RNA-seq analysis reveals narrow differential gene expression in MEP and MVA pathways responsible for phytochemical divergence in extreme genotypes of Thymus daenensis Celak

BACKGROUND

Here, we investigated the underlying transcriptional-level evidence behind phytochemical differences between two metabolically extreme genotypes of Thymus daenensis. The genotypes 'Zagheh-11' (thymol/carvacrol type, poor in essential oil [EO] [2.9%] but rich in triterpenic acids) and 'Malayer-21' (thymol type and rich in EO [3.8%]) were selected from an ongoing breeding program and then clonally propagated for further experimental use.

MATERIALS AND METHODS

GC-MS, GC-FID, and HPLC-PDA were utilized to monitor the fluctuation of secondary metabolites at four phenological stages (vegetative, bud burst, early, and full-flowering stages). The highest phytochemical divergence was observed at early flowering stage. Both genotypes were subjected to mRNA sequencing (approximately 100 million paired reads) at the aforementioned stage. The expression patterns of four key genes involved in the biosynthesis of terpenoids were also validated using qRT-PCR.

RESULTS

Carvacrol content in 'Zagheh-11' (26.13%) was approximately 23 times higher than 'Malayer-21' (1.12%). Reciprocally, about 10% higher thymol was found in 'Malayer-21' (62.15%). Moreover, the concentrations of three major triterpenic acids in 'Zagheh-11' were approximately as twice as those found in 'Malayer-21'. Transcriptome analysis revealed a total of 1840 unigenes that were differentially expressed, including terpene synthases, cytochrome P450, and terpenoid backbone genes. Several differentially expressed transcription factors (such as MYB, bZIP, HB-HD-ZIP, and WRKY families) were also identified. These results suggest that an active cytosolic mevalonate (MVA) pathway may be linked to higher levels of sesquiterpenes, triterpenic acids, and carvacrol in 'Zagheh-11'. The chloroplastic pathway of methyl erythritol phosphate (MEP) may have also contributed to a higher accumulation of thymol in Malayer-21. Indeed, 'Zagheh-11' showed higher expression of certain genes (HMGR, CYP71D180, β-amyrin 28-monooxygenase, and sesquiterpene synthases) in the MVA pathway, while some genes in the MEP pathway (including DXR, ispG, and γ-terpinene synthase) were distinctly expressed in Malayer-21. Future efforts in metabolic engineering of MVA/MEP pathways may benefit from these findings to produce increased levels of desired secondary metabolites at commercial scale.

Is apomixis occurring in walnut (Juglans regia L.)? New data from progeny molecular tests and cytological investigations shed light on its reproductive system

Introduction

Persian walnut (Juglans regia) is an economically important nut fruit species cultivated worldwide for its nutritious kernel and timber quality wood. Walnut trees are mostly hetero-dichogamous and, depending on the genotype, some cultivars are protogynous, while others are protandrous. Although selfing is possible when male and female blooms overlap, the dichogamy of the species promotes outcrossing. In addition to sexual reproduction, some reports indicate that elements of apomixis may occur in commercial orchards of walnut varieties and in the last two decades, nut production by apomixis has been reported in walnut. However, there are no reliable studies on the occurrence of apomictic reproduction based on cytoembryological observations and/or molecular marker-progeny tests. This study addresses the combined use of molecular and cytological analyses to gain new insights into the population genetics and reproduction systems of J. regia.

Methods

We systematically analyzed the reproductive origin of individual progeny plants from 8 different cultivated walnut genotypes using microsatellite genotyping and carried out cytohistological investigations of 5 cultivated walnut genotypes arising seed sets from isolated flowers, to shed light on the mode of reproduction.

Results and discussion

These cytometric and genotyping analyses did not support any asexual mode of reproduction or asexual propagation by seed and all individuals studied were identified as zygotic plants produced by crossing. Likewise, the cytological findings did not confirm completely the first component of apomixis, namely apomeiosis. On the other hand, according to histological evidence, adventitious embryony seems to take place at low frequency. Overall, our findings suggest that the occurrence of gametophytic apomixis is unlikely in J. regia, but sporophytic apomixis cannot be completely ruled out.

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Non-erroneous and well-optimized transcriptome assembly is a crucial prerequisite for authentic downstream analyses. Each de novo assembler has its own algorithm-dependent pros and cons to handle the assembly issues and should be specifically tested for each dataset. Here, we examined efficiency of seven state-of-art assemblers on ~ 30 Gb data obtained from mRNA-sequencing of Thymus daenensis. In an ensemble workflow, combining the outputs of different assemblers associated with an additional redundancy-reducing step could generate an optimized outcome in terms of completeness, annotatability, and ORF richness. Based on the normalized scores of 16 benchmarking metrics, EvidentialGene, BinPacker, Trinity, rnaSPAdes, CAP3, IDBA-trans, and Velvet-Oases performed better, respectively. EvidentialGene, as the best assembler, totally produced 316,786 transcripts, of which 235,730 (74%) were predicted to have a unique protein hit (on uniref100), and also half of its transcripts contained an ORF. The total number of unique BLAST hits for EvidentialGene was approximately three times greater than that of the worst assembler (Velvet-Oases). EvidentialGene could even capture 17% and 7% more average BLAST hits than BinPacker and Trinity. Although BinPacker and CAP3 produced longer transcripts, the EvidentialGene showed a higher collinearity between transcript size and ORF length. Compared with the other programs, EvidentialGene yielded a higher number of optimal transcript sets, further full-length transcripts, and lower possible misassemblies. Our finding corroborates that in non-model species, relying on a single assembler may not give an entirely satisfactory result. Therefore, this study proposes an ensemble approach of accompanying EvidentialGene pipelines to acquire a superior assembly for T. daenensis.

Biochemical and molecular responses of Rosa damascena mill. cv. Kashan to salicylic acid under salinity stress

BACKGROUND

Today, salinity stress is one of the most important abiotic stresses in the world, because it causes damage to many agricultural products and reduces their yields. Oxidative stress causes tissue damages in plants, which occurs with the production of reactive oxygen species (ROS) when plants are exposed to environmental stresses such as salinity. Today, it is recommended to use compounds that increase the resistance of plants to environmental stresses and improve plant metabolic activities. Salicylic acid (SA), as an intracellular and extracellular regulator of the plant response, is known as one of these effective compounds. Damask rose (Rosa damascena Mill.) is a medicinal plant from the Rosaceae, and its essential oils and aromatic compounds are used widely in the cosmetic and food industries in the world. Therefore, considering the importance of this plant from both medicinal and ornamental aspects, for the first time, we investigated one of the native cultivars of Iran (Kashan). Since one of the most important problems in Damask rose cultivation is the occurrence of salinity stress, for the first time, we investigated the interaction of several levels of NaCl salinity (0, 4, 8, and 12 ds m^- 1) with SA (0, 0.5, 1, and 2 mM) as a stress reducer.

RESULTS

Since salinity stress reduces plant growth and yield, in this experiment, the results showed that the increase in NaCl concentration caused a gradual decrease in photosynthetic and morphological parameters and an increase in ion leakage. Also, increasing the level of salinity stress up to 12 ds m^- 1 affected the amount of chlorophyll, root length and leaf total area, all of which reduced significantly compared to plants under no stress. However, many studies have highlighted the application of compounds that reduce the negative effects of stress and increase plant resistance and tolerance against stresses. In this study, the application of SA even at low concentration (0.5 mM) could neutralize the negative effects of salinity stress in the Rosa damascena. In this regard, the results showed that salinity increases the activity of antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD) and the concentration of proline, protein and glycine betaine (GB). Overexpression of antioxidant genes (Ascorbate Peroxidase (APX), CAT, Peroxidase (POD), Fe-SOD and Cu-SOD) showed an important role in salt tolerance in Damascus rose. In addition, 0.5 mm SA increased the activity of enzymatic and non-enzymatic systems and increased salinity tolerance.

CONCLUSIONS

The change in weather conditions due to global warming and increased dryness contributes to the salinization of the earth's surface soils. Therefore, it is of particular importance to measure the threshold of tolerance of roses to salinity stress and the effect of stress-reducing substances in plants. In this context, SA has various roles such as increasing the content of pigments, preventing ethylene biosynthesis, increasing growth, and activating genes involved in stress, which modifies the negative effects of salinity stress. Also, according to the results of this research, even in the concentration of low values, positive results can be obtained from SA, so it can be recommended as a relatively cheap and available material to improve production in saline lands.

Influence of kaolin application on most important fruit and leaf characteristics of two apple cultivars under sustained deficit irrigation

Background

Apple is one of the oldest and most valuable fruits. Water restriction is one of the major problems in the production of this fruit in some planting areas.

Methods

Effects of kaolin spray treatments were studied on two early apple cultivars of Golab and Shafi-Abadi under sustained deficit irrigation (SDI) in Alborz province, Iran during 2017 and 2018. Irrigation treatments were 100%, 85%, and 70% ETc and kaolin application were concentrations of 0, 3 and 6% in 2017 and 0, 1.5 and 3% in 2018.

Results

Results showed that 85% ETc treatment compared to other irrigation treatments improved apple tree crown volume in 2017. Deficit irrigation treatments significantly reduced fruit weight in both years. Application with 6% kaolin resulted in 33.3% increase in apple fruit weight compared to non-kaolin treatment at 100% ETc irrigation in the first year. Severe deficit irrigation (70% ETc) significantly reduced apple fruit length in both years, but 6% kaolin increased fruit length in both apple cultivars in 2017. Severe deficit irrigation treatment increased the firmness of apple fruit compared to control and mild deficit irrigation (85% ETc) in the first year of experiment. There was no significant difference between irrigation treatments for apple fruit firmness in the second year of experiment. Kaolin treatments of 1.5% and 3% at full irrigation increased the soluble solids content of apple fruit by 36.6% and 44.1% in 2018, respectively. Deficit irrigation treatments significantly increased leaf proline content compared to control in both years. In the first year, kaolin treatments increased leaf proline but in the second year, leaf proline was not significant. Deficit irrigation treatment of 70% ETc and 6% kaolin had the highest amount of glycine betaine content, malondialdehyde and hydrogen peroxide in apple leaf in the first year of experiment.

Conclusions

Severe deficit irrigation stress (70% ETc) increased the activity of nonenzymatic defense systems of apple trees. Kaolin as a drought stress reducing agent can be recommended in apple orchards of Golab and Shafi-Abadi cultivars as an effective and inexpensive method to improve tolerance to drought stress conditions.

Effect of foliar application with sodium selenate on selenium biofortification and fruit quality maintenance of 'Starking Delicious' apple during storage

BACKGROUND

Selenium (Se) is an essential micronutrient due to its anticarsinogenic properties and positive influence on human immune system. Fortification of some fruits based on their rates of consumption and availability all year round appears to be an effective way to supplement Se in the human diet. In this study the possibility of augmenting Se content in 'Starking Delicious' apple fruit during two growing seasons was investigated. In 2016, the impact of 0, 0.5, 1 and 1.5 mg Se L^-1 by foliar application on Se accumulation and fruit ripening as well as quality attributes was investigated. In 2017, the effects of 1.5 mg Se L^-1 foliar application on fruit Se content and changes in the antioxidant system and storability were studied with a 30-day interval during 6 months storage at 0 ± 1 °C.

RESULTS

Foliar application of Se significantly increased both leaf and fruit Se concentration. The increase in Se content enhanced the flesh firmness, titrable acidity, and soluble solid content of the fruit. The activities of antioxidant enzymes, superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) were markedly amplified by Se treatments as compared to the control, resulting in lower superoxide anion radical (O₂ ^-• ) and hydrogen peroxide (H₂ O₂ ) contents, correspondingly higher membrane integrity as revealed by lower ion leakage and malondialdehyde accumulation and the fruit with lower water core.

CONCLUSION

Application of Se was efficient in increasing fruit Se content and nutraceutical properties, retarding the flesh firmness reduction, and postponing fruit ripening resulting from lower ethylene biosynthesis rate, thereby positively affecting apple fruit quality and storability. © 2019 Society of Chemical Industry.

Effects of deficit irrigation and kaolin application on vegetative growth and fruit traits of two early ripening apple cultivars

Background

Drought is one of the main serious problems for agriculture production which its intensity is increasing in many parts of the world, hence, improving water use efficiency is a main goal for sustainable agriculture.

Results

Growth indices including relative shoot length growth (SL), relative stem diameter increase (SD) and relative trunk cross sectional area growth (TCSA) measured at the start and end of the season decreased by reducing the irrigation level. Chlorophyll index (CI) was decreased at 70% crop evapotranspiration, however water use efficiency (WUE), leaf and fruit total phenolic content (TPC), and fruit anthocyanin content (AC) were among the traits that showed increment by water deficit stress in both cultivars. Shafi-Abadi cultivar showed to be more sensitive to the water stress than ‘Golab’. Kaolin treatment improved SL, SD and CI traits, but this increase was statistically significant only for SD at 5% level. Kaolin had no significant effect on yield and water use efficiency (WUE), however, it had negative effect on yield efficiency (YE). Kaolin treatments also significantly increased fruit and leaf TPC (P < 0.01) but had no effect on leaf and fruit total antioxidant activity (AA), as well as fruit anthocyanin content (AC) and soluble proteins (SP).

Conclusions

Irrigation at 85% ETc showed better results than 100% and 70% ETc levels for yield attributes. It seems that the more pronounced effect of kaolin on vegetative traits but not on the fruits, might be attributed to the early ripening and harvest time of the examined cultivars.

Catalyst-Free Three-Component Synthesis of Spirobenzimidazolidines Bearing an Indole Scaffold

An efficient catalyst-free one-pot three-component reaction was developed for the synthesis of a new family of N- and S-containing spirocyclic compounds. Various derivatives of spirobenzimidazolidine containing an indole scaffold were synthesized for the first time in a modestly toxic solvent and under mild reaction conditions. The reaction times were of the order of several minutes, and all the products were obtained in moderate to high yields (overall yields 58–80%).

Physico-chemical analysis of drinking groundwater of around Tehran by seasonal variation

This study was a cross-sectional descriptive study and done in four seasons during April 2011 to March 2012.The objective of the present study was to examine Physico-chemical properties of groundwater around Tehran. The results are also compared with the guideline values of Iranian legislation. A total of 160 drinking water samples were collected from different drinking groundwater around the Tehran. Total Dissolved Solids (TDS), conductivity and pH, were measured by using standard methods and the concentration of ions Cl-, F-, NO3-, NO2-, Br-, SO4(2-), PO4(3-), Ca2+, K+, Na+ and NH4+ in groundwater was performed using Ion chromatography (Metrohm Company, USA) with standard method. This study showed that most of the parameters in groundwater were below the Iranian permissible limit except total dissolved solids (N = 2), conductivity (N = 2), nitrate as NO3- (N = 22), chloride (N = 3), sulphate (N = 2), fluoride (N = 3) and ammonia (N = 8). There were significant differences (p < 0.05) between physico-chemical parameters such as pH, nitrite (NO2-), sodium, potassium, sulphate, ammonia, bromide and phosphate in different seasons. These results are important, not only for the many people who drink groundwater but also for the health supervisory agencies such as Ministry of Health and Institute of Standards and Industrial of Iran (ISIRI) to have more effective control on groundwater.

A metabolomic study on the effect of intravascular laser blood irradiation on type 2 diabetic patients

Intravenous laser blood irradiation (ILBI) is widely applied in the treatment of different pathologies including diabetes mellitus. The aim of this study is to evaluate the effects of ILBI on the metabolites of blood in diabetic type 2 patients using metabolomics. We compared blood samples of nine diabetic type 2 patients, using metabolomics, before and after ILBI with blue light laser. The results showed significant decrease in glucose, glucose 6 phosphate, dehydroascorbic acid, R-3-hydroxybutyric acid, L-histidine, and L-alanine and significant increase in L-arginine level in blood and blood sugar in the patients have reduced significantly (p < 0.05). This study clearly demonstrated a significant positive effect of ILBI on metabolites of blood in diabetic type 2 patients. These findings support the therapeutic potential of ILBI in diabetic patients.

Early detection of immunization: a study based on an animal model using 1H nuclear magnetic resonance spectroscopy

Vaccines require a period of at least three months for clinical trials, hence a method that can identify elicitation of immune response a few days after the first dose is a necessity. Evolutionary variable selections are modeling approaches for proper manipulation of available data which were used to set up an animal model for classification of time dependent 1HNMR metabolomic profiles and pattern recognition of fluctuations of metabolites in two groups of male rabbits. One group of rabbits was immunized with human red blood cells and the other used as control. Blood was obtained every 48 h from each rabbit for a period of six weeks and the serum monitored for antibodies and metabolites by 1HNMR spectra. Evaluation of data was carried out using orthogonal signal correction followed by principal component analysis and partial least square. A neural network was also set up to predict immunization profiles. A distinct separation in patterns of significant metabolites was obtained between the two groups, just a few days after the first and the second dose. These metabolites were used as targets of neural networks where each sample was used as test, validation and training and their quantitative influence predicted by regression. This model could be used for prediction of immunization in rabbits a few days after the first dose with 96% accuracy. Similar animals and human vaccine trials would assist greatly in reaching early conclusions in advance of the usual two month immunization schedule; resulting in an appreciable saving of cost and time.

Genetic diversity of Iranian soft-seed pomegranate genotypes as revealed by fluorescent-AFLP markers

The amplified fragment length polymorphism (AFLP) technique was used to examine the genetic relationships among 21 Iranian soft-seeded pomegranate (Punica granatum L.) genotypes. Out of 72 fluorescent-AFLP primer combinations screened, 31 were selected to produce the 503 polymorphic markers used in this study. Genetic similarity estimates between genotypes, calculated by the Jaccard's similarity coefficient, ranged from 0.17 to 1.00, while the cophenetic correlation coefficient between the genetic similarities and the unweighted pair group method of arithmetic averages (UPGMA) dendrogram was 0.98. The AFLP-based UPGMA dendrogram revealed two groups within the genotypes at 0.33 similarity coefficient, which reflect fruit traits such as peel and aril color, and seed firmness, as well as region of origin. Our study shows that the use of molecular markers is essential during all steps of germplasm management to avoid genotype redundancy and mislabeling. The present study will be used as a reliable reference to discriminate among these genotypes, to aid management of germplasm collections used to breed new varieties for the Iranian pomegranate industry.

Evaluation of serum levels of essential trace elements in patients with pulmonary tuberculosis before and after treatment by age and gender

The purpose of this study was to evaluate the levels of Zinc, Copper, Iron and Copper/Zinc ratio in the serum of adult patients with pulmonary tuberculosis in Iran. Serum levels of Zinc and Copper were determined by flame atomic absorption spectrophotometer and scrum iron concentration was measured by using an Auto Analyzer. The study group consisted of 50 pulmonary tuberculosis patients before treatment and after 6 months of anti-tubercular therapy. Levels of scrum Zn (p < 0.001) and Fe (p < 0.001) in TB patients were significantly increased after 6 months of anti-tubercular therapy. However, serum Cu concentration (p < 0.01) and Cu/Zn ratio (p < 0.05) were decreased after 6 months of anti-tubercular therapy. Some studies indicated a strong association of Zn, Cu, Fe and the Cu/Zn ratio with TB. In this study, we found remarkable change in Cu/Zn ratio. Some researchers mentioned that serum Cu/Zn ratio could be used as an important laboratory marker for diagnosis and treatment of tuberculosis. They also mentioned that trace element levels must be closely monitored during the process of disease.

Evaluation of serum levels of zinc, copper, iron, and zinc/copper ratio in cutaneous leishmaniasis

BACKGROUND

The purpose of this study was to evaluate the levels of zinc (Zn), copper (Cu), iron (Fe) and zinc/ copper ratio in the serum of patients with cutaneous leishmaniasis in Qom Province, center of Iran.

METHODS

Serum levels of zinc and copper were determined by flame atomic absorption spectrophotometer and serum iron concentration was measured by using an Auto Analyzer. The study group consisted of 60 patients with cutaneous leishmaniasis and the control group of 100 healthy volunteers from the same area who were not exposed to cutaneous leishmaniasis.

RESULT

There were no statistically significant differences in age and body mass index between the two groups. Serum Zn (P< 0.001) and Fe (P< 0.05) levels were lower in patients with cutaneous leishmaniasis than the control group. We also found serum Cu concentration (P< 0.05) in the patient group was significantly higher than that of the control group. However, zinc/ copper ratio (P< 0.001) was lower in patients with cutaneous leishmaniasis than in the control group.

CONCLUSION

Our data indicated that Zn/Cu ratio was significantly lower in patients with CL as compared to the controls. Earlier reports suggest that, this ratio imbalance could be a useful marker for immune dysfunction in leishmaniasis. There was also strong association of Zn, Cu and Fe with CL. It suggests the use of blood zinc, copper, iron concentration and the copper/zinc ratio (Zn/Cu), as a means for estimating the prognosis of CL.