scholarly journals Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huanhuan Wu ◽  
Lei Zheng ◽  
Ghulam Qanmber ◽  
Mengzhen Guo ◽  
Zhi Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Gene Structure ◽  
Growth And Development ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Plant Growth And Development ◽  
Functional Studies ◽  
Cotton Species ◽  
Plant Homeodomain

Abstract Background The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. Results In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. Conclusion This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

scholarly journals Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

2020 ◽  
Author(s):  
Huanhuan Wu ◽  
Lei Zheng ◽  
Ghulam Qanmber ◽  
Mengzhen Guo ◽  
Zhi Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Gene Structure ◽  
Growth And Development ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Plant Growth And Development ◽  
Functional Studies ◽  
Cotton Species ◽  
Plant Homeodomain

Abstract Background: The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. Results: In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome, however, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. Conclusion: This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

scholarly journals Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

2020 ◽  
Author(s):  
Huanhuan Wu ◽  
Lei Zheng ◽  
Ghulam Qanmber ◽  
Mengzhen Guo ◽  
Zhi Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Gene Structure ◽  
Growth And Development ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Plant Growth And Development ◽  
Functional Studies ◽  
Cotton Species ◽  
Plant Homeodomain

Abstract Background: The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton.Results: In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions.Conclusion: This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

scholarly journals Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

2020 ◽  
Author(s):  
Huanhuan Wu ◽  
Lei Zheng ◽  
Ghulam Qanmber ◽  
Mengzhen Guo ◽  
Zhi Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Gene Structure ◽  
Growth And Development ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Plant Growth And Development ◽  
Functional Studies ◽  
Cotton Species ◽  
Plant Homeodomain

Abstract Background: The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton.Results: In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions.Conclusion: This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

scholarly journals Genome-Wide Identification and Comparative Analysis of ARF Family Genes in Three Apiaceae Species

2021 ◽  
Vol 11 ◽  
Author(s):  
Qiaoying Pei ◽  
Nan Li ◽  
Qihang Yang ◽  
Tong Wu ◽  
Shuyan Feng ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Growth And Development ◽  
Expression Patterns ◽  
Gene Families ◽  
Plant Growth And Development ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Functional Analyses ◽  
Significant Positive Selection

The family Apiaceae includes many important vegetables and medicinal plants. Auxin response factors (ARFs) play critical roles in regulating plant growth and development. Here, we performed a comprehensive analysis of the ARF gene family in three Apiaceae species, celery, coriander, and carrot, and compared the results with the ARF gene family of lettuce, Arabidopsis, and grape. We identified 156 ARF genes in all six species and 89 genes in the three Apiaceae species, including 28, 34, and 27 in celery, coriander, and carrot, respectively. The paralogous gene number in coriander was far greater than that in carrot and celery. Our analysis revealed that ARF genes of the three Apiaceae species in 34 branches of the phylogenetic tree underwent significant positive selection. Additionally, our findings indicated that whole-genome duplication played an important role in ARF gene family expansion. Coriander contained a greater number of ARF genes than celery and carrot because of more gene duplications and less gene losses. We also analyzed the expression of ARF genes in three tissues by RNA-seq and verified the results by quantitative real-time PCR. Furthermore, we found that several paralogous genes exhibited divergent expression patterns. Overall, this study provides a valuable resource for exploring how ARF family genes regulate plant growth and development in other plants. Since this is the first report of the ARF gene family in Apiaceae, our results will serve as a guide for comparative and functional analyses of ARF and other gene families in Apiaceae.

scholarly journals Identification and Analysis of GhEXO Gene Family Indicated That GhEXO7_At Promotes Plant Growth and Development Through Brassinosteroid Signaling in Cotton (Gossypium hirsutum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Shengdong Li ◽  
Zhao Liu ◽  
Guoquan Chen ◽  
Ghulam Qanmber ◽  
Lili Lu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Growth And Development ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Virus Induced Gene Silencing ◽  
Plant Growth And Development ◽  
Altered Expression ◽  
Protein Motifs

Brassinosteroids (BRs), an efficient plant endogenous hormone, significantly promotes plant nutrient growth adapting to biological and abiotic adversities. BRs mainly promote plant cell elongation by regulating gene expression patterns. EXORDIUM (EXO) genes have been characterized as the indicators of BR response genes. Cotton, an ancient crop, is of great economic value and its fibers can be made into all kinds of fabrics. However, EXO gene family genes have not been full identified in cotton. 175 EXO genes were identified in nine plant species, of which 39 GhEXO genes in Gossypium hirsutum in our study. A phylogenetic analysis grouped all of the proteins encoded by the EXO genes into five major clades. Sequence identification of conserved amino acid residues among monocotyledonous and dicotyledonous species showed a high level of conservation across the N and C terminal regions. Only 25% the GhEXO genes contain introns besides conserved gene structure and protein motifs distribution. The 39 GhEXO genes were unevenly distributed on the 18 At and Dt sub-genome chromosomes. Most of the GhEXO genes were derived from gene duplication events, while only three genes showed evidence of tandem duplication. Homologous locus relationships showed that 15 GhEXO genes are located on collinear blocks and that all orthologous/paralogous gene pairs had Ka > Ks values, indicating purifying selection pressure. The GhEXO genes showed ubiquitous expression in all eight tested cotton tissues and following exposure to three phytohormones, IAA, GA, and BL. Furthermore, GhEXO7_At was mainly expressed in response to BL treatment, and was predominantly expressed in the fibers. GhEXO7_At was found to be a plasma membrane protein, and its ectopic expression in Arabidopsis mediated BR-regulated plant growth and development with altered expression of DWF4, CPD, KCS1, and EXP5. Additionally, the functions of GhEXO7_At were confirmed by virus-induced gene silencing (VIGS) in cotton. This study will provide important genetic resources for future cotton breeding programs.

scholarly journals Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Khadiza Khatun ◽  
Sourav Debnath ◽  
Arif Hasan Khan Robin ◽  
Antt Htet Wai ◽  
Ujjal Kumar Nath ◽  
...  
Keyword(s):  
Stress Response ◽  
Plant Growth ◽  
Growth And Development ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background CONSTANS-like (CO-like, COL) are putative zinc-finger transcription factors known to play vital role in various plant biological processes such as control of flowering time, regulation of plant growth and development and responses to stresses. However, no systematic analysis of COL family gene regarding the plant development and stress response has been previously performed in any solanaceous crop. In the present study, a comprehensive genome-wide analysis of COL family genes in petunia has been conducted to figure out their roles in development of organs and stress response. Results A total of 33 COL genes, 15 PaCOL genes in P. axillaris and 18 PiCOL genes in P. inflata, were identified in petunia. Subsequently, a genome-wide systematic analysis was performed in 15 PaCOL genes. Considering the domain composition and sequence similarity the 15 PaCOL and 18 PiCOL genes were phylogenetically classified into three groups those are conserved among the flowering plants. Moreover, all of the 15 PaCOL proteins were localized in nucleus. Furthermore, differential expression patterns of PaCOL genes were observed at different developmental stages of petunia. Additionally, transcript expression of 15 PaCOL genes under various abiotic and phytohormone treatments showed their response against stresses. Moreover, several cis-elements related to stress, light-responsive, hormone signaling were also detected in different PaCOL genes. Conclusion The phylogenetic clustering, organ specific expression pattern and stress responsive expression profile of conserved petunia COL genes indicating their involvement in plant growth and development and stress response mechanism. This work provide a significant foundation for understanding the biological roles of petunia COL genes in plant growth, development and in stress response.

scholarly journals Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7950 ◽  
Author(s):  
Yongbin Wang ◽  
Lei Ling ◽  
Zhenfeng Jiang ◽  
Weiwei Tan ◽  
Zhaojun Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Genomic Data ◽  
Evolutionary Analysis ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
Genome Wide ◽  
Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

scholarly journals Genome-wide identification of HSF family in peach and functional analysis of PpHSF5 involvement in root and aerial organ development

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10961
Author(s):  
Bin Tan ◽  
Liu Yan ◽  
Huannan Li ◽  
Xiaodong Lian ◽  
Jun Cheng ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Growth ◽  
Gene Family ◽  
Growth And Development ◽  
Multiple Alignment ◽  
Heat Shock Factors ◽  
Plant Growth And Development ◽  
Peach Genome ◽  
Significant Difference ◽  
Length Changes

Background Heat shock factors (HSFs) play important roles during normal plant growth and development and when plants respond to diverse stressors. Although most studies have focused on the involvement of HSFs in the response to abiotic stresses, especially in model plants, there is little research on their participation in plant growth and development or on the HSF (PpHSF) gene family in peach (Prunus persica). Methods DBD (PF00447), the HSF characteristic domain, was used to search the peach genome and identify PpHSFs. Phylogenetic, multiple alignment and motif analyses were conducted using MEGA 6.0, ClustalW and MEME, respectively. The function of PpHSF5 was confirmed by overexpression of PpHSF5 into Arabidopsis. Results Eighteen PpHSF genes were identified within the peach genome. The PpHSF genes were nonuniformly distributed on the peach chromosomes. Seventeen of the PpHSFs (94.4%) contained one or two introns, except PpHSF18, which contained three introns. The in silico-translated PpHSFs were classified into three classes (PpHSFA, PpHSFB and PpHSFC) based on multiple alignment, motif analysis and phylogenetic comparison with HSFs from Arabidopsis thaliana and Oryza sativa. Dispersed gene duplication (DSD at 67%) mainly contributed to HSF gene family expansion in peach. Promoter analysis showed that the most common cis-elements were the MYB (abiotic stress response), ABRE (ABA-responsive) and MYC (dehydration-responsive) elements. Transcript profiling of 18 PpHSFs showed that the expression trend of PpHSF5 was consistent with shoot length changes in the cultivar ‘Zhongyoutao 14’. Further analysis of the PpHSF5 was conducted in 5-year-old peach trees, Nicotiana benthamiana and Arabidopsis thaliana, respectively. Tissue-specific expression analysis showed that PpHSF5 was expressed predominantly in young vegetative organs (leaf and apex). Subcellular localization revealed that PpHSF5 was located in the nucleus in N. benthamiana cells. Two transgenic Arabidopsis lines were obtained that overexpressed PpHSF5. The root length and the number of lateral roots in the transgenic seedlings were significantly less than in WT seedlings and after cultivation for three weeks. The transgenic rosettes were smaller than those of the WT at 2–3 weeks. The two transgenic lines exhibited a dwarf phenotype three weeks after transplanting, although there was no significant difference in the number of internodes. Moreover, the PpHSF5-OE lines exhibited enhanced thermotolerance. These results indicated that PpHSF5 might be act as a suppresser of growth and development of root and aerial organs.

scholarly journals Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei-Meng Zhang ◽  
Da Fang ◽  
Xiu-Zhu Cheng ◽  
Jun Cao ◽  
Xiao-Li Tan
Keyword(s):  
Brassica Napus ◽  
Plant Growth ◽  
Gene Family ◽  
Nuclear Localization ◽  
Growth And Development ◽  
Gene Organization ◽  
Type I ◽  
Type Ii ◽  
Plant Growth And Development ◽  
Type Iii

AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.

scholarly journals Genome-wide analysis of metallothionein gene family in maize to reveal its role in development and stress resistance to heavy metal

2022 ◽  
Vol 55 (1) ◽  
Author(s):  
Canhong Gao ◽  
Kun Gao ◽  
Huixian Yang ◽  
Tangdan Ju ◽  
Jingyi Zhu ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Plant Growth ◽  
Stress Resistance ◽  
Binding Sites ◽  
Growth And Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Specific Expression

Abstract Background Maize (Zea mays L.) is a widely cultivated cereal and has been used as an optimum heavy metal phytoremediation crop. Metallothionein (MT) proteins are small, cysteine-rich, proteins that play important roles in plant growth and development, and the regulation of stress response to heavy metals. However, the MT genes for maize have not been fully analyzed so far. Methods The putative ZmMT genes were identified by HMMER.The heat map of ZmMT genes spatial expression analysis was generated by using R with the log2 (FPKM + 1).The expression profiles of ZmMT genes under three kinds of heavy metal stresses were quantified by using qRT-PCR. The metallothionein proteins was aligned using MAFFT and phylogenetic analysis were constructed by ClustalX 2.1. The protein theoretical molecular weight and pI, subcellular localization, TFs binding sites, were predicted using ProtParam, PSORT, PlantTFDB, respectively. Results A total of 9 ZmMT genes were identified in the whole genome of maize. The results showed that eight of the nine ZmMT proteins contained one highly conserved metallothio_2 domain, while ZmMT4 contained a Metallothio_PEC domain. All the ZmMT proteins could be classified into three major groups and located on five chromosomes. The ZmMT promoters contain a large number of hormone regulatory elements and hormone-related transcription factor binding sites. The ZmMT genes exhibited spatiotemporal specific expression patterns in 23 tissues of maize development stages and showed the different expression patterns in response to Cu, Cd, and Pb heavy metal stresses. Conclusions We identified the 9 ZmMT genes, and explored their conserved motif, tissue expression patterns, evolutionary relationship. The expression profiles of ZmMT genes under three kinds of heavy metal stresses (Cu, Cd, Pb) were analyzed. In summary, the expression of ZmMTs have poteintial to be regulated by hormones. The specific expression of ZmMTs in different tissues of maize and the response to different heavy metal stresses are revealed that the role of MT in plant growth and development, and stress resistance to heavy metals.

Sign in / Sign up

Export Citation Format

Share Document