Genome-wide identification and expression analysis of the GSK gene family in Solanum tuberosum L. under abiotic stress and phytohormone treatments and functional characterization of StSK21 involvement in salt stress

Gene ◽  
2021 ◽  
Vol 766 ◽  
pp. 145156
Author(s):  
Shu-hua Huang ◽  
Yu-xiu Liu ◽  
Rui Deng ◽  
Tian-tian Lei ◽  
Ai-juan Tian ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Solanum Tuberosum ◽  
Gene Family ◽  
Expression Analysis ◽  
Solanum Tuberosum L ◽  
Functional Characterization ◽  
Genome Wide

scholarly journals Genome-wide identification and characterization of NF-Y gene family in peanut (Arachis hypogaea L.)

2019 ◽  
Author(s):  
Qian Wan ◽  
Lu Luo ◽  
Xiurong Zhang ◽  
Yuying Lv ◽  
Suqing Zhu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gene Duplication ◽  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Salt Stress Response

Abstract Background Nuclear factor Y (NF-Y) gene family consists of NF-YA, NF-YB and NF-YC subfamilies. Many members of NF-Y family have been involved in plant development processes, phytohormone signaling and tolerance to stresses in Arabidopsis and other plant species. However, little attention has been given in peanut. Results A total of 33 AhNF-Y genes (AhNF-Ys) were identified and distributed on 16 chromosomes. A phylogenetic analysis indicated that NF-Y genes prossessed highly conservatism in different plants. Gene duplication analyze indicated that only segmental duplication were detected. The abiotic stress-related regulatory elements analysis showed that AhNF-Ys, except for AhNF-YB6, contained at least one abiotic stress response element. With RNA-seq data, the tissue/organ-specific expression and differential expression profiling under salt stress were analyzed, indicating that six selected AhNF-Y gene may play potential roles in the regulation of salt stress response. qRT-PCR results suggested that these AhNF-Y genes also responded to osmotic, ABA (Abscisic Acid) and SA (Salicylic acid) stresses. Conclusions In this study, thirty three AhNF-Y genes were identified in cultivated peanut and the phylogeny, gene structures, motif composition, chromosomal location, gene duplication, stress-related regulatory elements, and expression patterns were also examined. These results may contribute to functional characterization of AhNF-Y genes in further research.

scholarly journals Investigation and Computational Analysis of Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights Into Sulfur Adjustment for Proper Development and Stimuli Responses

2021 ◽  
Author(s):  
Sahar Faraji ◽  
Parviz Heidari ◽  
Hoorieh Amouei ◽  
Ertugrul Filiz ◽  
Abdullah . ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Active Sites ◽  
Sulfur Metabolism ◽  
Solanum Tuberosum L ◽  
Functional Characterization ◽  
The Other ◽  
Protein Motifs ◽  
A Genome

Various kinds of primary metabolisms in plants are modulated through sulfate assimilation that the uptake of this inorganic compound can be regulated via the sulfate transporters, such as sulfotransfer-ases (SOTs), engaged in the sulfur metabolism. In the current study a genome-wide approach has been utilized for recognition and characterization of SOT family genes in the significant nutritional crop po-tato (Solanum tuberosum L.). As a result, 29 StSOT genes were identified in the potato genome, which were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure demonstrated two highly conserved 5' PSB region and 3' PB motif that are essential for sulfotransferase and catalytic ac-tivities. The protein-protein interaction networks also significantly demonstrated an interesting collabo-ration between SOTs and the other genes, such as PRTase, APS-kinase, protein phosphatase and APRs, in sulfur compounds biosynthesis and regulation of the flavonoid and brassinosteroid metabolic pro-cesses, which clearly detected the importance of sulfotransferases for potato proper growth/development and stress dealing. Notably, the homology modeling of StSOT proteins and dock-ing analysis of their ligand-binding sites revealed the presence of some stress-responsive residues, such as proline, glycine, serine and lysine, in their active sites. The expression assay of StSOT genes via the potato RNA-seq data clearly suggested the engagements of these gene family members in plants growth and extension as well as responses to various hormones and biotic/abiotic stimulus circum-stances. Our predictions can be informative for the functional characterization of the SOT genes in po-tato and may the other nutritional crops.

Functional characterization of the pollen-specific SBgLR promoter from potato (Solanum tuberosum L.)

Planta ◽  
2007 ◽  
Vol 227 (2) ◽  
pp. 387-396 ◽  
Author(s):  
Zhihong Lang ◽  
Peng Zhou ◽  
Jingjuan Yu ◽  
Guangming Ao ◽  
Qian Zhao
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Functional Characterization

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 Identification, Expression Profile and Evolution Analysis of Karyopherin β Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses

2020 ◽  
Vol 21 (3) ◽  
pp. 931
Author(s):  
Ya Xu ◽  
Lu Liu ◽  
Pan Zhao ◽  
Jing Tong ◽  
Naiqin Zhong ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Functional Characterization ◽  
Nucleocytoplasmic Trafficking ◽  
Genome Wide ◽  
Cellular Signal ◽  
Model Plant Arabidopsis Thaliana ◽  
Almost All

In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin β/Importin (KPNβ or Impβ) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in response to pathogen attack and environmental cues. Although achievements on understanding the roles of several KPNβs have been obtained from model plant Arabidopsis thaliana, comprehensive analysis of potato KPNβ gene family is yet to be elucidated. In our genome-wide identifications, a total of 13 StKPNβ (Solanum tuberosum KPNβ) genes were found in the genome of the doubled monoploid S. tuberosum Group Phureja DM1-3. Sequence alignment and conserved domain analysis suggested the presence of importin-β N-terminal domain (IBN_N, PF08310) or Exporin1-like domain (XpoI, PF08389) at N-terminus and HEAT motif at the C-terminal portion in most StKPNβs. Phylogenetic analysis indicated that members of StKPNβ could be classified into 16 subgroups in accordance with their homology to human KPNβs, which was also supported by exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis and quantitative real-time PCR experiments revealed that, except StKPNβ3d and StKPNβ4, almost all StKPNβs were ubiquitously expressed in all tissues analyzed, whereas transcriptional levels of several StKPNβs were increased upon biotic/abiotic stress or phytohormone treatments, reflecting their potential roles in plant growth, development or stress responses. Furthermore, we demonstrated that silencing of StKPNβ3a, a SA- and H2O2-inducible KPNβ genes led to increased susceptibility to environmental challenges, implying its crucial roles in plant adaption to abiotic stresses. Overall, our results provide molecular insights into StKPNβ gene family, which will serve as a strong foundation for further functional characterization and will facilitate potato breeding programs.

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