scholarly journals Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ruibin Wang ◽  
Jingfei Ma ◽  
Qian Zhang ◽  
Chunlai Wu ◽  
Hongyan Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Glutathione Transferase ◽  
Purifying Selection ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Qrt Pcr ◽  
Duplication Events

Abstract Background Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one of the most important crops, but the functions of GST genes in wheat were less studied. Results A total of 330 TaGST genes were identified from the wheat genome and named according to the nomenclature of rice and Arabidopsis GST genes. They were classified into eight classes based on the phylogenetic relationship among wheat, rice, and Arabidopsis, and their gene structure and conserved motif were similar in the same phylogenetic class. The 43 and 171 gene pairs were identified as tandem and segmental duplication genes respectively, and the Ka/Ks ratios of tandem and segmental duplication TaGST genes were less than 1 except segmental duplication gene pair TaGSTU24/TaGSTU154. The 59 TaGST genes were identified to have syntenic relationships with 28 OsGST genes. The expression profiling involved in 15 tissues and biotic and abiotic stresses suggested the different expression and response patterns of the TaGST genes. Furthermore, the qRT-PCR data showed that GST could response to abiotic stresses and hormones extensively in wheat. Conclusions In this study, a large GST family with 330 members was identified from the wheat genome. Duplication events containing tandem and segmental duplication contributed to the expansion of TaGST family, and duplication genes might undergo extensive purifying selection. The expression profiling and cis-elements in promoter region of 330 TaGST genes implied their roles in growth and development as well as adaption to stressful environments. The qRT-PCR data of 14 TaGST genes revealed that they could respond to different abiotic stresses and hormones, especially salt stress and abscisic acid. In conclusion, this study contributed to the further functional analysis of GST genes family in wheat.

scholarly journals Expression profiling of the Dof gene family under abiotic stresses in spinach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Spinacia Oleracea ◽  
Purifying Selection ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

AbstractDNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

scholarly journals Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Al Stress ◽  
Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

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 evolution of HECT genes in wheat

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10457
Author(s):  
Xianwen Meng ◽  
Ting Yang ◽  
Jing Liu ◽  
Mingde Zhao ◽  
Jiuli Wang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Profile Analysis ◽  
Purifying Selection ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Ubiquitin Proteasome ◽  
Proteasome Pathway

Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals Genome-wide analysis of WRKY transcription factors in wheat (Triticum aestivum L.) and differential expression under water deficit condition

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3232 ◽  
Author(s):  
Pan Ning ◽  
Congcong Liu ◽  
Jingquan Kang ◽  
Jinyin Lv
Keyword(s):  
Triticum Aestivum ◽  
Water Deficit ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Grain Filling ◽  
Triticum Aestivum L ◽  
Whole Wheat ◽  
Group I ◽  
Annotation Information ◽  
Specific Tissue

Background WRKY proteins, which comprise one of the largest transcription factor (TF) families in the plant kingdom, play crucial roles in plant development and stress responses. Despite several studies on WRKYs in wheat (Triticum aestivum L.), functional annotation information about wheat WRKYs is limited. Results Here, 171 TaWRKY TFs were identified from the whole wheat genome and compared with proteins from 19 other species representing nine major plant lineages. A phylogenetic analysis, coupled with gene structure analysis and motif determination, divided these TaWRKYs into seven subgroups (Group I, IIa–e, and III). Chromosomal location showed that most TaWRKY genes were enriched on four chromosomes, especially on chromosome 3B. In addition, 85 (49.7%) genes were either tandem (5) or segmental duplication (80), which suggested that though tandem duplication has contributed to the expansion of TaWRKY family, segmental duplication probably played a more pivotal role. Analysis of cis-acting elements revealed putative functions of WRKYs in wheat during development as well as under numerous biotic and abiotic stresses. Finally, the expression of TaWRKY genes in flag leaves, glumes, and lemmas under water-deficit condition were analyzed. Results showed that different TaWRKY genes preferentially express in specific tissue during the grain-filling stage. Conclusion Our results provide a more extensive insight on WRKY gene family in wheat, and also contribute to the screening of more candidate genes for further investigation on function characterization of WRKYs under various stresses.

scholarly journals In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Raju Mondal ◽  
Subhankar Biswas ◽  
Akanksha Srivastava ◽  
Suvajit Basu ◽  
Maitri Trivedi ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Signaling Pathways ◽  
Differential Expression ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Light Stress ◽  
Regulatory Elements ◽  
Qrt Pcr

Abstract Background S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. Results This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. Conclusions To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.

scholarly journals Expression Profiling of the Dof Gene Family Under Abiotic Stresses in Spinach

2021 ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Male Flowers

Abstract DNA-binding with one finger (Dof) transcription factors are plant-specific transcription factors involved in numerous pathways of plant development, especially in respond to abiotic stresses. Although genome-wide analysis of this gene family has been performed in many species, Dof genes in spinach have not been thoroughly analyzed. We performed a genome-wide analysis and characterization of Dof gene family in spinach. Twenty two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purify selection. Using Cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

scholarly journals Genome-Wide Identification, Evolution, and Expression Analysis of TPS and TPP Gene Families in Brachypodium distachyon

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 362 ◽  
Author(s):  
Song Wang ◽  
Kai Ouyang ◽  
Kai Wang
Keyword(s):  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Interaction Network ◽  
Purifying Selection ◽  
Gene Interaction ◽  
Gene Families ◽  
Gene Interaction Network ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Trehalose biosynthesis enzyme homologues in plants contain two families, trehalose-6-phosphate synthases (TPSs) and trehalose-6-phosphate phosphatases (TPPs). Both families participate in trehalose synthesis and a variety of stress-resistance processes. Here, nine BdTPS and ten BdTPP genes were identified based on the Brachypodium distachyon genome, and all genes were classified into three classes. The Class I and Class II members differed substantially in gene structures, conserved motifs, and protein sequence identities, implying varied gene functions. Gene duplication analysis showed that one BdTPS gene pair and four BdTPP gene pairs are formed by duplication events. The value of Ka/Ks (non-synonymous/synonymous) was less than 1, suggesting purifying selection in these gene families. The cis-elements and gene interaction network prediction showed that many family members may be involved in stress responses. The quantitative real-time reverse transcription (qRT-PCR) results further supported that most BdTPSs responded to at least one stress or abscisic acid (ABA) treatment, whereas over half of BdTPPs were downregulated after stress treatment, implying that BdTPSs play a more important role in stress responses than BdTPPs. This work provides a foundation for the genome-wide identification of the B. distachyon TPS–TPP gene families and a frame for further studies of these gene families in abiotic stress responses.

scholarly journals Genome-wide analysis of WRKY transcription factors in wheat (Triticum aestivum L.) and differential expression under water deficit treatment

2017 ◽  
Author(s):  
Pan Ning ◽  
Congcong Liu ◽  
Jingquan Kang ◽  
Jinyin Lv
Keyword(s):  
Triticum Aestivum ◽  
Transcription Factors ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Grain Filling ◽  
Triticum Aestivum L ◽  
Cis Acting ◽  
Group I ◽  
Annotation Information ◽  
Specific Tissue

WRKY proteins, comprising one of the largest transcription factor families in plant kingdom, play crucial roles in the plant development and stress responses. Despite several studies on WRKYs in wheat (Triticum aestivum L.) were investigated, functional annotation information about wheat WRKYs was limited. Here, 171 TaWRKY transcription factors (TFs) were identified from the whole wheat genome and compared with proteins from other 19 species representing nine major plant lineages. A phylogenetic analysis, coupled with gene structure analysis and motif determination, divided these TaWRKYs into seven subgroups (Group I, IIa-e, III). Chromosomal location showed that the most TaWRKY genes were enriched on four chromosomes, especially on chromosome 3B, and 85 (49.7%) genes were either tandem (5) or segmental duplication (80), which suggested that though tandem duplication has contributed to the expansion of TaWRKY family, segmental duplication probably played a more pivotal role. The cis-acting elements analysis revealed putative functions of WRKYs in wheat during development as well as under numerous biotic and abiotic stresses. Finally, the expression of TaWRKY genes in flag leaves, glumes and lemmas under water stress were analyzed, and we found different TaWRKY genes preferentially express in specific tissue during the grain-filling stage. Our results provide a more extensive knowledge on TaWRKYs, which helps to complete the information of WRKY gene family in wheat, and also contribute to screen more candidate genes for further investigation on function characterization of WRKYs under various stresses.

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