plant metabolism such as regulation of organic acids in fruits, movement of guard cells and inducing tolerance against aluminum stress. However, the systematic characterization of ALMT genes in loquat is yet to be performed. In the current study, 24 putative ALMT genes were identified in the genome of Eriobotrya japonica Lindl. To further investigate the role of those ALMT genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatics analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of EjALMT genes were conducted. The result revealed that the ALMT superfamily domain was conserved in all EjALMT proteins. EjALMT proteins were predicted to be localized in the plasma membrane. Genomic structural and motif analysis showed that the exon and motif number of each EjALMT gene ranged dramatically, from 5 to 7, and 6 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of the EjALMT gene family. The Ka and Ks values of duplicated genes depicted that EjALMT genes have undergone a strong purifying selection. Furthermore, the expression analysis of EjALMT genes was performed in the root, mature leaf, stem, full-bloom flower and ripened fruit of loquat. Some genes were expressed differentially in examined loquat tissues, signifying their differential role in plant growth and development. This study provides the first genome-wide identification, characterization, and relative expression of the ALMT gene family in loquat and provides the foundation for further functional analysis.

scholarly journals Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth

2020 ◽  
Vol 71 (19) ◽  
pp. 5880-5895
Author(s):  
Shangang Jia ◽  
Abou Yobi ◽  
Michael J Naldrett ◽  
Sophie Alvarez ◽  
Ruthie Angelovici ◽  
...  
Keyword(s):  
Cold Stress ◽  
Abiotic Stress Tolerance ◽  
Significant Proportion ◽  
Amino Acid Content ◽  
Differentially Expressed ◽  
Freezing Stress ◽  
Transcriptional Changes ◽  
Altered Response ◽  
Zein Reduction

Abstract Opaque kernels in maize may result from mutations in many genes, such as OPAQUE-2. In this study, a maize null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4) showed an opaque kernel phenotype, as well as plant developmental delay, male sterility, and altered response to cold stress. We found that in opaque kernels, all zein proteins were reduced and amino acid content was changed, including increased lysine. Transcriptomic and proteomic analysis confirmed the zein reduction and proteomic rebalancing of non-zein proteins, which was quantitatively and qualitatively different from opaque-2. Global transcriptional changes were found in endosperm and leaf, including many transcription factors and tissue-specific expressed genes. Furthermore, of the more than 8000 significantly differentially expressed genes in wild type in response to cold, a significant proportion (25.9% in moderate cold stress and 40.8% in near freezing stress) were not differentially expressed in response to cold in rdm4, suggesting RDM4 may participate in regulation of abiotic stress tolerance. This initial characterization of maize RDM4 provides a basis for further investigating its function in endosperm and leaf, and as a regulator of normal and stress-responsive development.

Isolation and characterization of the genes encoding antimicrobial neutrophil cationic peptides, defensins.

Ensho ◽  
1995 ◽  
Vol 15 (1) ◽  
pp. 33-41
Author(s):  
Isao Nagaoka ◽  
Noriko Ishihara ◽  
Akimasa Someya ◽  
Kazuhisa Iwabuchi ◽  
Shin Yomogida ◽  
...  
Keyword(s):  
Cationic Peptides ◽  
Isolation And Characterization ◽  
Genes Encoding

Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

2010 ◽  
Vol 36 (4) ◽  
pp. 688-694
Author(s):  
Yi-Jun WANG ◽  
Yan-Ping LÜ ◽  
Qin XIE ◽  
De-Xiang DENG ◽  
Yun-Long BIAN
Keyword(s):  
Sorghum Bicolor ◽  
Gene Family ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Characterization ◽  
I Gene

Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

2019 ◽  
Vol 14 (7) ◽  
pp. 591-601 ◽  
Author(s):  
Aravind K. Konda ◽  
Parasappa R. Sabale ◽  
Khela R. Soren ◽  
Shanmugavadivel P. Subramaniam ◽  
Pallavi Singh ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Wrky Transcription Factor ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Callose Deposition ◽  
Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

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