Comprehensive transcriptome resource for response to phytohormone-induced signaling in Capsicum annuum L.

Abstract Objectives Phytohormones are small signaling molecules with crucial roles in plant growth, development, and environmental adaptation to biotic and abiotic stress responses. Despite several previously published molecular studies focused on plant hormones, our understanding of the transcriptome induced by phytohormones remains unclear, especially in major crops. Here, we aimed to provide transcriptome dataset using RNA sequencing for phytohormone-induced signaling in plant. Data description We used high-throughput RNA sequencing profiling to investigate the pepper plant response to treatment with four major phytohormones (salicylic acid, jasmonic acid, ethylene, and abscisic acid). This dataset yielded 78 samples containing three biological replicates per six different time points for each treatment and the control, constituting 187.8 Gb of transcriptome data (2.4 Gb of each sample). This comprehensive parallel transcriptome data provides valuable information for understanding the relationships and molecular networks that regulate the expression of phytohormone-related genes involved in plant developments and environmental stress adaptation.

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Regulation of drought tolerance in Arabidopsis involves PLATZ4-mediated transcriptional suppression of PIP2;8

10.1101/2021.10.06.463369 ◽

2021 ◽

Author(s):

Miao Liu ◽

Chunyan Wang ◽

Zhen Ji ◽

Lei Zhang ◽

Chunlong Li ◽

...

Keyword(s):

Drought Tolerance ◽

Stress Responses ◽

Water Loss ◽

Stomatal Closure ◽

Xenopus Laevis Oocytes ◽

In Planta ◽

Biotic And Abiotic Stress ◽

Transcriptional Suppression ◽

Aba Sensitivity ◽

Growth Development

PLATZ transcription factors play important roles in plant growth, development, biotic and abiotic stress responses. However, how PLATZ regulates plant drought tolerance and ABA sensitivity remains largely unknown. Here, we show that PLATZ4 increases drought tolerance and ABA sensitivity in Arabidopsis thaliana by suppressing the expression of PIP2;8, while upregulating expression of ABI3, ABI4 and ABI5. PLATZ4 directly binds A/T-rich sequences within the PIP2;8 promoter. Consistent with this, PIP2;8 acts epistatically to PLATZ4. Furthermore, the aquaporin activity of PIP2;8 was confirmed in Xenopus laevis oocytes in response to osmotic stress. Analysis of water loss of seedlings overexpressing PIP2;8 or lacking PIP2;8 function indicated that PIP2;8-mediated water flow is particularly active in response to drought stress in planta. In platz4 mutant and PLATZ4-overexpressing plants, water loss and stomatal closure changed oppositely to those in pip2;8 mutants and PIP2;8-overexpressing plants, respectively. In addition, the interaction between PLATZ4 and AITR6 was confirmed by several assays, and the binding of PIP2;8 promoter by PLATZ4 was strengthened by an interaction with AITR6. Collectively, our findings reveal that PLATZ4 interacts with AITR6 to increase ABA sensitivity and drought tolerance by upregulating expression of ABI3, ABI4 and ABI5 while inhibiting the expression of PIP2;8 and associated genes.

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Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes

International Journal of Molecular Sciences ◽

10.3390/ijms21186872 ◽

2020 ◽

Vol 21 (18) ◽

pp. 6872

Author(s):

Woo-Jong Hong ◽

Xu Jiang ◽

Hye Ryun Ahn ◽

Juyoung Choi ◽

Seong-Ryong Kim ◽

...

Keyword(s):

Stress Response ◽

Cold Stress ◽

Stress Responses ◽

Oryza Sativa L ◽

Molecular Networks ◽

Transcriptome Data ◽

Environmental Stress Response ◽

Stay Green ◽

Systematic Analysis ◽

Functional Features

Rice (Oryza sativa L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein–protein interaction network encompassing four hub genes and analyzed the roles of the Stay-Green (SGR) gene in regulating crosstalk with sgr mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.

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An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

Protein and Peptide Letters ◽

10.2174/0929866527666200625202028 ◽

2020 ◽

Vol 27 ◽

Author(s):

Fırat Kurt

Keyword(s):

Stress Responses ◽

Chelating Agent ◽

Biological Processes ◽

Biotic And Abiotic Stress ◽

Oligopeptide Transporter ◽

Binding Residues ◽

Fe Homeostasis ◽

Proteins Interactions ◽

Insight Into ◽

Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

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Blood transcriptome analysis of patients with uncomplicated bacterial infection and sepsis

BMC Research Notes ◽

10.1186/s13104-021-05488-w ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Velma Herwanto ◽

Benjamin Tang ◽

Ya Wang ◽

Maryam Shojaei ◽

Marek Nalos ◽

...

Keyword(s):

Bacterial Infection ◽

Healthy Controls ◽

Beta Globin ◽

Transcriptome Data ◽

Valuable Resource ◽

Globin Mrna ◽

Blood Samples ◽

Data Description ◽

Pathway Activation ◽

Blood Transcriptome

Abstract Objectives Hospitalized patients who presented within the last 24 h with a bacterial infection were recruited. Participants were assigned into sepsis and uncomplicated infection groups. In addition, healthy volunteers were recruited as controls. RNA was prepared from whole blood, depleted from beta-globin mRNA and sequenced. This dataset represents a highly valuable resource to better understand the biology of sepsis and to identify biomarkers for severe sepsis in humans. Data description The data presented here consists of raw and processed transcriptome data obtained by next generation RNA sequencing from 105 peripheral blood samples from patients with uncomplicated infections, patients who developed sepsis, septic shock patients, and healthy controls. It is provided as raw sequenced reads and as normalized log2 transformed relative expression levels. This data will allow performing detailed analyses of gene expression changes between uncomplicated infections and sepsis patients, such as identification of differentially expressed genes, co-regulated modules as well as pathway activation studies.

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Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

Sustainability ◽

10.3390/su13052826 ◽

2021 ◽

Vol 13 (5) ◽

pp. 2826

Author(s):

Yan Tong ◽

Hui Huang ◽

YuHua Wang

Keyword(s):

Stress Responses ◽

Cold Treatment ◽

Dendrobium Officinale ◽

Functional Domain ◽

Cis Elements ◽

Genome Wide Analysis ◽

Functional Studies ◽

Genome Wide ◽

Growth Development ◽

Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

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Biotic and Abiotic Stress Responses of Domesticated Vigna Legumes: A Comprehensive Review

Microbial Mitigation of Stress Response of Food Legumes ◽

10.1201/9781003028413-3 ◽

2020 ◽

pp. 11-23

Author(s):

Difo Voukang Harouna

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Biotic And Abiotic Stress ◽

Comprehensive Review

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Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies

Plant Phenomics ◽

10.34133/2020/5801869 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13 ◽

Cited By ~ 2

Author(s):

Jordan Ubbens ◽

Mikolaj Cieslak ◽

Przemyslaw Prusinkiewicz ◽

Isobel Parkin ◽

Jana Ebersbach ◽

...

Keyword(s):

Image Processing ◽

Association Mapping ◽

Stress Responses ◽

Interspecific Cross ◽

Response To Treatment ◽

Brassica Napus L ◽

Nested Association Mapping ◽

Latent Space ◽

Using Data ◽

Candidate Loci

Association mapping studies have enabled researchers to identify candidate loci for many important environmental tolerance factors, including agronomically relevant tolerance traits in plants. However, traditional genome-by-environment studies such as these require a phenotyping pipeline which is capable of accurately measuring stress responses, typically in an automated high-throughput context using image processing. In this work, we present Latent Space Phenotyping (LSP), a novel phenotyping method which is able to automatically detect and quantify response-to-treatment directly from images. We demonstrate example applications using data from an interspecific cross of the model C4 grass Setaria, a diversity panel of sorghum (S. bicolor), and the founder panel for a nested association mapping population of canola (Brassica napus L.). Using two synthetically generated image datasets, we then show that LSP is able to successfully recover the simulated QTL in both simple and complex synthetic imagery. We propose LSP as an alternative to traditional image analysis methods for phenotyping, enabling the phenotyping of arbitrary and potentially complex response traits without the need for engineering-complicated image-processing pipelines.

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Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula

PeerJ ◽

10.7717/peerj.8471 ◽

2020 ◽

Vol 8 ◽

pp. e8471 ◽

Cited By ~ 1

Author(s):

Lei Ling ◽

Yue Qu ◽

Jintao Zhu ◽

Dan Wang ◽

Changhong Guo

Keyword(s):

Cicer Arietinum ◽

Medicago Truncatula ◽

Stress Responses ◽

Pcr Analysis ◽

Biotic And Abiotic Stress ◽

Systematic Analysis ◽

Genome Wide ◽

Specific Proteins ◽

Solid Foundation ◽

In Silico Analyses

Valine-glutamine (VQ) proteins are plant-specific proteins that play crucial roles in plant development as well as biotic and abiotic stress responses. VQ genes have been identified in various plants; however, there are no systematic reports in Cicer arietinum or Medicago truncatula. Herein, we identified 19 and 32 VQ genes in C. arietinum and M. truncatula, respectively. A total of these VQ genes were divided into eight groups (I–VIII) based on phylogenetic analysis. Gene structure analyses and motif patterns revealed that these VQ genes might have originated from a common ancestor. In silico analyses demonstrated that these VQ genes were expressed in different tissues. qRT-PCR analysis indicated that the VQ genes were differentially regulated during multiple abiotic stresses. This report presents the first systematic analysis of VQ genes from C. arietinum and M. truncatula and provides a solid foundation for further research of the specific functions of VQ proteins.

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Brassinosteroids in Plants: Crosstalk with Small-Molecule Compounds

Biomolecules ◽

10.3390/biom11121800 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1800

Author(s):

Dongliang Hu ◽

Lijuan Wei ◽

Weibiao Liao

Keyword(s):

Small Molecule ◽

Stress Responses ◽

Plant Hormone ◽

Photosynthetic Capacity ◽

Stem Elongation ◽

Adventitious Rooting ◽

Plant Growth And Development ◽

Growth Development ◽

Stress Damage ◽

Physiological And Biochemical

Brassinosteroids (BRs) are known as the sixth type of plant hormone participating in various physiological and biochemical activities and play an irreplaceable role in plants. Small-molecule compounds (SMCs) such as nitric oxide (NO), ethylene, hydrogen peroxide (H2O2), and hydrogen sulfide (H2S) are involved in plant growth and development as signaling messengers. Recently, the involvement of SMCs in BR-mediated growth and stress responses is gradually being discovered in plants, including seed germination, adventitious rooting, stem elongation, fruit ripening, and stress responses. The crosstalk between BRs and SMCs promotes plant development and alleviates stress damage by modulating the antioxidant system, photosynthetic capacity, and carbohydrate metabolism, as well as osmotic adjustment. In the present review, we try to explain the function of BRs and SMCs and their crosstalk in the growth, development, and stress resistance of plants.

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