Tissue-Specific RNA-Seq Analysis and Identification of Receptor-Like Proteins Related to Plant Growth in Capsicum annuum

Receptor-like proteins (RLPs) are a gene family of cell surface receptors that are involved in plant growth, development, and disease resistance. In a recent study, 438 pepper RLP genes were identified in the Capsicum annuum genome (CaRLPs) and determined to be present in response to multiple biotic stresses. To further understand the role of CaRLPs in plant growth and development, we analyzed expression patterns of all CaRLPs from various pepper tissues and developmental stages using RNA-seq. Ten CaRLP genes were selected for further analysis according to transcript levels with hierarchical clustering. The selected CaRLP genes displayed similarity of motifs within the same groups and structures typical of RLPs. To examine RLP function in growth and development, we performed loss-of-function analysis using a virus-induced gene silencing system. Three of the ten tested CaRLPs (CaRLP238, 253, and 360) in silenced plants exhibited phenotypic alteration with growth retardation compared to controls. All three gene-silenced peppers showed significant differences in root dry weight. Only CaRLP238 had significant differences in both root and shoot dry weight. Our results suggest that CaRLPs may play important roles in regulation of plant growth and development as well as function in defense responses to biotic stresses in the RLP gene family.

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

PeerJ ◽

10.7717/peerj.7950 ◽

2019 ◽

Vol 7 ◽

pp. e7950 ◽

Cited By ~ 2

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.

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Response of Poinsettia Growth and Development to Ratio of Radiant to Thermal Energy

HortScience ◽

10.21273/hortsci.33.3.508e ◽

1998 ◽

Vol 33 (3) ◽

pp. 508e-508

Author(s):

Bin Liu ◽

Royal D. Heins

Keyword(s):

Plant Growth ◽

Thermal Energy ◽

Growth And Development ◽

Model Simulation ◽

Interactive Effect ◽

Dry Weight ◽

Plant Spacing ◽

Plant Growth And Development ◽

Daily Light Integral ◽

Highly Correlated

A concept of ratio of radiant to thermal energy (RRT) has been developed to deal with the interactive effect of light and temperature on plant growth and development. This study further confirms that RRT is a useful parameter for plant growth, development, and quality control. Based on greenhouse experiments conducted with 27 treatment combinations of temperature, light, and plant spacing, a model for poinsettia plant growth and development was constructed using the computer program STELLA II. Results from the model simulation with different levels of daily light integral, temperature, and plant spacing showed that the RRT significantly affects leaf unfolding rate when RRT is lower than 0.025 mol/degree-day per plant. Plant dry weight is highly correlated with RRT; it increases linearly as RRT increases.

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

Frontiers in Genetics ◽

10.3389/fgene.2020.590535 ◽

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.

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

PeerJ ◽

10.7717/peerj.10961 ◽

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.

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Expression and function analysis of wheat expasin genes EXPA2 and EXPB1

Genetika ◽

10.2298/gensr1901261z ◽

2019 ◽

Vol 51 (1) ◽

pp. 261-274 ◽

Cited By ~ 1

Author(s):

Dong Zhu ◽

Yanlin Liu ◽

Man Jin ◽

Guanxing Chen ◽

Slaven Prodanovic ◽

...

Keyword(s):

Cell Wall ◽

Plant Growth ◽

Growth And Development ◽

Plant Cell Wall ◽

Function Analysis ◽

Structural Features ◽

Plant Growth And Development ◽

Cell Wall Loosening ◽

And Function ◽

Wall Loosening

Expansins are a group of plant cell wall loosening proteins that play important roles in plant growth and development. In this study, we performed the first study on the molecular characterization, transcriptional expression and functional properties of two wheat expansin genes TaEXPA2 and TaEXPB1. The results indicated that TaEXPA2 and TaEXPB1 genes had typical structural features of plant expansin gene family. As a member of ?-expansins, TaEXPA2 is closely related to rice OsEXPA17 while the ?- expansin member TaEXPB1 has closely phylogenetic relationships with rice OsEXPAB4. The genetic transformation to Arabidopsis showed that both TaEXPA2 and TaEXPB1 were located in cell wall and highly expressed in roots, leaves and seeds. Overexpression of TaEXPA2 and TaEXPB1 genes showed similar functions, causing rapid root elongation, early bolting, and increases in leaves number, rosette diameter and stems length. These results demonstrated that wheat expansin genes TaEXPA1 and TaEXPB2 can enhance plant growth and development.

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.714305 ◽

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.

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

10.21203/rs.2.22544/v2 ◽

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.

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Identification and Expression of SAUR Genes in the CAM Plant Agave

Genes ◽

10.3390/genes10070555 ◽

2019 ◽

Vol 10 (7) ◽

pp. 555

Author(s):

Gang Deng ◽

Xing Huang ◽

Li Xie ◽

Shibei Tan ◽

Thomas Gbokie ◽

...

Keyword(s):

Plant Growth ◽

Stress Responses ◽

Growth And Development ◽

Developmental Stages ◽

Auxin Signaling ◽

Plant Growth And Development ◽

Cam Plants ◽

African Countries ◽

Biotic Stresses ◽

Species Specific

Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave’s leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species.

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

10.21203/rs.2.22544/v3 ◽

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.

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