scholarly journals De novo assembly of Amorpha fruticosa L. transcriptome in response to drought stress provides insight into the tolerance mechanisms

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11044
Author(s):  
Xinzhu Sun ◽  
Songmiao Hu ◽  
Xin Wang ◽  
He Liu ◽  
Yun wei Zhou ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Drought Stress ◽  
Drought Resistance ◽  
Stress Responses ◽  
Hormonal Regulation ◽  
De Novo ◽  
Expression Patterns ◽  
Peg 6000 ◽  
Amorpha Fruticosa ◽  
Wall Signal

Background Amorpha fruticosa L. is a deciduous shrub that is native to North America and has been introduced to China as an ornamental plant. In order to clarify the drought resistance characteristics of Amorpha fruticosa L. and excavate the related genes involved in drought resistance regulation pathway, the mechanism of drought resistance stress of Amorpha fruticosa L. was revealed by the changes of transcriptome of Amorpha fruticosa L. under drought stress.Through the changes of the transcriptome of Amorpha fruticosa L. under drought stress, the mechanism of anti-stress of Amorpha fruticosa L. could be revealed. Methods Different concentrations of polyethylene glycol-6000 (PEG-6000) was used to simulate drought stress, and transcriptomic analysis was used to reveal the changes of gene expression patterns in Amorpha fruticosa L. seedlings. Results Results showed that Amorpha fruticosa L. seedlings were seriously affected by PEG-6000. As for the differently expressed genes (DEGs), most of them were up-regulated. The additional Go and KEGG analysis results showed that DEGs were functionally enriched in cell wall, signal transduction and hormonal regulation related pathways. DEGs like AfSOD, AfHSP, AfTGA, AfbZIP and AfGRX play roles in response to drought stress. Conclusion In conclusion, Amorpha fruticosa L. seedlings were sensitive to drought, which was different from Amorpha fruticosa L. tree, and the genes functions in drought stress responses via ABA-independent pathways. The up-regulation of Salicylic acid signal related DEGs (AfTGA and AfPR-1) indicated that Salicylic acid play a key role in response to drought stress in Amorpha fruticosa L.

scholarly journals De novo assembly of Amorpha fruticosa (Amorpha fruticosa L.) transcriptome in response to drought stress provides insight into the tolerance mechanisms

2019 ◽  
Author(s):  
Xinzhu SUN ◽  
He LIU ◽  
Songmiao HU ◽  
Yunwei ZHOU ◽  
Qingjie GUAN
Keyword(s):  
Salicylic Acid ◽  
Drought Stress ◽  
Stress Responses ◽  
Hormonal Regulation ◽  
De Novo ◽  
Expression Patterns ◽  
Peg 6000 ◽  
Amorpha Fruticosa ◽  
Drought Tolerant ◽  
Wall Signal

Abstract Background Amorpha fruticosa (Amorpha fruticosa L.) is a deciduous shrub that is native to North America and has been introduced to China as an ornamental plant.In order to cultivate drought-tolerant Amorpha fruticosa varieties, it is important to understand the drought-tolerant mechanism of Amorpha fruticosa. Through the changes of the transcriptome of Amorpha fruticosa under drought stress, the mechanism of anti-stress of Amorpha fruticosa could be revealed. Different concentrations of polyethylene glycol-6000 (PEG-6000) was used to simulate drought stress, and transcriptomic analysis was used to reveal the changes of gene expression patterns in Amorpha fruticosa seedlings.Results Results showed that Amorpha fruticosa seedlings were seriously affected by PEG-6000. As for the differently expressed genes (DEGs), most of them were up-regulated. The additional Go and KEGG analysis results showed that DEGs were functionally enriched in cell wall, signal transduction and hormonal regulation related pathways. DEGs like AfSOD, AfHSP, AfTGA, AfbZIP and AfGRX play roles in response to drought stress.Conclusion In conclusion, Amorpha fruticosa seedlings were sensitive to drought, which was different from Amorpha fruticosa tree, and the genes functions in drought stress responses via ABA‐independent pathways. The up-regulation of Salicylic acid signal related DEGs (AfTGA and AfPR-1) indicated that Amorpha fruticosa can resist drought stress through Salicylic acid.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

An ABA-flavonoid relationship contributes to the differences in drought resistance between different sea buckthorn subspecies

2020 ◽  
Author(s):  
Guori Gao ◽  
Zhongrui Lv ◽  
Guoyun Zhang ◽  
Jiayi Li ◽  
Jianguo Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Drought Resistance ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Normal Growth ◽  
Carotenoid Biosynthesis ◽  
Sea Buckthorn ◽  
Mutual Regulation ◽  
The Difference

Abstract Drought is the most severe abiotic stress and hinders the normal growth and development of plants. Sea buckthorn (Hippophae rhamnoides Linn.) is a typical drought-resistant tree species. In this study, the leaves of the H. rhamnoides ssp. sinensis (“FN”) and H. rhamnoides ssp. mongolica (“XY”) were selected during drought-recovery cycles for RNA sequencing, and physiological and biochemical analyses. The results revealed that drought stress significantly decreased leaf water potential, net photosynthetic rate, and stomatal conductance in both sea buckthorn subspecies. Similarly, the contents of flavone, flavonol, isoflavone and flavanone significantly decreased under drought stress in “XY.” Conversely, in “FN,” the flavone and abscisic acid (ABA) contents were significantly higher under drought stress and recovered after rehydration. Meanwhile, 4,618 and 6,100 differentially expressed genes (DEGs) were identified under drought stress in “FN” and “XY,” respectively. In total, 5,164 DEGs were observed in the comparison between “FN” and “XY” under drought stress. This was more than the 3,821 and 3,387 DEGs found when comparing the subspecies under control and rehydration conditions, respectively. These DEGs were mainly associated with carotenoid biosynthesis, flavonoid biosynthesis, photosynthesis, and plant hormone signal transduction. Six hub DEGs (ABCG5, ABCG22, ABCG32, ABCG36, ABF2 and PYL4) were identified to respond to drought stress based on WGCNA and BLAST analysis using DroughtDB. These six DEGs were annotated to play roles in the ABA-dependent signaling pathway. Sixteen RNA sequencing results involving eight genes and similar expression patterns (12/16) were validated using quantitative real-time PCR. The biochemical and molecular mechanisms underlying the regulation of drought responses by ABA and flavonoids in sea buckthorn were clarified. In this study, gene co-expression networks were constructed, and the results suggested that the mutual regulation of ABA and flavonoid signaling contributed to the difference in drought resistance between the different sea buckthorn subspecies.

scholarly journals Effects of Exogenous Salicylic Acid on Drought Response and Characterization of Dehydrins in Impatiens walleriana

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1589
Author(s):  
Dragana D. Antonić ◽  
Angelina R. Subotić ◽  
Milan B. Dragićević ◽  
Danijel Pantelić ◽  
Snežana M. Milošević ◽  
...  
Keyword(s):  
Lipid Peroxidation ◽  
Salicylic Acid ◽  
Drought Stress ◽  
De Novo ◽  
Foliar Application ◽  
Drought Response ◽  
Leaf Transcriptome ◽  
Relative Water ◽  
Impatiens Walleriana

Impatiens walleriana is a valued ornamental plant sensitive to drought stress. We investigated whether the foliar application of 2mM salicylic acid (SA) can protect potted I. walleriana plants from drought stress. The plants were divided into: watered plants, drought-stressed plants, watered plants treated with SA and drought-stressed plants treated with SA. The number of flowers and flower buds, relative water content (RWC), contents of malondialdehyde (MDA) and proline (Pro) and the activities of superoxide dismutases, catalases and peroxidases were recorded at different time points. Three dehydrin sequences were identified in de novo assembled leaf transcriptome: IwDhn1, IwDhn2.1 and IwDhn2.2. Drought stress caused wilting, floral abortion, reduction of RWC and increased MDA—an indicator of lipid peroxidation. In response to drought, Impatiens accumulated Pro and induced chloroplastic Cu/ZnSOD and two peroxidase isoforms. The most remarkable drought response was strong induction of IwDhn2.1 and IwDhn2.2. Rehydration restored RWC, Pro level, Cu/ZnSOD activity and dehydrins expression in drought-stressed plants approximately to the values of watered plants.SA had ameliorating effects on plants exposed to drought, including prevention of wilting, preservation of RWC, increased Pro accumulation, modulation of antioxidative activities and remarkable decrease of lipid peroxidation, but without effects on flowers’ preservation.

scholarly journals Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Shi ◽  
Wei Jiao ◽  
Lan Yun ◽  
Zhiqiang Zhang ◽  
Xiujuan Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Small Rna ◽  
Mirna Target ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Limiting Factor ◽  
Degradome Sequencing ◽  
Medicago Ruthenica

Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica (M. ruthenica) is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, microRNAs (miRNAs), and key miRNA-target pairs in M. ruthenica under drought and rewatering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed in three test conditions (CK: control, DS: plants under drought stress, and RW: plants rewatering after drought stress). The degradome sequencing (AllenScore < 4) analysis revealed that 104 miRNAs (11 novel and 93 conserved miRNAs) were identified with 263 target transcripts, forming 296 miRNA-target pairs in three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21, 18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

scholarly journals Physiological and Differential Proteomic Analyses of Imitation Drought Stress Response in Sorghum bicolor Root at the Seedling Stage

2020 ◽  
Vol 21 (23) ◽  
pp. 9174
Author(s):  
Hongbing Li ◽  
Yulin Li ◽  
Qingbo Ke ◽  
Sang-Soo Kwak ◽  
Suiqi Zhang ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Sorghum Bicolor ◽  
Stress Responses ◽  
Expression Patterns ◽  
Physiological Mechanism ◽  
Seedling Stage ◽  
Ros Scavenging ◽  
Root Response

Drought is one of the most important constraints on the growth and productivity of many crops, including sorghum. However, as a primary sensing organ, the plant root response to drought has not been well documented at the proteomic level. In the present study, we compared physiological alteration and differential accumulation of proteins in the roots of sorghum (Sorghum bicolor) inbred line BT×623 response to Polyethylene Glycol (PEG)-induced drought stress at the seedling stage. Drought stress (up to 24 h after PEG treatment) resulted in increased accumulation of reactive oxygen species (ROS) and subsequent lipid peroxidation. The proline content was increased in drought-stressed plants. The physiological mechanism of sorghum root response to drought was attributed to the elimination of harmful free radicals and to the alleviation of oxidative stress via the synergistic action of antioxidant enzymes, such as superoxide dismutase, peroxidase, and polyphenol oxidase. The high-resolution proteome map demonstrated significant variations in about 65 protein spots detected on Coomassie Brilliant Blue-stained 2-DE gels. Of these, 52 protein spots were identified by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS) representing 49 unique proteins; the levels of 43 protein spots were increased, and 22 were decreased under drought condition. The proteins identified in this study are involved in a variety of cellular functions, including carbohydrate and energy metabolism, antioxidant and defense response, protein synthesis/processing/degradation, transcriptional regulation, amino acid biosynthesis, and nitrogen metabolism, which contribute jointly to the molecular mechanism of outstanding drought tolerance in sorghum plants. Analysis of protein expression patterns and physiological analysis revealed that proteins associated with changes in energy usage; osmotic adjustment; ROS scavenging; and protein synthesis, processing, and proteolysis play important roles in maintaining root growth under drought stress. This study provides new insight for better understanding of the molecular basis of drought stress responses, aiming to improve plant drought tolerance for enhanced yield.

scholarly journals Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cuiling Yuan ◽  
Chunjuan Li ◽  
Xiaodong Lu ◽  
Xiaobo Zhao ◽  
Caixia Yan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Drought Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Nac Transcription Factor ◽  
Rna Seq ◽  
A Genome ◽  
Salt And Drought Stress

Abstract Background Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. Results We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. Conclusion Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.

scholarly journals Evaluation of drought resistance and transcriptome analysis for the identification of drought-responsive genes in Iris germanica

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jingwei Zhang ◽  
Dazhuang Huang ◽  
Xiaojie Zhao ◽  
Man Zhang
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Drought Resistance ◽  
Molecular Mechanisms ◽  
Cdna Libraries ◽  
Sequencing Analysis ◽  
Peg 6000 ◽  
Sequencing Platform ◽  
Iris Germanica ◽  
Drought Resistant

AbstractIris germanica, a species with very high ornamental value, exhibits the strongest drought resistance among the species in the genus Iris, but the molecular mechanism underlying its drought resistance has not been evaluated. To investigate the gene expression profile changes exhibited by high-drought-resistant I. germanica under drought stress, 10 cultivars with excellent characteristics were included in pot experiments under drought stress conditions, and the changes in the chlorophyll (Chl) content, plasma membrane relative permeability (RP), and superoxide dismutase (SOD), malondialdehyde (MDA), free proline (Pro), and soluble protein (SP) levels in leaves were compared among these cultivars. Based on their drought-resistance performance, the 10 cultivars were ordered as follows: ‘Little Dream’ > ‘Music Box’ > ‘X’Brassie’ > ‘Blood Stone’ > ‘Cherry Garden’ > ‘Memory of Harvest’ > ‘Immortality’ > ‘White and Gold’ > ‘Tantara’ > ‘Clarence’. Using the high-drought-resistant cultivar ‘Little Dream’ as the experimental material, cDNA libraries from leaves and rhizomes treated for 0, 6, 12, 24, and 48 h with 20% polyethylene glycol (PEG)-6000 to simulate a drought environment were sequenced using the Illumina sequencing platform. We obtained 1, 976, 033 transcripts and 743, 982 unigenes (mean length of 716 bp) through a hierarchical clustering analysis of the resulting transcriptome data. The unigenes were compared against the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and gene ontology (GO) databases for functional annotation, and the gene expression levels in leaves and rhizomes were compared between the 20% PEG-6000 stress treated (6, 12, 24, and 48 h) and control (0 h) groups using DESeq2. 7849 and 24,127 differentially expressed genes (DEGs) were obtained from leaves and rhizomes, respectively. GO and KEGG enrichment analyses of the DEGs revealed significantly enriched KEGG pathways, including ribosome, photosynthesis, hormone signal transduction, starch and sucrose metabolism, synthesis of secondary metabolites, and related genes, such as heat shock proteins (HSPs), transcription factors (TFs), and active oxygen scavengers. In conclusion, we conducted the first transcriptome sequencing analysis of the I. germanica cultivar ‘Little Dream’ under drought stress and generated a large amount of genetic information. This study lays the foundation for further exploration of the molecular mechanisms underlying the responses of I. germanica to drought stress and provides valuable genetic resources for the breeding of drought-resistant plants.

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