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

Exploring Chemical Variability in the Essential Oils of the Thymus Genus

Thyme remains an indispensable herb today, finding its place in gastronomy, medicine, cosmetics, and gardens worldwide. It is highly valued in herbal remedies and pharmaceutical formulations for its antibacterial, antifungal, and antioxidant properties derived from the richness of its essential oil, which comprises various volatile components. However, climate change poses a significant challenge today, potentially affecting the quality of thyme, particularly the extracted essential oil, along with other factors such as biotic influences and the plant's geographical distribution. Consequently, complex diversity in essential oil composition was observed, also influenced by genetic diversity within the same species, resulting in distinct chemotypes. Other factors contributing to this chemodiversity include the chosen agrotechnology and processing methods of thyme, the extraction of the essential oil, and storage conditions. In this review, we provide the latest findings on the factors contributing to the chemovariability of thyme essential oil.

Chromosome-level genome assembly provides insights into the genome evolution and functional importance of the phenylpropanoid-flavonoid pathway in Thymus mongolicus

BACKGROUND

Thymus mongolicus (family Lamiaceae) is a Thyme subshrub with strong aroma and remarkable environmental adaptability. Limited genomic information limits the use of this plant.

RESULTS

Chromosome-level 605.2 Mb genome of T. mongolicus was generated, with 96.28% anchored to 12 pseudochromosomes. The repetitive sequences were dominant, accounting for 70.98%, and 32,593 protein-coding genes were predicted. Synteny analysis revealed that Lamiaceae species generally underwent two rounds of whole genome duplication; moreover, species-specific genome duplication was identified. A recent LTR retrotransposon burst and tandem duplication might play important roles in the formation of the Thymus genome. Using comparative genomic analysis, phylogenetic tree of seven Lamiaceae species was constructed, which revealed that Thyme plants evolved recently in the family. Under the phylogenetic framework, we performed functional enrichment analysis of the genes on nodes that contained the most gene duplication events (> 50% support) and of relevant significant expanded gene families. These genes were highly associated with environmental adaptation and biosynthesis of secondary metabolites. Combined transcriptome and metabolome analyses revealed that Peroxidases, Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferases, and 4-coumarate-CoA ligases genes were the essential regulators of the phenylpropanoid-flavonoid pathway. Their catalytic products (e.g., apigenin, naringenin chalcone, and several apigenin-related compounds) might be responsible for the environmental tolerance and aromatic properties of T. mongolicus.

CONCLUSION

This study enhanced the understanding of the genomic evolution of T. mongolicus, enabling further exploration of its unique traits and applications, and contributed to the understanding of Lamiaceae genomics and evolutionary biology.

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.

A haplotype-resolved gap-free genome assembly provides novel insight into monoterpenoid diversification in Mentha suaveolens 'Variegata'

Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, a gap-free assembly with a genome size of 414.3 Mb and 31,251 coding genes was obtained for Mentha suaveolens 'Variegata'. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, with genome sizes of 401.9 and 405.7 Mb, respectively. The telomeres and centromeres of each haplotype were almost fully annotated. In addition, we detected a total of 41,135 structural variations. Enrichment analysis demonstrated that genes involved in terpenoid biosynthesis were affected by these structural variations. Analysis of volatile metabolites showed that M. suaveolens mainly produces piperitenone oxide rather than menthol. We identified three genes in the M. suaveolens genome which encode isopiperitenone reductase (ISPR), a key rate-limiting enzyme in menthol biosynthesis. However, the transcription levels of ISPR were low. Given that other terpenoid biosynthesis genes were expressed, M. suaveolens ISPRs may account for the accumulation of piperitenone oxide in this species. The findings of this study may provide a valuable resource for improving the detection rate and accuracy of genetic variants, thereby enhancing our understanding of their impact on gene function and expression. Moreover, our haplotype-resolved gap-free genome assembly offers novel insights into molecular marker-assisted breeding of Mentha.

Decoupling subgenomes within hybrid lavandin provide new insights into speciation and monoterpenoid diversification of Lavandula

Polyploidization and transposon elements contribute to shape plant genome diversity and secondary metabolic variation in some edible crops. However, the specific contribution of these variations to the chemo-diversity of Lamiaceae, particularly in economic shrubs, is still poorly documented. The rich essential oils (EOs) of Lavandula plants are distinguished by monoterpenoids among the main EO-producing species, L. angustifolia (LA), L. × intermedia (LX) and L. latifolia (LL). Herein, the first allele-aware chromosome-level genome was assembled using a lavandin cultivar 'Super' and its hybrid origin was verified by two complete subgenomes (LX-LA and LX-LL). Genome-wide phylogenetics confirmed that LL, like LA, underwent two lineage-specific WGDs after the γ triplication event, and their speciation occurred after the last WGD. Chloroplast phylogenetic analysis indicated LA was the maternal source of 'Super', which produced premium EO (higher linalyl/lavandulyl acetate and lower 1,8-cineole and camphor) close to LA. Gene expression, especially the monoterpenoid biosynthetic genes, showed bias to LX-LA alleles. Asymmetric transposon insertions in two decoupling 'Super' subgenomes were responsible for speciation and monoterpenoid divergence of the progenitors. Both hybrid and parental evolutionary analysis revealed that LTR (long terminal repeat) retrotransposon associated with AAT gene loss cause no linalyl/lavandulyl acetate production in LL, and multi-BDH copies retained by tandem duplication and DNA transposon resulted in higher camphor accumulation of LL. Advances in allelic variations of monoterpenoids have the potential to revolutionize future lavandin breeding and EO production.

Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles

Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.

A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria

Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.

Cannabis sativa: origin and history, glandular trichome development, and cannabinoid biosynthesis

Is Cannabis a boon or bane? Cannabis sativa has long been a versatile crop for fiber extraction (industrial hemp), traditional Chinese medicine (hemp seeds), and recreational drugs (marijuana). Cannabis faced global prohibition in the twentieth century because of the psychoactive properties of ∆9-tetrahydrocannabinol; however, recently, the perspective has changed with the recognition of additional therapeutic values, particularly the pharmacological potential of cannabidiol. A comprehensive understanding of the underlying mechanism of cannabinoid biosynthesis is necessary to cultivate and promote globally the medicinal application of Cannabis resources. Here, we comprehensively review the historical usage of Cannabis, biosynthesis of trichome-specific cannabinoids, regulatory network of trichome development, and synthetic biology of cannabinoids. This review provides valuable insights into the efficient biosynthesis and green production of cannabinoids, and the development and utilization of novel Cannabis varieties.

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.

Formation mechanism of glandular trichomes involved in the synthesis and storage of terpenoids in lavender

BACKGROUND

Lavender (genus Lavandula, family Lamiaceae) is an aromatic plant widely grown as an ornamental plant. The chemical composition of lavender is characterized by monoterpenoids, sesquiterpenoids, and other compounds, which are primarily synthesized and stored in epidermal secretory structures called glandular trichomes (GTs). Volatile organic compounds (VOCs) are responsible for the aroma characteristics of plant oil that drive consumer preference. Aroma is usually regarded as a characteristic trait for the classification of aromatic plants. Interestingly, VOCs are synthesized and stored in GTs. Lamiaceae species such as purple perilla, peppermint, basil, thyme, and oregano usually possess two types of GTs: peltate glandular trichomes (PGTs) and capitate glandular trichomes (CGTs). But the development process of PGTs in lavender has been reported in only a few studies to date.

RESULTS

In this study, we identified and quantified the VOCs in four lavender cultivars by headspace-solid phase micro extraction-gas chromatography mass spectrometry (HS-SPME-GC-MS). A total of 66 VOCs were identified in these four cultivars, the most prominent of which were linalyl acetate and linalool, and flowers were the main site of accumulation of these VOCs. Here, we examined the developmental process of PGTs, including the formation of their base, body, and apex. The apex cells contained secretory cavities, which produced VOCs. Based on the reference genome sequence of the lavender cultivar 'Jingxun 2', several R2R3-MYB subfamily genes related to GT formation were identified. These results will guide the engineering of GTs and molecular breeding of lavender for improving the VOC content.

CONCLUSIONS

In this study, we identified the VOCs in four lavender cultivars. We analyzed the formation of GTs, and compared the number and diameter size of PGTs among four lavender cultivars. Additionally, we identified four candidate genes belonging to the R2R3-MYB family.

Plant terpene specialized metabolism: complex networks or simple linear pathways?

From the perspectives of pathway evolution, discovery and engineering of plant specialized metabolism, the nature of the biosynthetic routes represents a critical aspect. Classical models depict biosynthesis typically from an end-point angle and as linear, for example, connecting central and specialized metabolism. As the number of functionally elucidated routes increased, the enzymatic foundation of complex plant chemistries became increasingly well understood. The perception of linear pathway models has been severely challenged. With a focus on plant terpenoid specialized metabolism, we review here illustrative examples supporting that plants have evolved complex networks driving chemical diversification. The completion of several diterpene, sesquiterpene and monoterpene routes shows complex formation of scaffolds and their subsequent functionalization. These networks show that branch points, including multiple sub-routes, mean that metabolic grids are the rule rather than the exception. This concept presents significant implications for biotechnological production.

Carvacrol-A Natural Phenolic Compound with Antimicrobial Properties

The main purpose of this article is to present the latest research related to selected biological properties of carvacrol, such as antimicrobial, anti-inflammatory, and antioxidant activity. As a monoterpenoid phenol, carvacrol is a component of many essential oils and is usually found in plants together with its isomer, thymol. Carvacrol, either alone or in combination with other compounds, has a strong antimicrobial effect on many different strains of bacteria and fungi that are dangerous to humans or can cause significant losses in the economy. Carvacrol also exerts strong anti-inflammatory properties by preventing the peroxidation of polyunsaturated fatty acids by inducing SOD, GPx, GR, and CAT, as well as reducing the level of pro-inflammatory cytokines in the body. It also affects the body's immune response generated by LPS. Carvacrol is considered a safe compound despite the limited amount of data on its metabolism in humans. This review also discusses the biotransformations of carvacrol, because the knowledge of the possible degradation pathways of this compound may help to minimize the risk of environmental contamination with phenolic compounds.

Comprehensive Analysis of Secondary Metabolites of Four Medicinal Thyme Species Used in Folk Medicine and Their Antioxidant Activities In Vitro

Thyme is a colloquial term for number of aromatic species belonging to the genus Thymus L., known for their expressed biological activities and therefore used worldwide for seasoning and in folk medicine. In the present paper, the content of the total polyphenols (TP), total flavonoids (TF), and antioxidant capacity were assessed in the extracts of four traditionally used thyme species. Moreover, a comprehensive metabolomic study of thyme bioactive compounds was performed, and the obtained data were processed using multivariate statistical tests. The results clearly demonstrated the positive correlation between the content of the TP, TF, and antioxidant activity, and TF was more significant than TP. The findings revealed that four selected thyme species contained 528 secondary metabolites, including 289 flavonoids and 146 phenolic acids. Thymus marschallianus had a higher concentration of active ingredients, which improve its antioxidant capacity. Differentially accumulated metabolites were formed by complex pathways such as flavonoid, flavone, flavonol, isoflavonoid, and anthocyanin biosynthesis. Correlation analysis showed that 59 metabolites (including 28 flavonoids, 18 phenolic acids, and 7 terpenoid compounds) were significantly correlated with obtained values of the antioxidant capacity. The results suggested that selected thyme species exhibit a great diversity in antioxidant-related components, whereas flavonoids may be responsible for the high antioxidant capacity of all studied thyme species. The present study greatly expands our understanding of the complex phytochemical profiles and related applications of selected medicinal plants.

Population diversity analyses provide insights into key horticultural traits of Chinese native thymes

Chinese native thymes (CNTs) in the genus Thymus (family Lamiaceae) are rich in bioactive terpenes, which exert antiviral, anti-inflammatory, antioxidation, immunological, and antimicrobial effects. Plants exhibit morphological variation, including erect-type and creeping-type growth forms; however, the molecular mechanisms underlying important horticultural traits have not been determined. Here, we collected 39 CNTs providing strategic plant resources for studies of lignin, terpenoids, and glandular trichomes of thymes. Using resequencing data as well as phenotypic, metabonomic, phylogenetic, population genetic, and transcriptomic analyses, we identified and characterized key genes involved in lignin biosynthesis, terpenoid biosynthesis, and glandular trichome formation. We found many regulatory genes or transcription factors related to these three important horticultural traits, including genes encoding caffeic acid O-methyltransferase (COMT), terpene synthase (TPS), v-myb avian myeloblastosis viral oncogene homolog (MYB), and homeodomain-leucine zipper (HD-ZIP). Population diversity analyses provided insights into growth form, terpenoid, and glandular trichome evolution in CNTs. Furthermore, our results revealed that T. mongolicus accessions might be wild ancestors, and T. quinquecostatus, T. quinquecostatus var. asiaticus, and T. quinquecostatus var. przewalskii might be transitional accessions that derived from T. mongolicus accessions. Finally, T. nervulosus, T. inaequalis, T. mandschuricus, T. curtus, T. amurensis, T. proximus, T. altaicus, T. roseus, and T. marschallianus showed high divergence. We found evidence for introgression between erect-type European cultivated thymes and CNTs. These findings improve our understanding of the determinants of variation in horticultural traits and provide candidate loci for research and breeding.

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.