Review on ethnobotany, phytochemical, molecular and pharmacological activity of Thymus daenensis Celak

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.

LC-MS/MS and GC-MS profiling, antioxidant, enzyme inhibition, and antiproliferative activities of Thymus leucostomus H ausskn. & V elen. extracts

The chemical composition as well as antioxidant, antiproliferative, and enzyme inhibition activities of extracts from aerial parts of Thymus leucostomus H ausskn. & V elen. obtained with hexane, methanol, and water were evaluated. Results showed that the methanol extract had significantly (p < 0.05) the highest total phenolic content (TPC; 107.80 mg GAE/g) and total flavonoids content (TFC; 25.21 mg RE/g) followed by the aqueous extract (102.72 mg GAE/g and 20.88 mg RE/g, respectively). LC-MS/MS-guided profiling of the three extracts revealed that rosmarinic acid (34.8%), hesperetin (42.9%), and linoleic acid (18%) were the dominant compounds in the methanol, aqueous and hexane extracts, respectively. GC-MS analysis of the hexane extract showed that ɣ-sitosterol (29.9%) was the major constituent. The methanol extract displayed significantly (p < 0.05) the highest Cu++ , Fe+++ , and Mo(VI) ions scavenging and reducing properties while the aqueous extract exerted significantly (p < 0.05) the highest metal chelating power (42.51 mg EDTAE/g). Both the hexane and methanol extracts effectively inhibited the acetylcholinesterase enzyme (2.63 and 2.65 mg GALAE/g, respectively) while the former extract exerted significantly (p < 0.05) the highest butyrylcholinesterase (2.32 mg GALAE/g), tyrosinase (19.73 mg KAE/g), and amylase (1.16 mmol ACAE/g) inhibition capacity. The aqueous extract exhibited the best glucosidase inhibition property (0.49 mmol ACAE/g). The methanol and hexane extracts exerted a higher cytotoxic effect on HT-29 (IC50 : 8.12 µg/mL) and HeLa (IC50  = 8.08 µg/mL) cells, respectively. In conclusion, these results provide valuable insight into the potential use of T. leucostomus bioactive extracts in different pharmaceutical applications.

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.

Phytochemical and biological activities of some Iranian medicinal plants

CONTEXT

Due to adverse effects of synthetic compounds, there is a growing interest in utilization of plant-derived natural products in the pharmaceutical and food industries. Iranian endemic medicinal plants widely used in traditional practice have attracted much attention as antibacterial and antioxidant agents.

OBJECTIVE

This review attempts to compile the accessible scientific research pertained to phytochemical compounds, antibacterial and antioxidant effects of essential oils obtained from some of the most widely used and distributed medicinal plants in Iran.

METHODS

This review has been compiled using references via reliable databases (Google Scholar, SID and Science Direct) from 2010 to 2020. This literature review was limited to references published in English and Persian languages.

RESULTS

Based on studies heretofore carried out, essential oils isolated from mentioned medicinal plants exhibited strong antioxidant activity which is attributed to their main phytochemical compounds; thymol, carvacrol, p-cymene and γ-terpinene. In addition, the antibacterial activities of essential oils of most plant species from Apiaceae and Asteraceae families were more susceptible against Gram-positive bacteria; Staphylococcus aureus and Bacillus cereus than Gram-negative bacteria; however, essential oils of other studied plant species manifested similar behaviours against both Gram-positive and -negative bacteria.

CONCLUSIONS

As there is rich ethnobotanical knowledge behind Iranian endemic medicinal plants, further scientific research is required to prove their safety and efficacy. This review revealed that there are numerous valuable medicinal plants adoptable in food and pharmaceutical industries in the near future.

Ethnopharmacological studies of medicinal plants in central Zagros, Lorestan Province, Iran

ETHNOPHARMACOLOGICAL RELEVANCE

Lorestan Province (Iran) has a great diversity of habitats and plant diversity and the people living in this province have a good knowledge of herbal therapies.

AIM OF THE STUDY

In this study, the authors aimed to identify and report the medicinal plants used in the folk medicine of Lorestan.

MATERIAL AND METHODS

The indigenous medicinal information was collected with a semi-structured open-ended questionnaire, interviews, and personal observations. The relative importance of the species were estimated through frequency of citations (FC).

RESULTS

and discussion: A total of 555 plants belonging to 91 families were identified. The plants belong to Asteraceae with 62 species followed by Lamiaceae (56), Apiaceae (44), Fabaceae (41), and Brassicaceae (31). The plants were mostly used as a decoction or eaten raw (32%). Leaves (22%) were the most utilized plant parts followed by shoots (16%), and seeds (13%). Thymus daenensis, Thymus eriocalyx, Mentha longifolia, Mentha spicata, Mentha piperitha, Alium sativum, Quercus infectoria, Quercus persica, Ziziphora clinopodioides, and Malus domestica had the highest FC values. Most of the plants were used for gastrointestinal, respiratory, and skin problems.

CONCLUSION

Lorestan is a region rich in medicinal plants. The local knowledge of herbal therapies can be used as complementary medicine, particularly by people in remote areas and as a guide for the future pharmacological and phytochemical studies. While the known medicinal plants can be harvested or cultivated for medical and pharmaceutical purposes, the less known plants with high FC scores can be investigated phytochemically and pharmacologically in the future studies.