scholarly journals Genome-Wide Analysis of the IQM Gene Family in Rice (Oryza sativa L.)

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1949
Author(s):  
Tian Fan ◽  
Tianxiao Lv ◽  
Chuping Xie ◽  
Yuping Zhou ◽  
Changen Tian
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Abiotic Stress Response ◽  
Biotic And Abiotic Stress ◽  
Yeast Two Hybrid ◽  
Iq Motif ◽  
Two Hybrid

Members of the IQM (IQ-Motif Containing) gene family are involved in plant growth and developmental processes, biotic and abiotic stress response. To systematically analyze the IQM gene family and their expression profiles under diverse biotic and abiotic stresses, we identified 8 IQM genes in the rice genome. In the current study, the whole genome identification and characterization of OsIQMs, including the gene and protein structure, genome localization, phylogenetic relationship, gene expression and yeast two-hybrid were performed. Eight IQM genes were classified into three subfamilies (I–III) according to the phylogenetic analysis. Gene structure and protein motif analyses showed that these IQM genes are relatively conserved within each subfamily of rice. The 8 OsIQM genes are distributed on seven out of the twelve chromosomes, with three IQM gene pairs involved in segmental duplication events. The evolutionary patterns analysis revealed that the IQM genes underwent a large-scale event within the last 20 to 9 million years. In addition, quantitative real-time PCR analysis of eight OsIQMs genes displayed different expression patterns at different developmental stages and in different tissues as well as showed that most IQM genes were responsive to PEG, NaCl, jasmonic acid (JA), abscisic acid (ABA) treatment, suggesting their crucial roles in biotic, and abiotic stress response. Additionally, a yeast two-hybrid assay showed that OsIQMs can interact with OsCaMs, and the IQ motif of OsIQMs is required for OsIQMs to combine with OsCaMs. Our results will be valuable to further characterize the important biological functions of rice IQM genes.

scholarly journals The DUB family in Populus: identification, characterization, evolution and expression patterns

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenqing Zheng ◽  
Liang Du
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Structure ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Foliar Spray ◽  
Regulatory Elements ◽  
Limited Information ◽  
Abiotic Stress Response

Abstract Background The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. Results In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. Conclusions The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.

scholarly journals Genome-wide Identification and Abiotic Stress Response Pattern Analysis of NF-Y Gene Family in Peanut (Arachis Hypogaea L.)

2021 ◽  
Author(s):  
Qian Wan ◽  
Lu Luo ◽  
Xiurong Zhang ◽  
Yuying Lv ◽  
Suqing Zhu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Regulatory Region ◽  
Amino Acid Sequences ◽  
Start Codon ◽  
Abiotic Stress Response ◽  
Specific Expression

AbstractThe nuclear factor Y (NF-Y) transcription factor (TF) family consists of three subfamilies NF-YA, NF-YB and NF-YC. Many studies have proven that NF-Y complex plays multiple essential roles in stress response in Arabidopsis and other plant species. However, little attention has been given to these genes in peanut. In this study, thirty-three AhNF-Y genes were identified in cultivated peanut and they were distributed on 16 chromosomes. A phylogenetic analysis of the NF-Y amino acid sequences indicated that the peanut NF-Y proteins were clustered in pairs at the end of the branches and showed high conservation with previous reported plant NF-Ys. Evolutionary history analysis showed that only segmental duplication contributed to expansion of this gene family. Analysis of the 1500-bp regulatory regions upstream the start codon showed that, except for AhNF-YB6, peanut NF-Ys contained at least one abiotic stress response element in their regulatory region. Expression patterns of peanut NF-Ys in 22 tissues and developmental stages were analyzed. A few NF-Ys showed universal expression patterns, while most NF-Ys showed specific expression patterns. Through RNA-seq and qRT-PCR analyses, expression of six AhNF-Y genes was induced under salt stress in leaves or roots. In addition, AhNF-YA4/8/11, NF-YB4 and NF-YC2/8 also responded to osmotic stress, ABA (abscisic acid) and salicylic acid (SA) treatment.

scholarly journals Identification of the Golden-2-like transcription factors gene family in Gossypium hirsutum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12484
Author(s):  
Zilin Zhao ◽  
Jiaran Shuang ◽  
Zhaoguo Li ◽  
Huimin Xiao ◽  
Yuling Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Qrt Pcr

Background Golden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response. Methods In this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments. Results Herein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton.

scholarly journals Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaomin Xu ◽  
Lili Zhang ◽  
Wan Zhao ◽  
Liang Fu ◽  
Yuxuan Han ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Salt Tolerance ◽  
Gene Family ◽  
Developmental Stages ◽  
Structural Characteristics ◽  
Expression Profiles ◽  
Abiotic Stress Response ◽  
Serine Carboxypeptidase ◽  
Drought And Salt Tolerance

Abstract Background The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family members have not yet been performed in wheat. Results In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat. Conclusions We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat.

Genome-wide identification, phylogeny and expression analysis of HSF gene family in barley during abiotic stress response and reproductive development

Plant Gene ◽  
2020 ◽  
Vol 23 ◽  
pp. 100231
Author(s):  
Sumit Kumar Mishra ◽  
Anuj Kumar Poonia ◽  
Reeku Chaudhary ◽  
Vinay K. Baranwal ◽  
Deepanksha Arora ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Expression Analysis ◽  
Reproductive Development ◽  
Abiotic Stress Response ◽  
Genome Wide

scholarly journals Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1617
Author(s):  
Jie Zhang ◽  
Junping Feng ◽  
Wei Liu ◽  
Zhongying Ren ◽  
Junjie Zhao ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Function Analysis ◽  
Histone Demethylase ◽  
Abiotic Stress Response ◽  
Cotton Species ◽  
Jmjc Domain ◽  
Allotetraploid Cotton

Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.

scholarly journals Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress

2019 ◽  
Vol 20 (22) ◽  
pp. 5676 ◽  
Author(s):  
Haifeng Yan ◽  
Mingzhi Li ◽  
Yuping Xiong ◽  
Jianming Wu ◽  
Jaime A. Teixeira da Silva ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Sequences ◽  
Santalum Album ◽  
Biotic And Abiotic Stress ◽  
Functional Identification ◽  
Wrky Protein

WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.

scholarly journals The DUBs Family in Populus: Identification, Characterization, Evolution and Expression Patterns

2020 ◽  
Author(s):  
Wenqing Zheng ◽  
Liang Du
Keyword(s):  
Abiotic Stress ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Genome Structure ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Motif Analysis ◽  
Duplication Events ◽  
The Stability

Abstract Background: The deubiquitinases (DUB) family are a class of enzymes that regulate the stability or reverse the ubiquitination modification of many proteins in the cell, participating in cell cycle regulation, cell division and differentiation, various physiological activities such as DNA damage repair, growth and development, and response to stress. However, little is known about these genes in the woody plants. Results: In the present study, 88 DUB genes were identified in woody model plant Populus trichocarpa, including 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM with similar domains. According to the phylogenetic analysis, the 44 PtrUBP genes were classified into 14 subfamily, three PtrUCHs were classified into two groups, 23 PtrOTUs had six groups, four PtrMJDs had two groups, and 14 PtrJAMMs had six groups. The structure and motif analysis indicated that the same subfamily had similar genome structure and motif distribution characteristics. Ks/Ka analysis showed that the segmental duplication events played a major role in the expansion of Populus DUB genes. Synteny analysis of Populus DUB genes and four other species provided deep perception into the evolutionary traits of DUB genes. Expression profiles derived from transcriptome data exhibited distinct expression patterns of DUB genes in various tissues. Based on the result of promoter cis-regulatory elements analysis, we selected 16 representative PtrUBP genes to test their response to different hormonal treatments. The results showed that most of PtrUBPs were upregulated in the ABA, SA, and MeJA treatments, implying that their potential roles in abiotic stress response in Populus. Conclusion: The results in this study broaden our understanding of the DUB gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the DUBs provide a solid foundation for exploring their specific functions in Populus as well as indicate potential role of PtrUBP gene in abiotic stress.

Sign in / Sign up

Export Citation Format

Share Document