Exploiting Differential Gene Expression to Discover Ionic and Osmotic-Associated Transcripts in the Halophyte Grass Aeluropus littoralis

Fatemi, Farzaneh; Hashemi-Petroudi, Seyyed Hamidreza; Nematzadeh, Ghorbanali; Askari, Hossein; Abdollahi, Mohammad Reza

doi:10.1186/s12575-019-0103-3

Cited by 13 publications

(16 citation statements)

References 44 publications

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“…Hence, it can be stated that 200 mM NaCl is not detected as stress condition, but 400 mM NaCl induces the most stress-related terms in the A. littoralis. Our results support previous findings that 200 mM NaCl enhances the biomass of A. littoralis in liquid MS culture medium 29 and also increases the root length in comparison with control plants 30 .…”

Section: Discussionsupporting

confidence: 92%

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

Younesi-Melerdi

Nematzadeh

Parizi

et al. 2020

Sci Rep

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the study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. the aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM nacl) by de novo RNA-sequencing. To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). The de novo assembled transcriptome by Bridger (k-mer 32) was chosen as final assembly for subsequent analysis. In general, 103290 transcripts were obtained. The differential expression analysis (log 2 fc > 1 and FDR < 0.01) showed that 1861 transcripts expressed differentially, including169 up and 316 down-regulated transcripts in 200 mM NaCl treatment and 1035 up and 430 down-regulated transcripts in 400 mM NaCl treatment compared to control. In addition, 89 transcripts were common in both treatments. The most important over-represented terms in the GO analysis of differentially expressed genes (FDR < 0.05) were chitin response, response to abscisic acid, and regulation of jasmonic acid mediated signaling pathway under 400 mM NaCl treatment and cell cycle, cell division, and mitotic cell cycle process under 200 mM treatment. in addition, the phosphatidylcholine biosynthetic process term was common in both salt treatments. Interestingly, under 400 mM salt treatment, the PRC1 complex that contributes to chromatin remodeling was also enriched along with vacuole as a general salinity stress responsive cell component. Among enriched pathways, the MAPK signaling pathway (ko04016) and phytohormone signal transduction (ko04075) were significantly enriched in 400 mM NaCl treatment, whereas DNA replication (ko03032) was the only pathway that significantly enriched in 200 mM NaCl treatment. Finally, our findings indicate the salt-concentration depended responses of A. littoralis, which wellknown salinity stress-related pathways are induced in 400 mM NaCl, while less considered pathways, e.g. cell cycle and DNA replication, are highlighted under 200 mM NaCl treatment. Soil salinity is an important challenge for food security and sustainable agriculture in the world 1. Salt stress negatively influences the growth, development, and yield of agricultural products 2-4. Higher plants adapt to different environmental stresses by complex molecular, cellular, and physiological mechanisms. The transcriptional alteration of stress-related genes is one of the key approaches at molecular level to cope with adverse conditions 5,6. Plants employ complicated strategies such as ion homeostasis, osmotic regulation, antioxidant systems, and signaling pathways of phytohormones and MAPK to tolerate salinity stress 6. Although our knowledge on this area is increasing continuously, but the molecular basis of salt resistance is not still well understood. Various omics technologies such as transcriptomics, proteomics, genomics and metabolomics are used for investigation of plant molecular responses 7,8. Am...

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Section: Discussionsupporting

confidence: 92%

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

Younesi-Melerdi

Nematzadeh

Parizi

et al. 2020

Sci Rep

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“…compared to a control [43]. The results also showed that potassium chloride was more toxic than sodium chloride, and the K + ion affected plant growth more than the Na + ion [43]. Another study of five selected landscape ornamental species demonstrated that plant growth decreased when irrigated with increasing NaCl + CaCl 2 concentrations [44].…”

Section: Introductionmentioning

confidence: 95%

“…In the case of Salicornia europaea L., good germination of large seeds occurred under NaCl between 0.5 and 2%, under Na 2 SO 4 and 2NaCl + KCl + CaCl 2 between 0.5 and 3%, and under 2Na 2 SO 4 + K 2 SO 4 + MgSO 4 between 0.5 and 5% [42]. Fatemi et al [43] indicated that salinity stresses induced by 200 mM and 400 mM KCl and polyethylene glycol (PEG, the nonpenetrant osmotic agent) significantly reduced the fresh weight of the halophyte grass Aeluropus littoralis (Gouan) Parl. compared to a control [43].…”

Section: Introductionmentioning

confidence: 96%

“…Fatemi et al [43] indicated that salinity stresses induced by 200 mM and 400 mM KCl and polyethylene glycol (PEG, the nonpenetrant osmotic agent) significantly reduced the fresh weight of the halophyte grass Aeluropus littoralis (Gouan) Parl. compared to a control [43]. The results also showed that potassium chloride was more toxic than sodium chloride, and the K + ion affected plant growth more than the Na + ion [43].…”

Section: Introductionmentioning

confidence: 99%

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Osmotic Stress or Ionic Composition: Which Affects the Early Growth of Crop Species More?

et al. 2021

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Salinization is a key soil degradation process. An estimated 20% of total cultivated lands and 33% of irrigated agricultural lands worldwide are affected by high salinity. Much research has investigated the influence of salt (mainly NaCl) on plants, but very little is known about how this is related to natural salinity and osmotic stress. Therefore, our study was conducted to determine the osmotic and ionic salt stress responses of selected C3 and C4 cultivated plants. We focused on the early growth stages as those critical for plant development. We applied natural brine to simulate natural salinity and to compare its effect to NaCl solution. We assessed traits related to germination ability, seedlings and plantlet morphology, growth indexes, and biomass and water accumulation. Our results demonstrate that the effects of salinity on growth are strongest among plantlets. Salinity most affected water absorption in C3 plants (28% of total traits variation), but plant length in C4 plants (17–27%). Compensatory effect of ions from brine were suggested by the higher model plants’ growth success of ca 5–7% under brine compared to the NaCl condition. However, trait differences indicated that osmotic stress was the main stress factor affecting the studied plants.

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“…Genome-wide transcript pro ling techniques play an important role in large-scale screening and characterization of the genes involved in various biological processes. Since the advent of the cDNA-AFLP transcript-pro ling technique in 1996 [22], owing to its advantages of good repeatability, high sensitivity and high throughput, this technique has been successfully applied to the eld of plant biology, such as abiotic stress response [23], plant-microorganism interaction [24], hormone signal [25] and development [26].…”

Section: Introductionmentioning

confidence: 99%

Transcript Profiling Provides Insights into the Molecular Mechanisms of Harvesting-activated Latex Regeneration in Virgin Rubber Trees

Fan

Xiao

Yang

et al. 2021

Preprint

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Background: Natural rubber, an important industrial raw material with wide applications, is harvested in the form of latex (cytoplasm of rubber-producing laticifers) from Hevea brasiliensis (para rubber tree) by the way of tapping, i.e. removing a slice of trunk bark by a special knife. In regularly tapped rubber trees, latex regeneration consists of one of the main yield-limiting factors for rubber productivity. Conspicuous stimulation on latex production for the first few tappings makes virgin (untapped before) rubber trees an ideal model to investigate the regulatory mechanisms of latex regeneration. To understand the underlying mechanisms, genome-wide transcript profiling was conducted with a silver-staining cDNA-AFLP technology against the latex samples for the first five tappings.Results: A total of 505 non-redundant differentially expressed (DE) transcript-derived fragments (TDFs) were identified, of which 217 were up-regulated, 180 down-regulated, and 108 bell type-regulated among the five tappings. About 72.5% of these DE-TDFs were functionally annotated, and classified into 11 functional categories, which were discussed with reference to harvesting-stimulated latex regeneration. The importance of sugar metabolism and rubber biosynthesis was highlighted, due to the fact that most of the DE-TDFs annotated in sucrose transport, sugar catabolism, glycolysis, tricarboxylic acid cycle and pentose-phosphate pathway and nine of the ten rubber biosynthesis pathway DE-TDFs were up-regulated by the tapping treatment. More than one tenth of the total DE-TDFs were randomly selected for expression validation by semi-quantitative RT-PCR, and 83.8% showed patterns consistent with their original cDNA-AFLP gel profiles. Moreover, quantitative RT-PCR analysis revealed an 89.7% consistency for the 29 latex-regeneration related DE-TDFs examined.Conclusions: In brief, our results indicate the tapping treatment incurs extensive physiological and molecular changes in the laticifers of virgin rubber trees. The vast numbers of tapping-responsive DE-TDFs identified here provide a basis for unravelling the gene regulatory network for latex regeneration in regularly harvested rubber trees.

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Exploiting Differential Gene Expression to Discover Ionic and Osmotic-Associated Transcripts in the Halophyte Grass Aeluropus littoralis

Cited by 13 publications

References 44 publications

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

Osmotic Stress or Ionic Composition: Which Affects the Early Growth of Crop Species More?

Transcript Profiling Provides Insights into the Molecular Mechanisms of Harvesting-activated Latex Regeneration in Virgin Rubber Trees

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