scholarly journals Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum)

2019 ◽  
Author(s):  
Hong Luo ◽  
Peipei Wu ◽  
Steven Cogill ◽  
Yijian Qiu ◽  
Zhigang Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Salinity Tolerance ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Perennial Grass ◽  
Differential Expression Analysis ◽  
Reduction Process ◽  
Seashore Paspalum ◽  
Paspalum Vaginatum

Abstract Background Seashore paspalum (Paspalum vaginatum), a halophytic warm-seasoned perennial grass, is tolerant of many environmental stresses, especially salt stress. To investigate molecular mechanisms underlying salinity tolerance in seashore paspalum, physiological characteristics and global transcription profiles of highly (Supreme) and moderately (Parish) salinity-tolerant cultivars under normal and salt stressed conditions were analyzed. Results Physiological characterization comparing highly (Supreme) and moderately (Parish) salinity-tolerant cultivars revealed that Supreme’s higher salinity tolerance is associated with higher Na+ and Ca2+ accumulation under normal conditions and further increase of Na+ under salt-treated conditions (400 mM NaCl), possibly by vacuolar sequestration. Moreover, K+ retention under salt treatment occurs in both cultivars, suggesting that it may be a conserved mechanism for prevention of Na+ toxicity. We sequenced the transcriptome of the two cultivars under both normal and salt-treated conditions (400 mM NaCl) using RNA-seq. De novo assembly of about 153 million high-quality reads and identification of Open Reading Frames (ORFs) uncovered a total of 82,608 non-redundant unigenes, of which 3,250 genes were identified as transcription factors (TFs). Gene Ontology (GO) annotation revealed the presence of genes involved in diverse cellular processes in seashore paspalum’s transcriptome. Differential expression analysis identified a total of 828 and 2,222 genes that are responsive to high salinity for Supreme and Parish, respectively. GO enrichment analysis demonstrated that genes involved in “oxidation-reduction process” and “nucleic acid binding” are significantly associated with salinity tolerance in both cultivars. Interestingly, compared to Parish, a number of salt stress induced transcription factors are enriched and show higher abundance in Supreme under normal conditions, possibly due to enhanced Ca2+ signaling transduction out of Na+ accumulation, which may be another contributor to Supreme’s higher salinity tolerance. Conclusion Physiological and genomics analyses of seashore paspalum reveal major molecular underpinnings contributing to plant response to salt stress in this halophytic warm-seasoned perennial grass. The data obtained provide valuable molecular resources for functional studies and developing strategies to engineer plant salinity tolerance.

scholarly journals Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum)

2020 ◽  
Author(s):  
Peipei Wu ◽  
Steven Cogill ◽  
Yijian Qiu ◽  
Zhigang Li ◽  
Man Zhou ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Salinity Tolerance ◽  
Molecular Mechanisms ◽  
Perennial Grass ◽  
Differential Expression Analysis ◽  
Reduction Process ◽  
Salt Treatment ◽  
Seashore Paspalum ◽  
Paspalum Vaginatum

Abstract Background: Seashore paspalum (Paspalum vaginatum), a halophytic warm-seasoned perennial grass, is tolerant of many environmental stresses, especially salt stress. To investigate molecular mechanisms underlying salinity tolerance in seashore paspalum, physiological characteristics and global transcription profiles of highly (Supreme) and moderately (Parish) salinity-tolerant cultivars under normal and salt stressed conditions were analyzed.Results: Physiological characterization comparing highly (Supreme) and moderately (Parish) salinity-tolerant cultivars revealed that Supreme’s higher salinity tolerance is associated with higher Na+ and Ca2+ accumulation under normal conditions and further increase of Na+ under salt-treated conditions (400 mM NaCl), possibly by vacuolar sequestration. Moreover, K+ retention under salt treatment occurs in both cultivars, suggesting that it may be a conserved mechanism for prevention of Na+ toxicity. We sequenced the transcriptome of the two cultivars under both normal and salt-treated conditions (400 mM NaCl) using RNA-seq. De novo assembly of about 153 million high-quality reads and identification of Open Reading Frames (ORFs) uncovered a total of 82,608 non-redundant unigenes, of which 3,250 genes were identified as transcription factors (TFs). Gene Ontology (GO) annotation revealed the presence of genes involved in diverse cellular processes in seashore paspalum’s transcriptome. Differential expression analysis identified a total of 828 and 2,222 genes that are responsive to high salinity for Supreme and Parish, respectively. “Oxidation-reduction process” and “nucleic acid binding” are significantly enriched GOs among differentially expressed genes in both cultivars under salt treatment. Interestingly, compared to Parish, a number of salt stress induced transcription factors are enriched and show higher abundance in Supreme under normal conditions, possibly due to enhanced Ca2+ signaling transduction out of Na+ accumulation, which may be another contributor to Supreme’s higher salinity tolerance.Conclusion: Physiological and genomics analyses of seashore paspalum reveal major molecular underpinnings contributing to plant response to salt stress in this halophytic warm-seasoned perennial grass. The data obtained provide valuable molecular resources for functional studies and developing strategies to engineer plant salinity tolerance.

scholarly journals Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum)

2019 ◽  
Author(s):  
Peipei Wu ◽  
Steven Cogill ◽  
Yijian Qiu ◽  
Zhigang Li ◽  
Man Zhou ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Salinity Tolerance ◽  
Molecular Mechanisms ◽  
Perennial Grass ◽  
Differential Expression Analysis ◽  
Reduction Process ◽  
Salt Treatment ◽  
Seashore Paspalum ◽  
Paspalum Vaginatum

Abstract Background: Seashore paspalum (Paspalum vaginatum), a halophytic warm-seasoned perennial grass, is tolerant of many environmental stresses, especially salt stress. To investigate molecular mechanisms underlying salinity tolerance in seashore paspalum, physiological characteristics and global transcription profiles of highly (Supreme) and moderately (Parish) salinity-tolerant cultivars under normal and salt stressed conditions were analyzed. Results: Physiological characterization comparing highly (Supreme) and moderately (Parish) salinity-tolerant cultivars revealed that Supreme’s higher salinity tolerance is associated with higher Na+ and Ca2+ accumulation under normal conditions and further increase of Na+ under salt-treated conditions (400 mM NaCl), possibly by vacuolar sequestration. Moreover, K+ retention under salt treatment occurs in both cultivars, suggesting that it may be a conserved mechanism for prevention of Na+ toxicity. We sequenced the transcriptome of the two cultivars under both normal and salt-treated conditions (400 mM NaCl) using RNA-seq. De novo assembly of about 153 million high-quality reads and identification of Open Reading Frames (ORFs) uncovered a total of 82,608 non-redundant unigenes, of which 3,250 genes were identified as transcription factors (TFs). Gene Ontology (GO) annotation revealed the presence of genes involved in diverse cellular processes in seashore paspalum’s transcriptome. Differential expression analysis identified a total of 828 and 2,222 genes that are responsive to high salinity for Supreme and Parish, respectively. “Oxidation-reduction process” and “nucleic acid binding” are significantly enriched GOs among differentially expressed genes in both cultivars under salt treatment. Interestingly, compared to Parish, a number of salt stress induced transcription factors are enriched and show higher abundance in Supreme under normal conditions, possibly due to enhanced Ca2+ signaling transduction out of Na+ accumulation, which may be another contributor to Supreme’s higher salinity tolerance. Conclusion: Physiological and genomics analyses of seashore paspalum reveal major molecular underpinnings contributing to plant response to salt stress in this halophytic warm-seasoned perennial grass. The data obtained provide valuable molecular resources for functional studies and developing strategies to engineer plant salinity tolerance.

scholarly journals De Novo Assembly and Discovery of Genes That Involved in Drought Tolerance in the Common Vetch

2019 ◽  
Vol 20 (2) ◽  
pp. 328 ◽  
Author(s):  
Yongqun Zhu ◽  
Qiuxu Liu ◽  
Wenzhi Xu ◽  
Jianhua Zhang ◽  
Xie Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Tolerance ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Reduction Process ◽  
Differentially Expressed ◽  
Forage Production ◽  
Common Vetch ◽  
Oxidoreductase Activity ◽  
The Common

The common vetch (Vicia sativa) is often used as feed for livestock because of its high nutritional value. However, drought stress reduces forage production through plant damage. Here, we studied the transcriptional profiles of common vetch exposed to drought in order to understand the molecular mechanisms of drought tolerance in this species. The genome of the common vetch has not been sequenced, therefore we used Illumina sequencing to generate de novo transcriptomes. Nearly 500 million clean reads were used to generate 174,636 transcripts, including 122,299 unigenes. In addition, 5313 transcription factors were identified and these transcription factors were classified into 79 different gene families. We also identified 11,181 SSR loci from di- to hexa-nucleotides whose repeat number was greater than five. On the basis of differentially expressed genes, Gene Ontology analysis identified many drought-relevant categories, including “oxidation-reduction process”, “lipid metabolic process” and “oxidoreductase activity”. In addition to these, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified pathways, such as “Plant hormone signal transduction”, “Glycolysis/Gluconeogenesis” and “Phenylpropanoid biosynthesis”, as differentially expressed in the plants exposed to drought. The expression results in this study will be useful for further extending our knowledge on the drought tolerance of common vetch.

scholarly journals Transcriptome analysis of immature xylem in Chinese fir at different developmental phases

2016 ◽  
Author(s):  
Yunxing Zhang ◽  
Xiaojiao Han ◽  
Jian Sang ◽  
Xuelian he ◽  
Mingying Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Southern China ◽  
Wood Formation ◽  
Chinese Fir ◽  
Nac Transcription Factors ◽  
Transcriptome Variation ◽  
Developmental Phases

Background: Chinese fir [Cunninghamia lanceolata (Lamb .) Hook.], is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results: We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome. Conclusion: Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.

scholarly journals Heterologous Expression of Transcription Factor AtWRKY57 Alleviates Salt Stress-Induced Oxidative Damage

2018 ◽  
Vol 12 (1) ◽  
pp. 204-218
Author(s):  
Wei Tang
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Salt Stress ◽  
Heterologous Expression ◽  
Stress Tolerance ◽  
Molecular Mechanisms ◽  
Abiotic Stress Tolerance ◽  
Thiobarbituric Acid Reactive Substance ◽  
Salt Stress Tolerance ◽  
Wrky Transcription Factors

Background:WRKY transcription factors play important roles in the responses to abiotic stresses, seed dormancy, seed germination, developmental processes, secondary metabolism, and senescence in plants. However, molecular mechanisms of WRKY transcription factors-related abiotic stress tolerance have not been fully understood.Methods:In this investigation, transcription factor AtWRKY57 was introduced into cell lines of rice (Oryza sativaL.), tobacco (Nicotiana tabacum), and white pine (Pinus strobesL.) for characterization of its function in salt stress tolerance. The purpose of this investigation is to examine the function of AtWRKY in a broad sample of plant species including monocotyledons, dicotyledons, and gymnosperms.Results:The experimental results demonstrated that heterologous expression of transcription factor AtWRKY57 improves salt stress tolerance by decreasing Thiobarbituric Acid Reactive Substance (TBARS), increasing Ascorbate Peroxidase (APOX) and Catalase (CAT) activity under salt stress. In rice, overexpression of transcription factor AtWRKY57 enhances expression of Ca2+-dependent protein kinase genesOsCPk6andOsCPk19to counteract salt stress.Conclusion:These results indicated that transcription factor AtWRKY57 might have practical application in genetic engineering of plant salt tolerance throughout the plant kingdom.

scholarly journals Performance of Two Seashore Paspalum (Paspalum vaginatum Sw.) Varieties Growing in Shallow Green Roof Substrate Depths and Irrigated with Seawater

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 250
Author(s):  
Nikolaos Ntoulas ◽  
Ioannis Varsamos
Keyword(s):  
Salt Stress ◽  
Saline Water ◽  
Recovery Period ◽  
Green Roof ◽  
Seashore Paspalum ◽  
Greenhouse Study ◽  
Irrigation Regimes ◽  
Mediterranean Countries ◽  
Paspalum Vaginatum ◽  
Seawater Irrigation

The continuing decline in global drinking water reserves necessitates finding alternative water sources for turfgrass irrigation, especially in southern semi-arid Mediterranean countries. The aim of the present study was to evaluate the potential of using seawater for irrigating two varieties of seashore paspalum (Paspalum vaginatum Sw.), “Marina” and “Platinum ΤΕ”, growing in shallow green roof substrates, and to determine their recuperative capacity after the termination of the salt stress period. The greenhouse study comprised of 48 lysimeters equipped with extensive green roof layering. Treatments included: (i) two substrate depths (7.5 cm or 15 cm) and (ii) three seawater irrigation regimes (7 mm, 15 mm, or 45 mm every two days). Measurements included the determination of green turf cover (GTC) as well as the leaching fraction (LF) and leachate electrical conductivity (ECL) draining from the lysimeters. It was found that during the 46-d salt stress period, none of the seawater irrigation regimes managed to maintain acceptable GTC levels for both seashore paspalum varieties. Increasing the green roof substrate depth from 7.5 cm to 15 cm resulted in GTC improvement. During the recovery period, the use of potable water as irrigation source improved GTC levels. After 40 d the recovery was complete since GTC exceeded 90% in all treatments for both varieties. Regression curves correlating GTC response to ECL can be used to estimate the leaching requirements of turfgrasses grown in shallow green roof systems when irrigated with saline water.

scholarly journals De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5681 ◽  
Author(s):  
Li Li ◽  
Mimi Li ◽  
Xiwu Qi ◽  
Xingli Tang ◽  
Yifeng Zhou
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Rna Sequencing ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Biosynthetic Pathways ◽  
Salt Stress Response ◽  
Glehnia Littoralis ◽  
Plant Signal Transduction

Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis.

scholarly journals AtCIPK16 Mediates Salt Stress Through Phytohormones and Transcription Factors

2020 ◽  
Author(s):  
Shanika L. Amarasinghe ◽  
Wenmian Huang ◽  
Nathan S. Watson-Haigh ◽  
Matthew Gilliham ◽  
Stuart J. Roy ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Salinity Tolerance ◽  
Food Production ◽  
Rna Seq ◽  
Productivity Losses ◽  
Global Food

AbstractSoil salinity causes large productivity losses for agriculture worldwide. “Next-generation crops” that can tolerate salt stress are required for the sustainability of global food production. Previous research in Arabidopsis thaliana aimed at uncovering novel factors underpinning improved plant salinity tolerance identified the protein kinase AtCIPK16. Overexpression of AtCIPK16 enhanced shoot Na+ exclusion and increased biomass in both Arabidopsis and barley. Here, a comparative transcriptomic study on Arabidopsis lines expressing AtCIPK16 was conducted in the presence and absence of salt stress, using an RNA-Seq approach, complemented by AtCIPK16 interaction and localisation studies. We are now able to provide evidence for AtCIPK16 activity in the nucleus. Moreover, the results manifest the involvement of a transcription factor, AtTZF1, phytohormones and the ability to quickly reach homeostasis as components important for improving salinity tolerance in transgenics overexpressing AtCIPK16. Furthermore, we suggest the possibility of both biotic and abiotic tolerance through AtCIPK16, and propose a model for the salt tolerance pathway elicited through AtCIPK16.

scholarly journals Comprehensive transcriptional analysis reveals salt stress-regulated key pathways, hub genes and time-specific responsive gene categories in common bermudagrass (Cynodon dactylon (L.) Pers.) roots

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
An Shao ◽  
Wei Wang ◽  
Shugao Fan ◽  
Xiao Xu ◽  
Yanling Yin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Molecular Mechanisms ◽  
Cynodon Dactylon ◽  
Expression Profiles ◽  
Transcriptional Analysis ◽  
Salt Treatment ◽  
Hub Genes ◽  
Salt Response ◽  
Common Bermudagrass

Abstract Background Despite its good salt-tolerance level, key genes and pathways involved with temporal salt response of common bermudagrass (Cynodon dactylon (L.) Pers.) have not been explored. Therefore, in this study, to understand the underlying regulatory mechanism following the different period of salt exposure, a comprehensive transcriptome analysis of the bermudagrass roots was conducted. Results The transcripts regulated after 1 h, 6 h, or 24 h of hydroponic exposure to 200 mM NaCl in the roots of bermudagrass were investigated. Dataset series analysis revealed 16 distinct temporal salt-responsive expression profiles. Enrichment analysis identified potentially important salt responsive genes belonging to specific categories, such as hormonal metabolism, secondary metabolism, misc., cell wall, transcription factors and genes encoded a series of transporters. Weighted gene co-expression network analysis (WGCNA) revealed that lavenderblush2 and brown4 modules were significantly positively correlated with the proline content and peroxidase activity and hub genes within these two modules were further determined. Besides, after 1 h of salt treatment, genes belonging to categories such as signalling receptor kinase, transcription factors, tetrapyrrole synthesis and lipid metabolism were immediately and exclusively up-enriched compared to the subsequent time points, which indicated fast-acting and immediate physiological responses. Genes involved in secondary metabolite biosynthesis such as simple phenols, glucosinolates, isoflavones and tocopherol biosynthesis were exclusively up-regulated after 24 h of salt treatment, suggesting a slightly slower reaction of metabolic adjustment. Conclusion Here, we revealed salt-responsive genes belonging to categories that were commonly or differentially expressed in short-term salt stress, suggesting possible adaptive salt response mechanisms in roots. Also, the distinctive salt-response pathways and potential salt-tolerant hub genes investigated can provide useful future references to explore the molecular mechanisms of bermudagrass.

scholarly journals Comprehensive transcriptional analysis reveals salt stress-regulated key pathways, hub genes and time-specific response categories in common bermudagrass (Cynodon dactylon (L.) Pers.) roots

2020 ◽  
Author(s):  
An Shao ◽  
Wei Wang ◽  
Shugao Fan ◽  
Xiao Xu ◽  
Yanling Yin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Molecular Mechanisms ◽  
Cynodon Dactylon ◽  
Transcriptional Analysis ◽  
Specific Response ◽  
Salt Treatment ◽  
Hub Genes ◽  
Salt Response ◽  
Common Bermudagrass

Abstract Background: Despite its good salt-tolerance level, key genes and pathways that are involved with temporal salt response of common bermudagrass (Cynodon dactylon (L.) Pers.) have not been explored. Therefore, in this study, to understand the underlying regulatory mechanism following the different period of salt exposure, a comprehensive transcriptome analysis of the bermudagrass roots was conducted.Results: The transcripts regulated after 1 h, 6 h, or 24 h of hydroponic exposure to 200 mM NaCl in the roots of bermudagrass were investigated. Dataset series analysis revealed 16 distinct salt-responsive temporal transcripts. Enrichment analysis identified common and distinct stress response themes such as hormonal metabolism, secondary metabolism, misc, cell wall, transcription factors and genes encoded a series of transporters. Weighted gene co-expression network analysis (WGCNA) revealed that lavenderblush2 and brown4 modules were significantly positively correlated with the proline content and peroxidase activity and hub genes within these two modules were further determined. Besides, after 1 h of salt treatment, categories such as signalling receptor kinase, transcription factors, tetrapyrrole synthesis and lipid metabolism were immediately and exclusively up-enriched compared to the subsequent time points, which indicated fast-acting and immediate physiological responses. Other specific categories involved in secondary metabolite biosynthesis such as simple phenols, glucosinolates, isoflavones and tocopherol biosynthesis were exclusively up-regulated after 24 h of salt treatment, suggesting a slightly slower reaction of metabolic adjustment.Conclusion: Here, we revealed salt response themes that were commonly or differentially expressed in short-term salt stress, suggesting possible adaptive salt response mechanisms in the roots. Also, the distinctive salt-response pathways and potential salt-tolerant hub genes investigated can provide useful future references to explore the molecular mechanisms of bermudagrass.

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