Creation of new germplasm resources, development of SSR markers, and screening of monoterpene synthases in thyme

BACKGROUND

Thyme derived essential oil and its components have numerous applications in pharmaceutical, food, and cosmetic industries, owing to their antibacterial, antifungal, and antiviral properties. To obtain thyme essential oil with different terpene composition, we developed new germplasm resources using the conventional hybridization approach.

RESULTS

Phenotypic characteristics, including essential oil yield and composition, glandular trichome density, plant type, and fertility, of three wild Chinese and seven European thyme species were evaluated. Male-sterile and male-fertile thyme species were crossed in different combinations, and two F₁ populations derived from Thymus longicaulis (Tl) × T. vulgaris 'Fragrantissimus' (Tvf) and T. vulgaris 'Elsbeth' (Tve) × T. quinquecostatus (Tq) crosses were selected, with essential oil yield and terpene content as the main breeding goals. Simultaneously, simple sequence repeat (SSR) primers were developed based on the whole-genome sequence of T. quinquecostatus to authenticate the F₁ hybrids. A total of 300 primer pairs were selected, and polymerase chain reaction (PCR) was carried out on the parents of the two hybrid populations (Tl, Tvf, Tve, and Tq). Based on the chemotype of the parents and their F₁ progenies, we examined the expression of genes encoding two γ-terpinene synthases, one α-terpineol synthase, and maybe one geraniol synthase in all genotypes by quantitative real-time PCR (qRT-PCR).

CONCLUSION

We used hybridization to create new germplasm resources of thyme, developed SSR markers based on the whole-genome sequence of T. quinquecostatus, and screened the expression of monoterpene synthase genes in thyme. The results of this study provide a strong foundation for the creation of new germplasm resources, construction of the genetic linkage maps, and identification of quantitative trait loci (QTLs), and help gain insight into the mechanism of monoterpenoids biosynthesis in thyme.

Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme

Thyme has medicinal and aromatic value because of its potent antimicrobial and antioxidant properties. However, the absence of a fully sequenced thyme genome limits functional genomic studies of Chinese native thymes. Thymus quinquecostatus Čelak., which contains large amounts of bioactive monoterpenes such as thymol and carvacrol, is an important wild medicinal and aromatic plant in China. Monoterpenoids are abundant in glandular secretory trichomes. Here, high-fidelity and chromatin conformation capture technologies were used to assemble and annotate the T. quinquecostatus genome at the chromosome level. The 13 chromosomes of T. quinquecostatus had a total length of 528.66 Mb, a contig N50 of 8.06 Mb, and a BUSCO score of 97.34%. We found that T. quinquecostatus had experienced two whole-genome duplications, with the most recent event occurring ∼4.34 million years ago. Deep analyses of the genome, in conjunction with comparative genomic, phylogenetic, transcriptomic, and metabonomic studies, uncovered many regulatory factors and genes related to monoterpenoids and glandular secretory trichome development. Genes encoding terpene synthase (TPS), cytochrome P450 monooxygenases (CYPs), short-chain dehydrogenase/reductase (SDR), R2R3-MYB, and homeodomain-leucine zipper (HD-ZIP) IV were among those present in the T. quinquecostatus genome. Notably, Tq02G002290.1 (TqTPS1) was shown to encode the terpene synthase responsible for catalyzing production of the main monoterpene product γ-terpinene from geranyl diphosphate (GPP). Our study provides significant insight into the mechanisms of glandular secretory trichome formation and monoterpenoid biosynthesis in thyme. This work will facilitate the development of molecular breeding tools to enhance the production of bioactive secondary metabolites in Lamiaceae.

Effect of Methyl Jasmonate on Thymol, Carvacrol, Phytochemical Accumulation, and Expression of Key Genes Involved in Thymol/Carvacrol Biosynthetic Pathway in Some Iranian Thyme Species

Thyme species are a good source of thymol and carvacrol, which play a key role in controlling diseases. For the first time, the expression patterns of γ-terpinene synthase (TPS2), CYP71D178, and CYP71D180 genes and the amount of phenolics compounds were evaluated in T. migricus and T. daenensis after different methyl jasmonate (MeJA) treatments. The highest thymol and carvacrol contents were observed in T. migricus (86.27%) and T. daenensis (17.87%) at MeJA 100 µM, which was consistent with the expression patterns of the three investigated genes. All species treated showed high total phenolic and flavonoid content compared to control plants for which the highest amounts were observed in T. vulgaris treated with 100 µM and 10 µM MeJA. Furthermore, in the 100 µM MeJA treatment, the relative expression of TPS2 and CYP71D178 in T. migricus increased 7.47 and 9.86-fold compared with the control, respectively. The highest level of CYP71D180 transcripts (5.15-fold) was also observed for T. daenensis treated. This finding highlights the notion that thymol was known as the dominant component of the essential oil rather than carvacrol in diffident thyme species. This implies that MeJA at different concentrations influenced metabolic pathways and induced expression changes, resulting in a rise in essential oil levels.

Evaluation and validation of housekeeping genes in two contrast species of thyme plant to drought stress using real-time PCR

To decrease errors and increase accuracy and reliability of quantitative real-time PCR (qRT-PCR) results, the use of a reference gene is inevitable. Despite the industrial importance of genus Thymus, not any validated reference gene has not been reported for T. kotschyanus and T. vulgaris which could limit such investigations. In this study, the expression stability of seven housekeeping genes including Actin, Cyclophilin-18, elongation factor-1A, glyceraldehyde-3-phosphate dehydrogenase, 18S ribosomal RNA, Cullin, and Polypyrimidine tract-binding protein were evaluated in T. kotschyanus and T. vulgaris which grown at four levels of drought stress using geNorm, NormFinder, and BestKeeper algorithms. Histone deacetylase-6 (HDA-6) gene was also used for validation of evaluated reference genes. In T. vulgaris, all of the algorithms similarly ranked elongation factor-1A and glyceraldehyde-3-phosphate dehydrogenase as the two most stably expressed genes. In T. kotschyanus, only NormFinder and BestKeeper had a similar ranking and identified Actin and glyceraldehyde-3-phosphate dehydrogenase as the two most stably expressed genes, but geNorm algorithm ranked elongation factor-1A and glyceraldehyde-3-phosphate dehydrogenase as the best two reference genes. On the other hand, all algorithms ranked 18S rRNA and Cyclophilin-18 as the least stable genes in T. kotschyanus and T. vulgaris, respectively. Validation results indicated that there was a significant change (0.53-3.19 fold change) in relative expression of HDA-6 normalized by the best stable gene compare to the least ranked gene. Our study presented the first systematic validation of reference gene(s) selection in T. kotschyanus and T. vulgaris and provided useful information to obtain more accurate qRT-PCR results in these species.

The expression of monoterpene synthase genes and their respective end products are affected by gibberellic acid in Thymus vulgaris

Thymus vulgaris L. (Lamiaceae), a well-known aromatic medicinal herb, has many important essential constituents in its oil, including γ-terpinene, carvacrol, thymol, and p-cymene. Gibberellins comprise hundreds of components, which regulate several various growths and underlying developmental processes, such as cell division and elongation, shoot elongation, seed germination, and gene expression. In this study, we investigated the influence of sprayed gibberellic acid (GA₃) treatments on the internode length, leaf morphology, length of new shoot, expression of monoterpene synthase genes and monoterpenes content during two plant growth stages. Our results showed that increasing of internode length was a clear effect of GA₃ that was varied with internode position. The results also showed that all internodes displayed a dramatic increase in the highest concentration of GA₃. Also, the foliar application of GA₃ resulted in not only an increased expression level of monoterpene synthase genes, but also the improved production of a monoterpene, especially in the moderate concentration of GA₃ that they were up-regulated. In the lowest GA₃ concentrations, relative expression levels were similar or lower than the control plants and a notable downregulation in those genes was observed in the application of the highest concentration of GA₃ rather than the moderate concentrations. Overall, the expression of two out of five monoterpene synthase genes, TPS and CYP71D181, showed a correlation with the level of γ-terpinene and carvacrol, respectively, indicating that they are regulated at the transcriptional levels.

Molecular cloning and functional characterization of a monoterpene synthase isolated from the aromatic wild shrub Thymus albicans

The essential oil of Thymus albicans Hoffmanns. & Link, a native shrub from the Iberian Peninsula, is mainly composed of monoterpenes. In this study, a 1,8-cineole synthase was isolated from the 1,8-cineole chemotype. A partial sequence that lacked the complete plastid transit peptide but contained an extended C-terminal when compared to other related terpene synthases was generated by PCR and Rapid Amplification of cDNA Ends (RACE). The predicted mature polypeptide was 593 amino acids in length and shared 78% and 77% sequence similarity with the homologue 1,8-cineole synthase from Rosmarinus officinalis and Salvia officinalis, respectively. The putative protein possessed the characteristic conserved motifs of plant monoterpene synthases including the RRx₈W and DDxxD motifs and phylogenetic analysis indicated that the amplified 1,8-cineole synthase bears greater sequence similarity with other 1,8-cineole synthases from Lamiaceae family relative to the terpene synthases from the genus Thymus. Functional expression of the recombinant protein in Escherichia coli revealed that in the presence of geranyl diphosphate (GPP) 1,8-cineole was the major product but that its production was too low for robust quantification. Other minor conversion products included α-pinene, β-pinene, sabinene and β-myrcene suggesting the isolated 1,8-cineole synthase may be a multi-product enzyme. To our knowledge, this is the first report of a functionally characterized monoterpene synthase from Thymus albicans.

Extraction of thymol from different varieties of thyme plants using green solvents

BACKGROUND

Thymol (2-isopropyl-5-methylphenol) is the main monoterpene phenol found in thyme essential oil. This compound has revealed several biological properties, including antibacterial, anti-inflammatory and antioxidant activities. In this work, a comparison was made between the performance of different green solvents (ethanol, limonene and ethyl lactate), by pressurized liquid extraction (PLE) and supercritical fluid extraction (SFE) at different conditions, to extract thymol from three different varieties of thyme (Thymus vulgaris, Thymus zygis and Thymus citriodorus). Additionally, new solubility data of thymol in limonene and ethanol at ambient pressure and temperatures in the range 30-43 °C are reported.

RESULTS

The highest thymol recoveries were attained with T. vulgaris (7-11 mg g(-1)). No thymol could be quantified in the PLE samples of T. citriodorus. The highest concentrations of thymol in the extracts were obtained with limonene. Thymol is very soluble in both solvents, particularly in ethanol (∼900 mg g(-1) at ∼40 °C), and is the main compound (in terms of peak area) present in the essential oil extracts obtained.

CONCLUSION

The three solvents show good capacity to extract thymol from T. vulgaris and T. zygis by PLE. Although PLE proved to be a suitable technology to extract thymol from thyme plants, the highest concentrations of thymol were obtained by SFE with supercritical CO2 .

Identification and characterization of a second isogene encoding γ-terpinene synthase in Thymus caespititius

Thymus caespititius Brot. is an Iberian endemic species, whose essential oils possess high polymorphism. They consist mostly of mono- and sesquiterpene, some of them with interest for the pharmaceutical and food industries. The search for terpene synthase genes was performed in three in vitro T. caespititius genotypes. For these plants, the expression of a previously described γ-terpinene synthase gene, Tctps2, was confirmed, occurring concomitantly with a new gene encoding an enzyme with similar activity, named Thymus caespititius terpene synthase 4 (Tctps4). The two isogenes were isolated and functionally characterized in the three plant genotypes. Alignment of the two Tctps revealed a transit peptide much shorter in Tctps4 than in Tctps2 (3-4 amino acids instead of 47). The Tctps4 open reading frame is shorter than Tctps2 (1665 bp versus 1794 bp). The amino acid sequence of both γ-terpinene synthases shared an 88% pairwise identity. The fact that T. caespititius carries two isogenes for γ-terpinene synthases, suggests gene duplication along the evolutionary process, followed by mutations leading to the differentiation of both genes. These mutations didn't compromise protein activity. A high accumulation of transcripts from both genes was found in shoots of in vitro plantlets, while in roots they could not be detected. Still, γ-terpinene levels in aerial parts were reduced, probably due to fast conversion into carvacrol and thymol, the main components from T. caespititius essential oils. This study is a contribution to the identification of terpene synthase genes in Lamiaceae.

RAPD and phytochemical analysis of Thymus moroderi plantlets after cryopreservation

Cryopreservation is at present the most reliable strategy to preserve plant germplasm. When aromatic plants are the object of conservation it is necessary to assess not only the genetic but also the phytochemical stability to ensure that plant material maintains its qualities after storage. In this work we present molecular and phytochemical stability data related to a previously described vitrification-based cryopreservation protocol for Thymus moroderi Pau ex Martínez. RAPD markers have been used to assess the genetic stability of T. moroderi explants and revealed 0.34 percent of variation in the cryopreserved material studied. Phytochemical data collected from GC-MS analysis of dichloromethane extracts from cryopreserved plantlets rendered a profile in which 1,8-cineole (14.5 percent), camphor (5.9 percent) and borneol (5.2 percent) were the major components. Both data confirmed the suitability of the cryopreservation protocol applied.

Evolution of a genetic polymorphism with climate change in a Mediterranean landscape

Many species show changes in distribution and phenotypic trait variation in response to climatic warming. Evidence of genetically based trait responses to climate change is, however, less common. Here, we detected evolutionary variation in the landscape-scale distribution of a genetically based chemical polymorphism in Mediterranean wild thyme (Thymus vulgaris) in association with modified extreme winter freezing events. By comparing current data on morph distribution with that observed in the early 1970s, we detected a significant increase in the proportion of morphs that are sensitive to winter freezing. This increase in frequency was observed in 17 of the 24 populations in which, since the 1970s, annual extreme winter freezing temperatures have risen above the thresholds that cause mortality of freezing-sensitive morphs. Our results provide an original example of rapid ongoing evolutionary change associated with relaxed selection (less extreme freezing events) on a local landscape scale. In species whose distribution and genetic variability are shaped by strong selection gradients, there may be little time lag associated with their ecological and evolutionary response to long-term environmental change.

Essential oil composition and preliminary molecular study of four Hungarian Thymus species

Chemical and genetic differences of twenty taxa belonging to four Thymus species were studied in order to determine whether molecular characters and essential oil components could be used as taxonomic markers and to examine the correlation between them. Plant samples, representing different taxa and geographic regions, were collected from experimentally grown populations. Essential oil samples were analysed by GC/MS and cluster analysis of volatile composition resulted in segregation of thymol chemotypes from sesquiterpenic ones. Thymol was characteristic for all the populations of Thymus glabrescens and T. pannonicus as well as for certain taxa belonging to T. praecox and T. pulegioides. Sesquiterpenes occurred in only two taxa of T. glabrescens, in each sample of T. praecox and in three taxa of T. pulegioides. Plant samples were analysed by random amplified polymorphic DNA (RAPD). The obtained dendrogram revealed high gene diversity. The 13 primers resulted 114 polymorphic RAPD bands, and the average percentage of polymorphism was 80.8%. The RAPD dendogram showed separation neither at interspecific nor at interpopulational levels. Therefore, further specific molecular studies involving more taxa are suggested. Partial correlation have been found between molecular and chemical assessments.

Additive antimicrobial [corrected] effects of the active components of the essential oil of Thymus vulgaris--chemotype carvacrol

Herbal remedies are multicomponent mixtures by their nature as well as by pharmaceutical definition. Being a multicomponent mixture is not only a crucial property of herbal remedies, it also represents a precondition for interactions such as synergism or antagonism. Until now, only a few phytomedicines are accurately described concerning the interactions of their active components. The aim of this study was to search for interactions within such a naturally given multi-component mixture and to discuss the pharmaceutical and clinical impacts. The thyme oil chosen for the examination belongs to the essential oils with the most pronounced antimicrobial activity. Antibiotic activity of thyme oil and single active components were tested against six different strains of microorganisms. The checkerboard assay was used to search for interactions. The time-kill assay was used to verify the observed effects and to get information about the temporal resolution of the antimicrobial activity. The degree of the detected interactions corresponded with the demarcating FICI measure of 0.5, which separates the additive from the over-additive (synergistic) effects. Therefore, the observed effect was called a "borderline case of synergism" or, respectively, "partial synergism". Partial synergism was observed only in the presence of Klebsiella pneumoniae. Additive antimicrobial activity was observed for the combination of the two monosubstances carvacrol plus linalool and thymol plus linalool as well as with the combination of the two essential oils of the carvacrol and linalool chemotypes. An increase of the carvacrol oil concentration from one to two times the MIC resulted in a considerable acceleration of the kill-rate. Thyme oil is composed of several different components that show antimicrobial activity (at least: carvacrol, thymol and linalool). The antimicrobial activity of thyme oil is partly based on additive effects, which might especially enhance the rapidity of the antimicrobial action. In addition, a mixture of several active ingredients that varies in its composition from year to year and from lot to lot as is the case with herbal remedies may be more stable concerning the antimicrobial activity than mixtures containing just a single active component.

[Patch diversity and spatial structure of wild Thymus quinquecostatus]

With the combination of ISSR (inter-simple sequence repeats), SRAP (sequence-related amplified polymorphism) and spatial autocorrelation, the genetic diversity and spatial structure per unit patch of three Huaiyuan populations of Thymus quinquecostatus in southeast China were analyzed. The results showed that there existed higher levels of genetic and clonal diversity among the patches within the wild T. quinquecostatus populations, with the percentage of polymorphic loc being 75.75%, Nei's gene diversity being 0.2537, Shannon's information index being 0.3811, percent of genetype (G/N) being 0.61, Simpson index (D) being 0.96, and Fager index (E) being 0.91. Analysis of molecular variance (AMOVA) showed that only 9.65% of genetic variation resided among the populations, while 90.35% of it resided among the individuals within the populations. No genotype patches in common were observed among the three populations. The spatial distribution of the same patches showed a concentrated distribution about 0-25 m, and that of different patches showed an inlaid distribution. Except for some locations that showed par correlations in the Huaiyuan populations of T. quinquecostatus, most locations lacked in spatial structure according to spatial autocorrelation analysis. The possible mechanism causing the establishment of the patches of T. quinquecostatus populations was due to seed dispersing, and the following clonal reproduction played important roles in patch development and population expanding.

Allelic configuration and polysomic inheritance of highly variable microsatellites in tetraploid gynodioecious Thymus praecox agg

Polyploidy plays a pivotal role in plant evolution. However, polyploids with polysomic inheritance have hitherto been severely underrepresented in plant population genetic studies, mainly due to a lack of appropriate molecular genetic markers. Here we report the establishment and experimental validation of six fully informative microsatellite markers in tetraploid gynodioecious Thymus praecox agg. Sequence data of 150 microsatellite alleles and their flanking regions revealed high variation, which may be characteristic for polyploids with a reticulate evolutionary history. Understanding the patterns of mutation (indels and substitutions) in microsatellite flanking-sequences was a prerequisite for the development of co-dominant markers for fragment analyses. Allelic segregation patterns among progeny arrays from ten test crosses revealed tetrasomic inheritance in T. praecox agg. No evidence of frequent double reduction was detected. Polymerase chain reaction (PCR) based dosage effects allowed for precise assignment of allelic configuration at all six microsatellite loci. The quantification of allele copy numbers in PCR was verified by comparisons of observed and expected gametic allele frequencies and heterozygosities in test crosses. Our study illustrates how PCR based markers can provide reliable estimates of heterozygosity and, thus, powerful tools for breeding system and population genetic analyses in polyploid organisms.

A Chemical Polymorphism in a Multitrophic Setting: Thyme Monoterpene Composition and Food Web Structure

We investigated the effects of chemical variation in thyme (Thymus vulgaris L.) on its interactions with competitors, herbivores, and herbivore predators. Four different thyme monoterpene phenotypes (chemotypes) were grown in a 4x2x2 factorial of chemotype, caging (sham half-cages vs. full cages), and competition (control vs. the grass Bromus madritensis L.). Cages reduced numbers of arthropod predators. Thyme-feeding aphids Aphis serpylli Koch passed through full cage walls to increase more than fourfold. As a result, freed from their predators, aphids had a large negative effect on thyme size and flowering. Similarly, competition from Bromus had a negative effect on thyme size and flowering. Individual effects of aphids and competition were nonadditive, however, and their combined effect was significantly less than that predicted by a multiplicative null model. Differential thyme sizes among chemotypes were not mediated by herbivores or competitors, but differential flowering was due to the effects of chemotype on aphids. We thus document differential selection by aphids among thyme chemotypes and the influence of Bromus on the strength of these negative effects of aphids.

In vitro inhibitory activities of essential oils from two KoreanThymus species against antibiotic-resistant pathogens

The in vitro inhibitory activities of essential oils from Thymus magnus and T. quinquecostatus as well as their main constituents were evaluated against susceptible and resistant species of Streptococcus pneumoniae, Staphylococcus aureus, Salmonella enteritidis, and Salmonella typhimurium. Notably, the essential oil fraction of T. magnus and its main components displayed significant inhibitory action against both antibiotic-susceptible and resistant strains of S. pneumoniae, S. aureus, and S. typhimurium with minimum inhibitory concentrations (MICs) ranging from 0.125 to 8 mg/mL. The differential MIC values imply that the oil fraction and its main components exhibit distinct patterns of activity against the tested bacterial species. Moreover, the disk diffusion test revealed that the inhibitory activities of oil fraction and components were dose-dependent. Data from the checkerboard titer test confirmed synergism between the antibiotic, norfloxacin, and T. magnus oil or thymol, particularly against the resistant strains of S. aureus.

Qualitative and quantitative variation in monoterpene co-occurrence and composition in the essential oil of Thymus vulgaris chemotypes

Thymus vulgaris has a chemical polymorphism with six different chemotypes that show marked spatial segregation in nature. Although some populations have a single chemotype in majority, many have two or three chemotypes. In this study we analyze the quantitative variation among T. vulgaris populations in the percentage of oil composed of the dominant monoterpene(s) for each chemotype. In general, phenolic chemotypes (thymol and carvacrol), which occur at the end of the biosynthetic chain, have a significantly lower proportion of their oil composed of their dominant monoterpene than nonphenolic chemotypes (geraniol, alpha-terpineol, and linalool). This is due to the presence of high amounts of precursors (gamma-terpinene and paracymene) in the oil of phenolic chemotypes. The essential oil of the nonphenolic thuyanol chemotype has four characteristic monoterpenes that together make up a lower proportion of the oil than the single dominant monoterpene of the other nonphenolic chemotypes. For all chemotypes, the percentage composition of the dominant monoterpene decreased significantly at sites where the chemotype is not the majority type. This decrease is correlated with a significant increase in either the proportion of the two precursors for the thymol chemotype or the monoterpenes characteristic of the other chemotypes at the site. The latter result suggests that a plant with dominant genes is responsible for the production of different monoterpenes can produce several molecules.

Comparison of planar chromatographic methods (TLC, OPLC, AMD) applied to essential oils of wild thyme and seven chemotypes of thyme

Essential oils analysis is more often realized by gas chromatography. However, thin-layer chromatography (TLC) remains the reference for Pharmacopoeia. Nevertheless classical TLC has its own limitations but it is always a good technique because it is simple, rapid and less expensive. Actually the reproducibility, the separation quality and the possibility to obtain good and reproducible quantitative determinations have been improved significantly with automated sample applicator, scanner densitometers and two new chromatographic planar methods: the optimum performance laminar chromatography (OPLC) and automated multiple development (AMD). In this work, we show and compare the performance of these methods and TLC through a study of seven thyme chemotypes and wild thyme essential oil.