scholarly journals Comparative Transcriptome Analysis of Sophora japonica (L.) Roots Reveals Key Pathways and Genes in Response to PEG-Induced Drought Stress under Different Nitrogen Conditions

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 650
Author(s):  
Jing Tian ◽  
Yue Pang ◽  
Zhong Zhao
Keyword(s):  
Drought Stress ◽  
Differential Expression ◽  
Stress Responses ◽  
De Novo ◽  
Average Length ◽  
N Uptake ◽  
High Stress ◽  
Sophora Japonica ◽  
N Starvation ◽  
Starvation Conditions

Sophora japonica is a native leguminous tree species in China. The high stress tolerance contributes to its long lifespan of thousands of years. The lack of genomic resources greatly limits genetic studies on the stress responses of S. japonica. In this study, RNA-seq was conducted for S. japonica roots grown under short-term 20% polyethylene glycol (PEG) 6000-induced drought stress under normal N and N starvation conditions (1 and 0 mM NH4NO3, respectively). In each of the libraries, we generated more than 25 million clean reads, which were then de novo assembled to 46,852 unigenes with an average length of 1310.49 bp. In the differential expression analyses, more differentially expressed genes (DEGs) were found under drought with N starvation than under single stresses. The number of transcripts identified under N starvation and drought in S. japonica was nearly the same, but more upregulated genes were induced by drought, while more downregulated genes were induced by N starvation. Genes involved in “phenylpropanoid biosynthesis” and “biosynthesis of amino acids” pathways were upregulated according to KEGG enrichment analyses, irrespective of the stress treatments. Additionally, upregulated N metabolism genes were enriched upon drought, and downregulated photosynthesis genes were enriched under N starvation. We found 4372 and 5430 drought-responsive DEGs under normal N and N starvation conditions, respectively. N starvation may aggravate drought by downregulating transcripts in the “carbon metabolism”, “ribosome”, “arginine biosynthesis pathway”, “oxidative phosphorylation” and “aminoacyl-tRNA biosynthesis” pathways. We identified 78 genes related to N uptake and assimilation, 38 of which exhibited differential expression under stress. A total of 395 DEGs were categorized as transcription factors, of which AR2/ERF-ERF, WRKY, NAC, MYB, bHLH, C3H and C2C2-Dof families played key roles in drought and N starvation stresses. The transcriptome data obtained, and the genes identified facilitate our understanding of the mechanisms of S. japonica responses to drought and N starvation stresses and provide a molecular foundation for understanding the mechanisms of its long lifespan for breeding resistant varieties for greening.

scholarly journals De NovoAssembly and Characterization ofSophora japonicaTranscriptome Using RNA-seq

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Liucun Zhu ◽  
Ying Zhang ◽  
Wenna Guo ◽  
Xin-Jian Xu ◽  
Qiang Wang
Keyword(s):  
Protein Interactions ◽  
De Novo ◽  
Average Length ◽  
Genomic Analysis ◽  
Interaction Network ◽  
Protein Protein Interactions ◽  
Gene Expressions ◽  
Sophora Japonica ◽  
Protein Protein Interaction ◽  
Functional Genomic Analysis

Sophora japonicaLinn (Chinese Scholar Tree) is a shrub species belonging to the subfamily Faboideae of the pea family Fabaceae. In this study, RNA sequencing ofS. japonicatranscriptome was performed to produce large expression datasets for functional genomic analysis. Approximate 86.1 million high-quality clean reads were generated and assembledde novointo 143010 unique transcripts and 57614 unigenes. The average length of unigenes was 901 bps with an N50 of 545 bps. Four public databases, including the NCBI nonredundant protein (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Cluster of Orthologous Groups (COG), were used to annotate unigenes through NCBI BLAST procedure. A total of 27541 of 57614 unigenes (47.8%) were annotated for gene descriptions, conserved protein domains, or gene ontology. Moreover, an interaction network of unigenes inS. japonicawas predicted based on known protein-protein interactions of putative orthologs of well-studied plant genomes. The transcriptome data ofS. japonicareported here represents first genome-scale investigation of gene expressions in Faboideae plants. We expect that our study will provide a useful resource for further studies on gene expression, genomics, functional genomics, and protein-protein interaction inS. japonica.

scholarly journals De novo characterization of Platycladus orientalis transcriptome and analysis of its gene expression during aging

2017 ◽  
Author(s):  
Ermei Chang ◽  
Xiamei Yao ◽  
Jin Zhang ◽  
Nan Deng ◽  
Zeping Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Potential Candidate ◽  
Platycladus Orientalis ◽  
Oxidation Reduction ◽  
Mda Content ◽  
As Stress

Platycladus orientalis in China has a lifespan of one to several thousands of years. The long lifespans of trees have attracted interest in aging at the molecular level. There is little information on how the global process is controlled. In this study, the MDA content, SOD and POD activities were higher in ancient P. orientalis than in 20-year-old Platycladus orientalis, and the content of protein showed the inverse trend. We obtained 48,044 unigenes having an average length of 896 bp from pooled samples of P. orientalis by transcriptome sequencing. Microarray analysis produced a high-resolution age-course profile of gene expression levels in different age of P. orientalis. In total, 418 differentially expressed genes were identified. The use of highly informative clustering revealed distinct time points at which oxidation reduction and photosynthesis pathways changed. Eight clusters with distinctive expression patterns were identified, the expression of metabolism, photosynthesis, oxidation reduction and transporters related genes were downregulated and protein synthesis, transcription, signal transduction and senescence related genes were upregulated with increasing age. Total chlorophyll, chlorophyll a, and chlorophyll b levels were decreased steadily with age. This study discovery of potential candidate genes affecting photosynthesis in different P. orientalis ages and at senescence, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses.

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.

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.

De novo transcriptome profiling of mustard aphid (Lipaphis erysimi) and differential expression of transcripts associated with developmental stages, feeding and non-feeding conditions

2019 ◽  
Author(s):  
Rubina Chongtham ◽  
Kirti Kulkarni ◽  
Rohit Nandan Shukla ◽  
Gopal Joshi ◽  
Amar Kumar ◽  
...  
Keyword(s):  
Differential Expression ◽  
Target Genes ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Indian Subcontinent ◽  
Expression Profiles ◽  
Lipaphis Erysimi ◽  
Adult Feeding ◽  
Aphid Control

AbstractLipaphis erysimi is a Brassicaceae specialist aphid, which causes significant losses in yield and/or reduction of oil content of vegetable and oilseed brassicas and is a major pest in the Indian subcontinent. This study reports the de novo transcriptome of L. erysimi for the first time. We also present a comparative analysis of nymphs and adult transcriptomes to study the differential expression profiles associated with different developmental stages as well as different feeding conditions. For this, RNA-seq was performed on three different biological samples adults, nymphs (with all nymph stages pooled) and adults starved for 3 hours (referred to as Adult Feeding, AF; Nymphs Feeding, NF, and Adult Starved_3 hr, ANF samples henceforth). A final transcriptome comprising 52,652 transcripts of 1064bp average length and N50 value of 1806 bp was generated. A total of 27,112 transcripts were annotated with insect proteins from SwissProt, of which 4128 transcripts were components of 165 KEGG pathways. A total of 17,296 transcripts were classified based on their Gene Ontology. Potential transcripts for host selection, detoxification, salivary proteins and effectors, molecular chaperones and developmental genes were identified. A total of 23,532 transcripts that remained unannotated were subjected to BLAST against aphid sequences available at AphidBase and a total of 3091 transcripts had hits with sequences of other aphids in the database, out of which 1380 had protein hits. A total of 20441 found to share no homology to any sequence available in the public domain and could therefore represent novel aphid genes or sequences that are unique to L. erysimi. This is an exploratory study with no biological replicates. However, the significant repertoire of feeding- and development-related genes and their differential expression profiles generated in this study adds to the limited data available on L. erysimi and it would facilitate studies on the molecular basis of aphid feeding and development. This could also allow identification of novel target genes for development of RNAi-based aphid control methods.

scholarly journals De novo characterization of Platycladus orientalis transcriptome and analysis of its gene expression during aging

2017 ◽  
Author(s):  
Ermei Chang ◽  
Xiamei Yao ◽  
Jin Zhang ◽  
Nan Deng ◽  
Zeping Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Potential Candidate ◽  
Platycladus Orientalis ◽  
Oxidation Reduction ◽  
Mda Content ◽  
As Stress

Platycladus orientalis in China has a lifespan of one to several thousands of years. The long lifespans of trees have attracted interest in aging at the molecular level. There is little information on how the global process is controlled. In this study, the MDA content, SOD and POD activities were higher in ancient P. orientalis than in 20-year-old Platycladus orientalis, and the content of protein showed the inverse trend. We obtained 48,044 unigenes having an average length of 896 bp from pooled samples of P. orientalis by transcriptome sequencing. Microarray analysis produced a high-resolution age-course profile of gene expression levels in different age of P. orientalis. In total, 418 differentially expressed genes were identified. The use of highly informative clustering revealed distinct time points at which oxidation reduction and photosynthesis pathways changed. Eight clusters with distinctive expression patterns were identified, the expression of metabolism, photosynthesis, oxidation reduction and transporters related genes were downregulated and protein synthesis, transcription, signal transduction and senescence related genes were upregulated with increasing age. Total chlorophyll, chlorophyll a, and chlorophyll b levels were decreased steadily with age. This study discovery of potential candidate genes affecting photosynthesis in different P. orientalis ages and at senescence, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses.

Differential Expression of Rice Two-Component Element Genes under Drought Stress

2009 ◽  
Vol 35 (9) ◽  
pp. 1628-1636 ◽  
Author(s):  
Ya-Jiao PAN ◽  
Di WANG ◽  
Ling-Hua ZHU ◽  
Bin-Ying FU ◽  
Zhi-Kang LI
Keyword(s):  
Drought Stress ◽  
Differential Expression ◽  
Two Component ◽  
Component Element

scholarly journals Spermine: Its Emerging Role in Regulating Drought Stress Responses in Plants

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 261
Author(s):  
Md. Mahadi Hasan ◽  
Milan Skalicky ◽  
Mohammad Shah Jahan ◽  
Md. Nazmul Hossain ◽  
Zunaira Anwar ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Defense Mechanisms ◽  
Antioxidant Defense ◽  
Severe Drought ◽  
New Information ◽  
Effects Of Drought

In recent years, research on spermine (Spm) has turned up a lot of new information about this essential polyamine, especially as it is able to counteract damage from abiotic stresses. Spm has been shown to protect plants from a variety of environmental insults, but whether it can prevent the adverse effects of drought has not yet been reported. Drought stress increases endogenous Spm in plants and exogenous application of Spm improves the plants’ ability to tolerate drought stress. Spm’s role in enhancing antioxidant defense mechanisms, glyoxalase systems, methylglyoxal (MG) detoxification, and creating tolerance for drought-induced oxidative stress is well documented in plants. However, the influences of enzyme activity and osmoregulation on Spm biosynthesis and metabolism are variable. Spm interacts with other molecules like nitric oxide (NO) and phytohormones such as abscisic acid, salicylic acid, brassinosteroids, and ethylene, to coordinate the reactions necessary for developing drought tolerance. This review focuses on the role of Spm in plants under severe drought stress. We have proposed models to explain how Spm interacts with existing defense mechanisms in plants to improve drought tolerance.

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