scholarly journals Transcriptome Analysis of Salt Stress in Hibiscus hamabo Sieb. et Zucc Based on Pacbio Full-Length Transcriptome Sequencing

2021 ◽  
Vol 23 (1) ◽  
pp. 138
Author(s):  
Longjie Ni ◽  
Zhiquan Wang ◽  
Xiangdong Liu ◽  
Shuting Wu ◽  
Jianfeng Hua ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Differentially Expressed Genes ◽  
Single Molecule ◽  
Treatment Time ◽  
Full Length ◽  
Differentially Expressed ◽  
Illumina Platform ◽  
Mangrove Plant

Hibiscus hamabo Sieb. et Zucc is an important semi-mangrove plant with great morphological features and strong salt resistance. In this study, by combining single molecule real time and next-generation sequencing technologies, we explored the transcriptomic changes in the roots of salt stressed H. hamabo. A total of 94,562 unigenes were obtained by clustering the same isoforms using the PacBio RSII platform, and 2269 differentially expressed genes were obtained under salt stress using the Illumina platform. There were 519 differentially expressed genes co-expressed at each treatment time point under salt stress, and these genes were found to be enriched in ion signal transduction and plant hormone signal transduction. We used Arabidopsis thaliana (L.) Heynh. transformation to confirm the function of the HhWRKY79 gene and discovered that overexpression enhanced salt tolerance. The full-length transcripts generated in this study provide a full characterization of the transcriptome of H. hamabo and may be useful in mining new salt stress-related genes specific to this species, while facilitating the understanding of the salt tolerance mechanisms.

scholarly journals Transcriptome Analysis of Salt-Sensitive and Tolerant Genotypes Reveals Salt-Tolerance Metabolic Pathways in Sugar Beet

2019 ◽  
Vol 20 (23) ◽  
pp. 5910 ◽  
Author(s):  
Gui Geng ◽  
Chunhua Lv ◽  
Piergiorgio Stevanato ◽  
Renren Li ◽  
Hui Liu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Sugar Beet ◽  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Defense Responses ◽  
Transport Processes ◽  
Differentially Expressed ◽  
Salt Tolerant ◽  
Gene Markers

Soil salinization is a common environmental problem that seriously affects the yield and quality of crops. Sugar beet (Beta vulgaris L.), one of the main sugar crops in the world, shows a strong tolerance to salt stress. To decipher the molecular mechanism of sugar beet under salt stress, we conducted transcriptomic analyses of two contrasting sugar beet genotypes. To the best of our knowledge, this is the first comparison of salt-response transcriptomes in sugar beet with contrasting genotypes. Compared to the salt-sensitive cultivar (S710), the salt-tolerant one (T710MU) showed better growth and exhibited a higher chlorophyll content, higher antioxidant enzyme activity, and increased levels of osmotic adjustment molecules. Based on a high-throughput experimental system, 1714 differentially expressed genes were identified in the leaves of the salt-sensitive genotype, and 2912 in the salt-tolerant one. Many of the differentially expressed genes were involved in stress and defense responses, metabolic processes, signal transduction, transport processes, and cell wall synthesis. Moreover, expression patterns of several genes differed between the two cultivars in response to salt stress, and several key pathways involved in determining the salt tolerance of sugar beet, were identified. Our results revealed the mechanism of salt tolerance in sugar beet and provided potential metabolic pathways and gene markers for growing salt-tolerant cultivars.

scholarly journals Ectopic Expression of a Thellungiella salsuginea Aquaporin Gene, TsPIP1;1, Increased the Salt Tolerance of Rice

2018 ◽  
Vol 19 (8) ◽  
pp. 2229 ◽  
Author(s):  
Wei Li ◽  
Xiao-Jing Qiang ◽  
Xiao-Ri Han ◽  
Lin-Lin Jiang ◽  
Shu-Hui Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Small Molecules ◽  
Differentially Expressed Genes ◽  
Osmotic Potential ◽  
Soluble Sugars ◽  
Ectopic Expression ◽  
Differentially Expressed ◽  
Thellungiella Salsuginea ◽  
Transgenic Lines

Aquaporins play important regulatory roles in the transport of water and small molecules in plants. In this study, a Thellungiella salsuginea TsPIP1;1 aquaporin was transformed into Kitaake rice, and three transgenic lines were evaluated by profiling the changes of the physiological metabolism, osmotic potential, and differentially expressed genes under salt stress. The TsPIP1;1 protein contains six transmembrane domains and is localized in the cytoplasm membrane. Overexpression of the TsPIP1;1 gene not only increased the accumulation of prolines, soluble sugars and chlorophyll, but also lowered the osmotic potential and malondialdehyde content in rice under salt stress, and alleviated the amount of salt damage done to rice organs by regulating the distribution of Na/K ions, thereby promoting photosynthetic rates. Transcriptome sequencing confirmed that the differentially expressed genes that are up-regulated in rice positively respond to salt stimulus, the photosynthetic metabolic process, and the accumulation profiles of small molecules and Na/K ions. The co-expressed Rubisco and LHCA4 genes in rice were remarkably up-regulated under salt stress. This data suggests that overexpression of the TsPIP1;1 gene is involved in the regulation of water transport, the accumulation of Na/K ions, and the translocation of photosynthetic metabolites, thus conferring enhanced salt tolerance to rice.

scholarly journals RNA-Seq And WGCNA Analysis Identifies Salt-Responsive Genes In Pear (Pyrus Ussuriensis Maxim)

2021 ◽  
Author(s):  
Qiming Chen ◽  
Huizhen Dong ◽  
Zhihua Xie ◽  
Kaijie Qi ◽  
Xiaosan Huang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Plant Hormone ◽  
Enrichment Analysis ◽  
Salt Resistance ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Signal Transduction Pathways ◽  
Rna Seq

Abstract Background: Pear is one of the most abundant fruit crops and has been cultivated world-wide. However, the salt injury events caused by increased salinity limited the distribution and sustainable production of pear crops. Therefore, it is needed to take further efforts to understand the genetics and mechanisms of salt tolerance to improved salt resistance and productivity.Results: In this work, we analyzed the dynamic transcriptome of pear (Pyrus ussuriensis Maxim) under salt stress by using RNA-Seq and WGCNA. A total of 3540, 3831, 8374, 6267 and 5381 genes were identified that were differentially expressed after exposure to 200mM NaCl for 4, 6, 12, 24 and 48 hours, respectively, and 1163 genes were shared among the five comparisons. KEGG enrichment analysis of these DEGs (differentially expressed genes) revealed that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly enriched. Meanwhile, 622 DEGs identified from WGCNA were highly correlated with these pathways, and some of them were able to indicate the salt tolerance of pear varieties. In addition, we provide a network to demonstrate the time-sequence of these co-expressed MAPK and hormone related genes.Conclusion: A comprehensive analysis about salt-responsive pear transcriptome were performed by using RNA-Seq and WGCNA. We demonstrated that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly recruited during salt stress, and provided new insights into the metabolism of plant hormones related signaling at transcriptome level underlying salt resistance in pear. The dynamic transcriptome data obtained from this study and these salt-sensitive DEGs may provide potential genes as suitable targets for further biotechnological manipulation to improve pear salt tolerance.

scholarly journals Transcriptomic Analysis Reveals Genes Mediating Salt Tolerance through Calcineurin/CchA-Independent Signaling inAspergillus nidulans

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Sha Wang ◽  
Hongchang Zhou ◽  
Jun Wu ◽  
Jiangyu Han ◽  
Shasha Li ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Salt Stress ◽  
Cell Division ◽  
Heat Shock ◽  
Salt Tolerance ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Induced Genes ◽  
Calcineurin Pathway

Adaptation to changes in the environment is crucial for the viability of all organisms. Although the importance of calcineurin in the stress response has been highlighted in filamentous fungi, little is known about the involvement of ion-responsive genes and pathways in conferring salt tolerance without calcium signaling. In this study, high-throughput RNA-seq was used to investigate salt stress-induced genes in the parent, ΔcnaB, and ΔcnaBΔcchAstrains ofAspergillus nidulans, which differ greatly in salt adaption. In total, 2,884 differentially expressed genes including 1,382 up- and 1,502 downregulated genes were identified. Secondary transporters, which were upregulated to a greater extent in ΔcnaBΔcchAthan in the parent or ΔcnaBstrains, are likely to play important roles in response to salt stress. Furthermore, 36 genes were exclusively upregulated in the ΔcnaBΔcchAunder salt stress. Functional analysis of differentially expressed genes revealed that genes involved in transport, heat shock protein binding, and cell division processes were exclusively activated in ΔcnaBΔcchA. Overall, our findings reveal that secondary transporters and stress-responsive genes may play crucial roles in salt tolerance to bypass the requirement for the CchA-calcineurin pathway, contributing to a deeper understanding of the mechanisms that influence fungal salt stress adaption inAspergillus.

scholarly journals Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Surendra Bhattarai ◽  
Yong-Bi Fu ◽  
Bruce Coulman ◽  
Karen Tanino ◽  
Chithra Karunakaran ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Medicago Sativa ◽  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Genetic Improvement ◽  
Rna Extraction ◽  
Differentially Expressed ◽  
Differential Expression Pattern ◽  
Root Tissues

Abstract Background Alfalfa (Medicago sativa L.) production decreases under salt stress. Identification of genes associated with salt tolerance in alfalfa is essential for the development of molecular markers used for breeding and genetic improvement. Result An RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with salt stress in two alfalfa cultivars: salt tolerant ‘Halo’ and salt intolerant ‘Vernal’. Leaf and root tissues were sampled for RNA extraction at 0 h, 3 h, and 27 h under 12 dS m− 1 salt stress maintained by NaCl. The sequencing generated a total of 381 million clean sequence reads and 84.8% were mapped on to the alfalfa reference genome. A total of 237 DEGs were identified in leaves and 295 DEGs in roots of the two alfalfa cultivars. In leaf tissue, the two cultivars had a similar number of DEGs at 3 h and 27 h of salt stress, with 31 and 49 DEGs for ‘Halo’, 34 and 50 for ‘Vernal’, respectively. In root tissue, ‘Halo’ maintained 55 and 56 DEGs at 3 h and 27 h, respectively, while the number of DEGs decreased from 42 to 10 for ‘Vernal’. This differential expression pattern highlights different genetic responses of the two cultivars to salt stress at different time points. Interestingly, 28 (leaf) and 31 (root) salt responsive candidate genes were highly expressed in ‘Halo’ compared to ‘Vernal’ under salt stress, of which 13 candidate genes were common for leaf and root tissues. About 60% of DEGs were assigned to known gene ontology (GO) categories. The genes were involved in transmembrane protein function, photosynthesis, carbohydrate metabolism, defense against oxidative damage, cell wall modification and protection against lipid peroxidation. Ion binding was found to be a key molecular activity for salt tolerance in alfalfa under salt stress. Conclusion The identified DEGs are significant for understanding the genetic basis of salt tolerance in alfalfa. The generated genomic information is useful for molecular marker development for alfalfa genetic improvement for salt tolerance.

scholarly journals Transcriptome revealed the molecular mechanism of Glycyrrhiza inflata root to maintain growth and development, absorb and distribute ions under salt stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Xu ◽  
Jia-hui Lu ◽  
Jia-de Zhang ◽  
Deng-kui Liu ◽  
Yue Wang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Glycerol Metabolism ◽  
Salt Tolerant ◽  
High Concentration ◽  
Stress Induction ◽  
Glycyrrhiza Inflata

Abstract Background Soil salinization extensively hampers the growth, yield, and quality of crops worldwide. The most effective strategies to counter this problem are a) development of crop cultivars with high salt tolerance and b) the plantation of salt-tolerant crops. Glycyrrhiza inflata, a traditional Chinese medicinal and primitive plant with salt tolerance and economic value, is among the most promising crops for improving saline-alkali wasteland. However, the underlying molecular mechanisms for the adaptive response of G. inflata to salinity stress remain largely unknown. Result G. inflata retained a high concentration of Na+ in roots and maintained the absorption of K+, Ca2+, and Mg2+ under 150 mM NaCl induced salt stress. Transcriptomic analysis of G. inflata roots at different time points of salt stress (0 min, 30 min, and 24 h) was performed, which resulted in 70.77 Gb of clean data. Compared with the control, we detected 2645 and 574 differentially expressed genes (DEGs) at 30 min and 24 h post-salt-stress induction, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that G. inflata response to salt stress post 30 min and 24 h was remarkably distinct. Genes that were differentially expressed at 30 min post-salt stress induction were enriched in signal transduction, secondary metabolite synthesis, and ion transport. However, genes that were differentially expressed at 24 h post-salt-stress induction were enriched in phenylpropane biosynthesis and metabolism, fatty acid metabolism, glycerol metabolism, hormone signal transduction, wax, cutin, and cork biosynthesis. Besides, a total of 334 transcription factors (TFs) were altered in response to 30 min and 24 h of salt stress. Most of these TFs belonged to the MYB, WRKY, AP2-EREBP, C2H2, bHLH, bZIP, and NAC families. Conclusion For the first time, this study elucidated the salt tolerance in G. inflata at the molecular level, including the activation of signaling pathways and genes that regulate the absorption and distribution of ions and root growth in G. inflata under salt stress conditions. These findings enhanced our understanding of the G. inflata salt tolerance and provided a theoretical basis for cultivating salt-tolerant crop varieties.

scholarly journals Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud.

2020 ◽  
Author(s):  
Jingjing Wang ◽  
Cong An ◽  
Hailin Guo ◽  
Xiangyang Yang ◽  
Jingbo Chen ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Stress Response ◽  
Salt Tolerance ◽  
Molecular Mechanisms ◽  
Salt Tolerant ◽  
Zoysia Japonica ◽  
Salt Stress Response ◽  
Leaves And Roots ◽  
Time Point

Abstract Background: Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown. Results: The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K+/Na+ ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family. Conclusions: Z011 may have improved salt tolerance by reducing Na+ transport from the roots to the leaves, increasing K+ absorption in the roots and reducing K+ secretion from the leaves to maintain a significantly greater K+/Na+ ratio. Twenty-four hours might be a relatively important time point for the salt-stress response of zoysiagrass. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation. This study provides fundamental information concerning the salt-stress response of Zoysia and improves the understanding of molecular mechanisms in salt-tolerant plants.

scholarly journals The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

2019 ◽  
Author(s):  
Wenbin Ye ◽  
Taotao Wang ◽  
Wei Wei ◽  
Shuaitong Lou ◽  
Faxiu Lan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Alternative Splicing ◽  
Salt Tolerance ◽  
Protein Kinases ◽  
Spartina Alterniflora ◽  
High Salt ◽  
Full Length ◽  
Salt Tolerant ◽  
High Salt Tolerance

ABSTRACTSpartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used PacBio full-length single molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt-gradient experiments (0, 350, 500 and 800 mM NaCl). We systematically analyzed the gene expression diversity and deciphered possible roles of ion transporters, protein kinases and photosynthesis in salt tolerance. Moreover, the co-expression network analysis revealed several hub genes in salt stress regulatory networks, including protein kinases such as SaOST1, SaCIPK10 and three SaLRRs. Furthermore, high salt stress affected the gene expression of photosynthesis through down-regulation at the transcription level and alternative splicing at the post-transcriptional level. In addition, overexpression of two Spartina salt-tolerant genes SaHSP70-I and SaAF2 in Arabidopsis significantly promoted the salt tolerance of transgenic lines. Finally, we built the SAPacBio website for visualizing the full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes, and alternative splicing events in Spartina. Overall, this study sheds light on the high salt tolerance mechanisms of monocotyledonous-halophyte and demonstrates the potential of Spartina genes for engineering salt-tolerant plants.

scholarly journals De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rasmita Rani Das ◽  
Seema Pradhan ◽  
Ajay Parida
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Differentially Expressed Genes ◽  
Salinity Stress ◽  
Abiotic Stress Tolerance ◽  
Differentially Expressed ◽  
Little Millet ◽  
Drought And Salt Stress

AbstractScreening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.

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