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

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.

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

BMC Genomics ◽

10.1186/s12864-021-07844-3 ◽

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.

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

Plants ◽

10.3390/plants9111617 ◽

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.

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

Plants ◽

10.3390/plants10091949 ◽

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.

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

Tropical Plant Biology ◽

10.1007/s12042-021-09295-2 ◽

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.

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Genome-wide Characterization and Expression Analysis of YABBY Gene Family in Three Cultivars of Cucurbita Linn. And Their Response of Salt Stress in Cucurbita Moschata

10.21203/rs.3.rs-121953/v1 ◽

2020 ◽

Author(s):

Jingping Yuan ◽

Changwei Shen ◽

Jingjing Xin ◽

Zhenxia Li ◽

Xinzheng Li ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Plant Growth ◽

Gene Family ◽

Expression Analysis ◽

Expression Patterns ◽

Pcr Analysis ◽

Abiotic Stress Response ◽

Element Analysis ◽

Qrt Pcr

Abstract BackgroundPlant specific YABBY transcription factors have important biological roles in plant growth and abiotic stress. However, the identification of Cucurbita Linn. YABBY and their response to salt stress have not yet been reported. The gene number, gene distribution on chromosome, gene structure, protein conserved structure, protein motif and the cis-acting element of YABBY in three cultivars of Cucurbita Linn. were analyzed by bioinformatics tools, and their tissue expression patterns and expression profile under salt stress were analyzed.ResultsIn this study, 34 YABBY genes (11 CmoYABBYs in Cucurbita moschata, 12 CmaYABBYs in Cucurbita maxima, and 11 CpeYABBYs in Cucurbita pepo) were identified and they were divided into five subfamilies (YAB1/YAB3, YAB2, INO, CRC and YAB5). YABBYs in the same subfamily usually have similar gene structures (intron-exon distribution) and conserved domains. Chromosomal localization analysis showed that these CmoYABBYs, CmaYABBYs, and CpeYABBYs were unevenly distributed in 8, 9, and 9 chromosomes of 21 chromosomes, respectively. Total of 6 duplicated gene pairs, and they all experienced segmental duplication events. Cis-acting element analysis showed that some Cucurbita Linn. YABBYs were associated with at least one of plant hormone response, plant growth, and abiotic stress response. Transcriptional profiles of CmoYABBYs and CmaYABBYs in roots, stems, leaves, and fruits, and CpeYABBYs in seed and fruit mesocarp showed that YABBYs of Cucurbita Linn. had tissue specificity. Finally, the transcriptional profile of 11 CmoYABBYs in leaf and qRT-PCR analysis of CmoYABBYs in root under salt stress indicated that some genes may play an important role in salt stress.ConclusionsGenome-wide identification and expression analysis of YABBYs revealed the characteristics of YABBY gene family in three cultivars of Cucurbita Linn.. Transcriptome and qRT-PCR analysis revealed the response of the CmoYABBYs to salt stress.This provides a theoretical basis for the functional research and utilization of YABBY genes in Cucurbita Linn..

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

10.21203/rs.2.11389/v1 ◽

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.

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Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

BMC Genomics ◽

10.1186/s12864-020-07152-2 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Mohammad Aslam ◽

Bello Hassan Jakada ◽

Beenish Fakher ◽

Joseph G. Greaves ◽

Xiaoping Niu ◽

...

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Stress Response ◽

Flowering Time ◽

Current Knowledge ◽

Ectopic Expression ◽

Ananas Comosus ◽

Biological Processes ◽

Abiotic Stress Response ◽

Bhlh Genes

Abstract Background Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory functions. Cryptochrome-interacting bHLH (CIB) and cryptochromes form an extensive regulatory network to mediate a plethora of pathways. Although bHLHs regulate critical biological processes in plants, the information about pineapple bHLHs remains unexplored. Results Here, we identified a total of 121 bHLH proteins in the pineapple genome. The identified genes were renamed based on the ascending order of their gene ID and classified into 18 subgroups by phylogenetic analysis. We found that bHLH genes are expressed in different organs and stages of pineapple development. Furthermore, by the ectopic expression of AcCIB2 in Arabidopsis and complementation of Atcib2 mutant, we verified the involvement of AcCIB2 in photomorphogenesis and abiotic stress response. Conclusions Our findings revealed that AcCIB2 plays an essential role in flowering time regulation and abiotic stress response. The present study provides additional insights into the current knowledge of bHLH genes and suggests their potential role in various biological processes during pineapple development.

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

Plant Gene ◽

10.1016/j.plgene.2020.100231 ◽

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

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Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

10.7287/peerj.preprints.27819 ◽

2019 ◽

Author(s):

Yong Zhou ◽

Yuan Cheng ◽

Chunpeng Wan ◽

Youxin Yang ◽

Jinyin Chen

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Expression Patterns ◽

Future Research ◽

Biological Processes ◽

Biological Functions ◽

Specific Expression ◽

Qrt Pcr ◽

Genome Wide ◽

Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

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A comprehensive analysis of cotton VQ gene superfamily reveals their potential and extensive roles in regulating cotton abiotic stress

10.21203/rs.3.rs-38226/v1 ◽

2020 ◽

Author(s):

Shuxun Yu ◽

Pengyun Chen ◽

Fei wei ◽

Shuaishuai Cheng ◽

Liang Ma ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Expression Patterns ◽

Regulatory Elements ◽

Abiotic Stress Response ◽

Salt And Drought Stress ◽

Solid Foundation ◽

Underlying Mechanisms ◽

Peg Stress ◽

Insight Into

Abstract Background Valine-glutamine (VQ) motif-containing proteins play important roles in plant growth, development and abiotic stress response. For many plant species, the VQ genes have been identified and their functions have been described. However, little is known about the origin, evolution, and functions (and underlying mechanisms) of the VQ family genes in cotton. Results In this study, we comprehensively analyzed the characteristics of 268 VQ genes from four Gossypium genomes and found that the VQ proteins evolved into ten clades, and each clade had a similar structural and conservative motif. The expansion of the VQ gene was mainly through segmental duplication, followed by dispersal. Expression analysis revealed that the VQ genes play important roles in response to salt and drought stress, especially GhVQ18 and GhVQ84 were significantly high expression in PEG stress and salt stress. Further analysis showed that GhVQ genes were co-expressed with GhWRKY transcription factors (TFs), and microRNAs (miRNAs) could hybridize to their cis-regulatory elements. Conclusions The results in this study broaden our understanding of the VQ gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the VQ genes provide a solid foundation for exploring their specific functions in the abiotic stress responses in cotton. Our study provides significant insight into the potential functions of VQ genes in cotton.

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