Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses

SIMILAR TO RCD-ONEs (SROs) comprise a small plant-specific gene family which play important roles in regulating numerous growth and developmental processes and responses to environmental stresses. However, knowledge of SROs in sesame (Sesamum indicum L.) is limited. In this study, four SRO genes were identified in the sesame genome. Phylogenetic analysis showed that 64 SROs from 10 plant species were divided into two groups (Group I and II). Transcriptome data revealed different expression patterns of SiSROs over various tissues. Expression analysis showed that Group II SROs, especially SiSRO2b, exhibited a stronger response to various abiotic stresses and phytohormones than those in Group I, implying their crucial roles in response to environmental stimulus and hormone signals. In addition, the co-expression network and protein-protein interaction network indicated that SiSROs are associated with a wide range of stress responses. Moreover, transgenic yeast harboring SiSRO2b showed improved tolerance to salt, osmotic and oxidative stress, indicating SiSRO2b could confer multiple tolerances to transgenic yeast. Taken together, this study not only lays a foundation for further functional dissection of the SiSRO gene family, but also provides valuable gene candidates for genetic improvement of abiotic stress tolerance in sesame.

Download Full-text

Genome-wide analysis and expression profile of the bZIP gene family in poplar

BMC Plant Biology ◽

10.1186/s12870-021-02879-w ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kai Zhao ◽

Song Chen ◽

Wenjing Yao ◽

Zihan Cheng ◽

Boru Zhou ◽

...

Keyword(s):

Salt Stress ◽

Systems Biology ◽

Gene Family ◽

Stress Responses ◽

Metal Ion ◽

Gene Networks ◽

Expression Patterns ◽

Gene Set Enrichment Analysis ◽

Specific Gene ◽

Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

Download Full-text

Genome-Wide Analysis of the Shi-Related Sequence Family and Functional Identification of GmSRS18 Involving in Drought and Salt Stresses in Soybean

International Journal of Molecular Sciences ◽

10.3390/ijms21051810 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1810

Author(s):

Shu-Ping Zhao ◽

Xin-Yuan Song ◽

Lin-Lin Guo ◽

Xiang-Zhan Zhang ◽

Wei-Jun Zheng

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Expression Patterns ◽

Functional Verification ◽

Marker Genes ◽

Functional Identification ◽

Related Sequence ◽

Genome Wide Analysis ◽

Group I ◽

Genome Wide

The plant-special SHI-RELATED SEQUENCE (SRS) family plays vital roles in various biological processes. However, the genome-wide analysis and abiotic stress-related functions of this family were less reported in soybean. In this work, 21 members of soybean SRS family were identified, which were divided into three groups (Group I, II, and III). The chromosome location and gene structure were analyzed, which indicated that the members in the same group may have similar functions. The analysis of stress-related cis-elements showed that the SRS family may be involved in abiotic stress signaling pathway. The analysis of expression patterns in various tissues demonstrated that SRS family may play crucial roles in special tissue-dependent regulatory networks. The data based on soybean RNA sequencing (RNA-seq) and quantitative Real-Time PCR (qRT-PCR) proved that SRS genes were induced by drought, NaCl, and exogenous abscisic acid (ABA). GmSRS18 significantly induced by drought and NaCl was selected for further functional verification. GmSRS18, encoding a cell nuclear protein, could negatively regulate drought and salt resistance in transgenic Arabidopsis. It can affect stress-related physiological index, including chlorophyll, proline, and relative electrolyte leakage. Additionally, it inhibited the expression levels of stress-related marker genes. Taken together, these results provide valuable information for understanding the classification of soybean SRS transcription factors and indicates that SRS plays important roles in abiotic stress responses.

Download Full-text

Genome-wide analysis of the WRKY gene family and its response to abiotic stress in buckwheat (Fagopyrum tataricum)

Open Life Sciences ◽

10.1515/biol-2019-0010 ◽

2019 ◽

Vol 14 (1) ◽

pp. 80-96 ◽

Cited By ~ 6

Author(s):

Xia He ◽

Jing-jian Li ◽

Yuan Chen ◽

Jia-qi Yang ◽

Xiao-yang Chen

Keyword(s):

Abiotic Stress ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth Regulation ◽

Expression Patterns ◽

Functional Characterization ◽

Tartary Buckwheat ◽

Wrky Gene ◽

Fagopyrum Tataricum

AbstractThe WRKY gene family is an ancient plant transcription factor (TF) family with a vital role in plant growth and development, especially in response to biotic and abiotic stresses. Although many researchers have studied WRKY TFs in numerous plant species, little is known of them in Tartary buckwheat (Fagopyrum tataricum). Based on the recently reported genome sequence of Tartary buckwheat, we identified 78 FtWRKY proteins that could be classified into three major groups. All 77 WRKY genes were distributed unevenly across all eight chromosomes. Exon–intron analysis and motif composition prediction revealed the complexity and diversity of FtWRKYs, indicating that WRKY TFs may be of significance in plant growth regulation and stress response. Two separate pairs of tandem duplication genes were found, but no segmental duplications were identified. Overall, most orthologous gene-pairs between Tartary and common buckwheat evolved under strong purifying selection. qRT-PCR was used to analyze differences in expression among four FtWRKYs (FtWRKY6, 74, 31, and 7) under salt, drought, cold, and heat treatments. The results revealed that all four proteins are related to abiotic stress responses, although they exhibited various expression patterns. In particular, the relative expression levels of FtWRKY6, 74, and 31 were significantly upregulated under salt stress, while the highest expression of FtWRKY7 was observed from heat treatment. This study provides comprehensive insights into the WRKY gene family in Tartary buckwheat, and can support the screening of additional candidate genes for further functional characterization of WRKYs under various stresses.

Download Full-text

Identification and characterization of HAK/KUP/KT potassium transporter gene family in barley and their expression under abiotic stress

BMC Genomics ◽

10.1186/s12864-021-07633-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Kangfeng Cai ◽

Fanrong Zeng ◽

Junmei Wang ◽

Guoping Zhang

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Responses ◽

Brachypodium Distachyon ◽

Expression Patterns ◽

Tissue Expression ◽

Potassium Deficiency ◽

Potassium Transporter ◽

Transporter Family ◽

A Genome

Abstract Background HAK/KUP/KT (High-affinity K+ transporters/K+ uptake permeases/K+ transporters) is the largest potassium transporter family in plants, and plays pivotal roles in K+ uptake and transport, as well as biotic and abiotic stress responses. However, our understanding of the gene family in barley (Hordeum vulgare L.) is quite limited. Results In the present study, we identified 27 barley HAK/KUP/KT genes (hereafter called HvHAKs) through a genome-wide analysis. These HvHAKs were unevenly distributed on seven chromosomes, and could be phylogenetically classified into four clusters. All HvHAK protein sequences possessed the conserved motifs and domains. However, the substantial difference existed among HAK members in cis-acting elements and tissue expression patterns. Wheat had the most orthologous genes to barley HAKs, followed by Brachypodium distachyon, rice and maize. In addition, six barley HAK genes were selected to investigate their expression profiling in response to three abiotic stresses by qRT-PCR, and their expression levels were all up-regulated under salt, hyperosmotic and potassium deficiency treatments. Conclusion Twenty seven HAK genes (HvHAKs) were identified in barley, and they differ in tissue expression patterns and responses to salt stress, drought stress and potassium deficiency.

Download Full-text

Genome-wide characterization and expression profiling analysis of the xyloglucan endotransglycosylase/hydrolase gene family in Brachypodium distachyon

10.21203/rs.3.rs-41833/v1 ◽

2020 ◽

Author(s):

Hongyan Shen ◽

Qiuping Tan ◽

Wei Xiao ◽

Wenpeng Deng ◽

Xiaoyan Yu ◽

...

Keyword(s):

Gene Family ◽

Plant Hormones ◽

Stress Responses ◽

Brachypodium Distachyon ◽

Expression Patterns ◽

Growth Stages ◽

Xyloglucan Endotransglycosylase ◽

Motif Analysis ◽

Group I ◽

Genome Wide

Abstract Background: Xyloglucan endotransglucosylase/hydrolases (XTHs) are a class of cell wall-associated enzymes involved in the construction and remodeling of cellulose/xyloglucan crosslinks. However, knowledge of this gene family in the model monocot Brachypodium distachyon is limited. Results: A total of 29 BdXTH genes were identified from the reference genome, and these were further divided into three main groups (Group I/II, Group III, and the Ancestral Group) through comparative phylogenetic analysis. Gene structure and protein motif analysis indicate that closely clustered BdXTH genes are relatively conserved within each group. A highly conserved amino acid domain (DEIDFEFLG) responsible for catalytic activity was identified in all BdXTH proteins. We detected three pairs of segmentally duplicated BdXTH genes and five groups of tandemly duplicated BdXTH genes, which have played important roles in the expansion of the BdXTH gene family. Cis -elements related to hormones, growth, and abiotic stress responses were identified in the promoters of each BdXTH gene. Most BdXTH genes have distinct expression patterns in different tissues and growth stages. Furthermore, when roots were treated with two abiotic stresses (salinity and drought) and four plant hormones (IAA, auxin; GA3, gibberellin; ABA, abscisic acid and BR, brassinolide), the expression levels of many BdXTH genes changed significantly, suggesting possible roles in response to various environmental stimuli and plant hormones. Conclusion: In this study, we performed genome-wide identification, characterization, and expression pattern analysis of the XTH gene family in Brachypodium, which provide valuable information for further elucidation of the biological functions of BdXTH genes in the model grass B. distachyon.

Download Full-text

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

BMC Genomics ◽

10.1186/s12864-021-08043-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shutao He ◽

Xiaomeng Hao ◽

Shuli He ◽

Xiaoge Hao ◽

Xiaonan Chen

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Gene Family ◽

Sweet Potato ◽

Stress Responses ◽

Expression Patterns ◽

Gene Promoters ◽

Biotic And Abiotic Stress ◽

Protein Motifs ◽

Genome Wide

Abstract Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

Download Full-text

Genome-wide investigation of Hydroxycinnamoyl CoA: Shikimate Hydroxycinnamoyl Transferase (HCT) gene family in Carthamus tinctorius L.

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha49312489 ◽

2021 ◽

Vol 49 (3) ◽

pp. 12489

Author(s):

Sun FAN ◽

Naveed AHMAD ◽

Jin LIBO ◽

Zhang XINYUE ◽

Ma XINTONG ◽

...

Keyword(s):

Abiotic Stress ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth And Development ◽

Carthamus Tinctorius ◽

Plant Growth And Development ◽

Monolignol Biosynthesis ◽

Genome Wide ◽

Wide Range

Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) is mainly associated with monolignol biosynthesis, a central precursor to producing guaiacyl and syringyl lignins in plants. However, the explicit regulatory mechanism of HCT-mediated monolignol biosynthesis in plants still remained unclear. Here, the genome-wide analysis of the HCT gene family in Carthamus tinctorius as a target for understanding growth, development, and stress-responsive mechanisms was investigated. A total of 82 CtHCT genes were identified and characterized. Most of the CtHCTs proteins demonstrated the presence of two common conserved domains, including HXXXD and DFGWG. In addition, the conserved structure of protein motifs, PPI network, cis-regulatory units, and gene structure analysis demonstrated several genetic determinants reflecting the wide range of functional diversity of CtHCT-encoding genes. The observed expression analysis of CtHCT genes in different flowering stages under normal conditions partially highlighted their putative roles in plant growth and development pathways. Moreover, CtHCT genes appeared to be associated with abiotic stress responses as validated by the expression profiling in various flowering phases under light irradiation and MeJA treatment. Altogether, these findings provide new insights into identifying crucial molecular targets associated with plant growth and development and present practical information for understanding abiotic stress-responsive mechanisms in plants.

Download Full-text

Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses

BMC Plant Biology ◽

10.1186/s12870-021-03206-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Wenjing Hu ◽

Qiaoyu Ren ◽

Yali Chen ◽

Guoliang Xu ◽

Yexiong Qian

Keyword(s):

Transcription Factor ◽

Abiotic Stress ◽

Gene Family ◽

Stress Responses ◽

Regulatory Network ◽

Abiotic Stresses ◽

Interaction Analysis ◽

Expression Patterns ◽

Wrky Transcription Factor ◽

Rna Seq

Abstract Background The WRKY transcription factor family plays significant roles in biotic and abiotic stress responses, which has been associated with various biological processes in higher plants. However, very little is known regarding the structure and function of WRKY genes in maize. Results In this study, a total of 140 ZmWRKY proteins encoded by 125 ZmWRKY genes were eventually identified in maize. On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were divided into three main groups (Groups I, II and III) and the Group II was further classified into five subgroups. The characteristics of exon-intron structure of these putative ZmWRKY genes and conserved protein motifs of their encoded ZmWRKY proteins were also presented respectively, which was in accordance with the group classification results. Promoter analysis suggested that ZmWRKY genes shared many abiotic stress-related elements and hormone-related elements. Gene duplication analysis revealed that the segmental duplication and purifying selection might play a significant role during the evolution of the WRKY gene family in maize. Using RNA-seq data, transcriptome analysis indicated that most of ZmWRKY genes displayed differential expression patterns at different developmental stages of maize. Further, by quantitative real-time PCR analysis, twenty-one ZmWRKY genes were confirmed to respond to two different abiotic stress treatments, suggesting their potential roles in various abiotic stress responses. In addition, RNA-seq dataset was used to conduct weighted gene co-expression network analysis (WGCNA) in order to recognize gene subsets possessing similar expression patterns and highly correlated with each other within different metabolic networks. Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential regulatory network. Conclusions Taken together, the present study will serve to present an important theoretical basis for further exploring function and regulatory mechanism of ZmWRKY genes in the growth, development, and adaptation to abiotic stresses in maize.

Download Full-text

Genome-wide identification and expression analyses of C2H2 zinc finger transcription factors in Pleurotus ostreatus

PeerJ ◽

10.7717/peerj.12654 ◽

2022 ◽

Vol 10 ◽

pp. e12654

Author(s):

Qiangqiang Ding ◽

Hongyuan Zhao ◽

Peilei Zhu ◽

Xiangting Jiang ◽

Fan Nie ◽

...

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Stress Tolerance ◽

Zinc Finger ◽

Stress Responses ◽

Pleurotus Ostreatus ◽

Abiotic Stress Tolerance ◽

Expression Patterns ◽

Amino Acid Sequences ◽

Heat And Cold Stress

The C2H2-type zinc finger proteins (C2H2-ZFPs) regulate various developmental processes and abiotic stress responses in eukaryotes. Yet, a comprehensive analysis of these transcription factors which could be used to find candidate genes related to the control the development and abiotic stress tolerance has not been performed in Pleurotus ostreatus. To fill this knowledge gap, 18 C2H2-ZFs were identified in the P. ostreatus genome. Phylogenetic analysis indicated that these proteins have dissimilar amino acid sequences. In addition, these proteins had variable protein characteristics, gene intron-exon structures, and motif compositions. The expression patterns of PoC2H2-ZFs in mycelia, primordia, and young and mature fruiting bodies were investigated using qRT-PCR. The expression of some PoC2H2-ZFs is regulated by auxin and cytokinin. Moreover, members of PoC2H2-ZFs expression levels are changed dramatically under heat and cold stress, suggesting that these genes may participate in abiotic stress responses. These findings could be used to study the role of P. ostreatus-derived C2H2-ZFs in development and stress tolerance.

Download Full-text

MicroRNA and cDNA-Microarray as Potential Targets against Abiotic Stress Response in Plants: Advances and Prospects

Agronomy ◽

10.3390/agronomy12010011 ◽

2021 ◽

Vol 12 (1) ◽

pp. 11

Author(s):

Tariq Pervaiz ◽

Muhammad Waqas Amjid ◽

Ashraf El-kereamy ◽

Shi-Hui Niu ◽

Harry X. Wu

Keyword(s):

Abiotic Stress ◽

Cdna Microarray ◽

Stress Responses ◽

Abiotic Stresses ◽

Abiotic Stress Tolerance ◽

Expression Patterns ◽

Machine Learning Algorithms ◽

Current Status ◽

Developmental Cycle ◽

Altered Expression

Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.

Download Full-text