scholarly journals Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Yuntian Ye ◽  
Yongqiang Liu ◽  
Xiaolong Li ◽  
Qing Chen ◽  
Yong Zhang ◽  
...  
Keyword(s):  
Blue Light ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Light Treatment ◽  
Rna Seq ◽  
Function Annotation ◽  
Data Resource ◽  
Kegg Pathways ◽  
Flowering Regulation ◽  
Go Terms

Blue light is an important signal that regulates the flowering of strawberry plants. To reveal the mechanism of early flowering under blue light treatment at the transcriptional regulation level, seedlings of cultivated strawberry (Fragaria × ananassa Duch.) “Benihoppe” were subjected to a white light treatment (WL) and blue light treatment (BL) until their flowering. To detect the expression patterns of genes in response to BL, a transcriptome analysis was performed based on RNA-Seq. The results identified a total of 6875 differentially expressed genes (DEGs) that responded to BL, consisting of 3138 (45.64%) downregulated ones and 3737 (54.36%) upregulated ones. These DEGs were significantly enriched into 98 GO terms and 71 KEGG pathways based on gene function annotation. Among the DEGs, the expression levels of genes that might participate in light signaling (PhyB, PIFs, and HY5) and circadian rhythm (FKF1, CCA1, LHY, and CO) in plants were altered under BL. The BBX transcription factors which responded to BL were also identified. The result showed that the FaBBX29, one of strawberry’s BBX family genes, may play an important role in flowering regulation. Our results provide a timely, comprehensive view and a reliable reference data resource for further study of flowering regulation under different light qualities.

scholarly journals Global Transcriptomic Profile Analysis of Genes Involved in Lignin Biosynthesis and Accumulation Induced by Boron Deficiency in Poplar Roots

Biomolecules ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 156 ◽  
Author(s):  
Wan-Long Su ◽  
Na Liu ◽  
Li Mei ◽  
Jie Luo ◽  
Yi-Jie Zhu ◽  
...  
Keyword(s):  
Histidine Kinase ◽  
Theoretical Basis ◽  
Reference Data ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Boron Deficiency ◽  
Rna Seq ◽  
Lignin Accumulation

To uncover the transcriptomic mechanism of lignin accumulation caused by boron deficiency (BD), Nanlin895 (Populus × euramericana “Nanlin895”) was subjected to control (CK, 0.25 mg·L−1) and BD (0 mg·L−1) treatments for 3 days. RNA-Seq was carried out to survey the expression patterns of the lignin-regulated biosynthetic genes in response to BD. The results showed that 5946 genes were identified as differentially expressed genes (DEGs), 2968 (44.2%) of which were upregulated and 3318 (55.8%) of which were downregulated in response to BD. Among them, the expression of lignin monomer biosynthetic (PAL, CCR, CAD, COMT, F5H, PER/LAC) and modulated genes, for example, transcription factors (MYBs) and hormone signal regulating genes (GIDs, histidine kinase 1, coronatine-insensitive protein 1), were upregulated, and some hormone signal regulating genes, such as AUXs and BR-related (sterol methyltransferases), were downregulated under BD treatment. There are also some genes that were screened as candidates for an association with wood formation, which will be used for the further analysis of the function of lignin formation. These results provide an important theoretical basis and reference data in plant for further research on the mechanism of lignin accumulation under BD.

Expression characterisation of cyclophilin BrROC1 during light treatment and abiotic stresses response in Brassica rapa subsp. rapa ‘Tsuda’

2018 ◽  
Vol 45 (12) ◽  
pp. 1223 ◽  
Author(s):  
Haifang Yan ◽  
Bo Zhou ◽  
Wei He ◽  
Yuzhe Nie ◽  
Yuhua Li
Keyword(s):  
Blue Light ◽  
Brassica Rapa ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Transcript Level ◽  
Light Treatment ◽  
Anthocyanin Synthesis ◽  
Root Epidermis ◽  
High Or Low Temperature ◽  
Level Analysis

ROC1 is a prototypic peptidyl prolyl cis/trans isomerase (PPIase) of the plant cytosol belonging to the large subfamily of cyclophilins that are associated with diverse functions through foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins have been reported, the molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. To characterise the roles of BrROC1 during light treatment and their responses in various abiotic stresses, we identified BrROC1 genes and characterised their expression patterns in Brassica rapa subsp. rapa ‘Tsuda’. Our results showed that BrROC1 genes are multi-family genes. Transcript level analysis showed BrROC1-2 expressed higher than BrROC1-1 in 0 to 6-day-old seedlings under natural light. Moreover, BrROC1-2 genes were also induced to highly express in the cotyledon, upper hypocotyls and lower hypocotyls of seedlings under UV-A and blue-light treatment. In addition, the transcript level of BrROC1-1 was higher in pigment tissues than that in unpigment tissues (cotyledon and lower hypocotyl) under UV-A and blue-light treatment. Furthermore, when the unpigment epidermis (shaded light) of 2-month-old ‘Tsuda’ turnip roots was exposed to UV-A light, transcript levels of the BrROC1-1 and BrROC1-2 were significantly increased with time prolongation. These two BrROC1 genes might be involved in UV-A-induced anthocyanin synthesis in the root epidermis of ‘Tsuda’ turnip, which accumulates high levels of anthocyanin. These two BrROC1 genes were also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. Then, the results indicate that BrROC1 genes are involved in light induction response and may play important roles in adaptation of plants to various environmental stresses.

scholarly journals Transcriptomic analysis reveals responses to Cycloastragenol in Arabidopsis thaliana

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0242986
Author(s):  
Wissem Mhiri ◽  
Merve Ceylan ◽  
Neslihan Turgut-Kara ◽  
Barbaros Nalbantoğlu ◽  
Özgür Çakır
Keyword(s):  
Telomerase Activity ◽  
Cytochrome P450s ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Transcriptional Responses ◽  
Kegg Pathways ◽  
Signaling Mechanisms ◽  
Genome Wide ◽  
Go Terms ◽  
Cag A

Cycloastragenol (CAG), a molecule isolated from ‘Astragalus membranaceus’, stimulates the telomerase activity and cell proliferation significantly. It has been proven that CAG has the ability to prevent some diseases in humans. In this study, we aimed to figure out the CAG effects on the different signaling mechanisms in plants and to broadly analyze the genome-wide transcriptional responses in order to demonstrate CAG as a new key molecule that can potentially help plants to overcome different environmental stresses. RNA-seq strategy was employed to assess the transcriptional profiles in A. thaliana calli. Our work primarily focused on an overall study on the transcriptomic responses of A. thaliana to CAG. A total of 22593 unigenes have been detected, among which 1045 unigenes associated with 213 GO terms were differentially expressed and were assigned to 118 KEGG pathways. The up-regulated genes are principally involved in cellular and metabolic processes in addition to the response to a stimulus. The data analysis revealed genes associated with defense signaling pathways such as cytochrome P450s transporter, antioxidant system genes, and stress-responsive protein families were significantly upregulated. The obtained results can potentially help in better understanding biotic and/or abiotic tolerance mechanisms in response to CAG.

scholarly journals Light Irradiation Coupled with Exogenous Metal Ions to Enhance Exopolysaccharide Synthesis from Agaricus sinodeliciosus ZJU-TP-08 in Liquid Fermentation

2021 ◽  
Vol 7 (11) ◽  
pp. 992
Author(s):  
Hongyun Lu ◽  
Siyu Liu ◽  
Shengliang Zhang ◽  
Qihe Chen
Keyword(s):  
Oxidative Stress ◽  
Metal Ions ◽  
Blue Light ◽  
Light Treatment ◽  
Light Shift ◽  
Rna Seq ◽  
Gene Expressions ◽  
Shift Strategy ◽  
And Oxidative Stress ◽  
Exopolysaccharides Production

To promote Agaricus sinodeliciosus var. Chaidam ZJU-TP-08 growth and metabolites accumulation, a novel integrated strategy was developed by adopting high levels of metal ions coupled with light treatment. The results revealed that yellow and blue light could significantly promote biomass and exopolysaccharides production, respectively. Furthermore, the yellow–blue light shift strategy could stimulate exopolysaccharides formation. Ca2+ ions coupled with blue light mostly promoted exopolysaccharides production related to oxidative stress, which was 42.00% and 58.26% higher than that of Ca2+ ions coupled with the non-light and dark cultivation without Ca2+ ions in 5-L bioreactor. RNA-seq was performed to uncover the underlined molecular mechanism regulated by light-induced gene expressions in exopolysaccharides biosynthesis and oxidative stress. The findings of this work provide valuable insights into adopting metal ions coupled with the light-assisted method for the macrofungus submerged fermentation for exopolysaccharides production.

scholarly journals Transcriptome Analysis of Spleen in Chickens Administered β-glucan Derived From Yeast Cell Wall

2021 ◽  
Author(s):  
Liting Cao ◽  
Jianrong Zhang ◽  
Yiwen Qu ◽  
Weihao Li ◽  
Yue Ma ◽  
...  
Keyword(s):  
Cell Wall ◽  
Oral Administration ◽  
Yeast Cell ◽  
Yeast Cell Wall ◽  
Rna Seq ◽  
Cell Wall Polysaccharides ◽  
Kegg Pathways ◽  
Expression Of Genes ◽  
Multiple Signaling ◽  
Go Terms

Abstract Background: Our previous study shown that oral administration of a product contained yeast cell wall polysaccharides enhanced immune responses elicited by Newcastle disease virus and changed microbial community of cecum in chickens.Results: The present study was design to investigate the potential molecular mechanism in relation to the immunomodulation of β-glucan in chickens. Using RNA-sequence (RNA-seq) technique, we identified 198 DEGs in spleen in chickens after oral administration of β-glucan. In addition, these DEGs were significantly enriched in 205 GO terms and 7 KEGG pathways. Conclusions: β-glucan might regulate chicken immune system by regulating expression of genes involved in cognition, cytokines, binding, enzyme activities and multiple signaling pathway.

scholarly journals Genome-Wide Identification and Expression Profile Analysis of the NF-Y Transcription Factor Gene Family in Petunia hybrida

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 336 ◽  
Author(s):  
Qian Wei ◽  
Shiyun Wen ◽  
Chuying Lan ◽  
Yixun Yu ◽  
Guoju Chen
Keyword(s):  
Stress Response ◽  
Gene Family ◽  
Stress Responses ◽  
Petunia Hybrida ◽  
Profile Analysis ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Draft Genome ◽  
Rna Seq ◽  
Expression Profile Analysis

Nuclear Factor Ys (NF-Ys) are a class of heterotrimeric transcription factors that play key roles in many biological processes, such as abiotic stress responses, flowering time, and root development. The petunia (Petunia hybrida) is a model ornamental plant, and its draft genome has been published. However, no details regarding the NF-Y gene family in petunias are available. Here, 27 NF-Y members from the petunia genome were identified, including 10 PhNF-YAs, 13 PhNF-YBs, and 4 PhNF-YCs. Multiple alignments showed that all PhNF-Y proteins had clear conserved core regions flanked by non-conserved sequences. Phylogenetic analyses identified five pairs of orthologues NF-YB proteins from Petunia and Arabidopsis, and six pairs of paralogues NF-Y proteins in Petunia. Analysis of the gene structure and conserved motifs further confirmed the closer relationship in each subfamily. Bioinformatics analysis revealed that 16 PhNF-Ys could be targeted by 18 miRNA families. RNA-seq results showed that expression patterns of PhNF-Ys among four major organs (leaf, stem, flower, and root) were clustered into six major groups. The stress response pattern of PhNF-Ys was identified under cold, heat, drought, and salinity treatments. Based on the RNA-seq data, we found that 3 genes responded to drought, 4 genes responded to salt, 10 genes responded to cold, and 9 genes responded to hot. In conclusion, this study provides useful information for further studying the functions of NF-Ys in stress response.

scholarly journals Transcriptome Analysis and Identification of Insecticide Tolerance-Related Genes after Exposure to Insecticide in Sitobion avenae

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 951
Author(s):  
Ning Wei ◽  
Yongzhi Zhong ◽  
Lulu Lin ◽  
Minghui Xie ◽  
Guangling Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Expression Patterns ◽  
Sitobion Avenae ◽  
Rna Seq ◽  
Kegg Pathways ◽  
Qrt Pcr ◽  
Stress Response Genes ◽  
Grain Aphid ◽  
Insecticide Tolerance ◽  
Polymerase Chain

Aphids cause serious losses to the production of wheat. The grain aphid, Sitobion avenae, which is the dominant species of aphid in all wheat regions of China, is resistant to a variety of insecticides, including imidacloprid and chlorpyrifos. However, the resistance and mechanism of insecticide tolerance of S. avenae are still unclear. Therefore, this study employed transcriptome analysis to compare the expression patterns of stress response genes under imidacloprid and chlorpyrifos treatment for 15 min, 3 h, and 36 h of exposure. S. avenae adult transcriptome was assembled and characterized first, after which samples treated with insecticides for different lengths of time were compared with control samples, which revealed 60–2267 differentially expressed unigenes (DEUs). Among these DEUs, 31–790 unigenes were classified into 66–786 categories of gene ontology (GO) functional groups, and 24–760 DEUs could be mapped into 54–268 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Finally, 11 insecticide-tolerance-related unigenes were chosen to confirm the relative expression by quantitative real-time polymerase chain reaction (qRT-PCR) in each treatment. Most of the results between qRT-PCR and RNA sequencing (RNA-Seq) are well-established. The results presented herein will facilitate molecular research investigating insecticide resistance in S. avenae, as well as in other wheat aphids.

scholarly journals Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Chunsheng Gao ◽  
Chaohua Cheng ◽  
Lining Zhao ◽  
Yongting Yu ◽  
Qing Tang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Differentially Expressed Genes ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Rna Seq ◽  
Kegg Pathways

Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.

scholarly journals GhCO and GhCRY1 accelerate floral meristem initiation in response to blue light to shorten cotton breeding

2022 ◽  
Author(s):  
Shuxun Yu ◽  
XIAO li ◽  
Yuanlong Wu ◽  
Zhenping Liu ◽  
Zhonghua Li ◽  
...  
Keyword(s):  
Blue Light ◽  
Apical Meristem ◽  
Light Treatment ◽  
Rna Seq ◽  
Early Maturity ◽  
Treatment Analysis ◽  
Light Signals ◽  
Fate Decision ◽  
Floral Meristems

The shoot apical meristem (SAM) is a special category of tissue with pluripotency that forms new organs and individuals, especially floral individuals. However, little is known about the fate of cotton SAMs as a tunica corpus structure. Here, we demonstrate that cotton SAM fate decisions depend on light signals and circadian rhythms, and the genes GhFKF1, GhGI, GhCRY1 and GhCO were responsible for SAM fate decisions and highlighted via RNA sequencing (RNA-seq) analysis of different cotton cultivars, as confirmed by genetic analysis via the CRISPR-Cas9 system. In situ hybridization (ISH) analysis showed that the GhCO gene, induced by a relatively high blue light proportion, was highly upregulated during the initiation of floral meristems (FMs). Further blue light treatment analysis showed that the transition from vegetative to reproductive growth of SAM was promoted by a high proportion of blue light, coupled with high expression of the blue light-responsive genes GhCO and GhCRY1. Taken together, our study suggests that blue light signalling plays a key role in the fate decision of cotton SAM. These results provide a strategy to regulate the SAM differentiation of cotton by using the CRISPR-Cas9 system to change the ratio of red and blue light absorption to breed early-maturity cotton.

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