Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues

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 terpene synthase supergene locus determines chemotype in Melaleuca alternifolia (tea tree)

Leaf oil terpenes vary categorically in many plant populations, leading to discrete phenotypes of adaptive and economic significance, but for most species, a genetic explanation for the concerted fluctuation in terpene chemistry remains unresolved. To uncover the genetic architecture underlying multi-component terpene chemotypes in Melaleuca alternifolia (tea tree), a genome-wide association study was undertaken for 148 individuals representing all six recognised chemotypes. A number of single nucleotide polymorphisms in a genomic region of c. 400 kb explained large proportions of the variation in key monoterpenes of tea tree oil. The region contained a cluster of 10 monoterpene synthase genes, including four genes predicted to encode synthases for 1,8-cineole, terpinolene, and the terpinen-4-ol precursor, sabinene hydrate. Chemotype-dependent null alleles at some sites suggested structural variants within this gene cluster, providing a possible basis for linkage disequilibrium in this region. Genotyping in a separate domesticated population revealed that all alleles surrounding this gene cluster were fixed after artificial selection for a single chemotype. These observations indicate that a supergene accounts for chemotypes in M. alternifolia. A genetic model with three haplotypes, encompassing the four characterised monoterpene synthase genes, explained the six terpene chemotypes, and was consistent with available biparental cross-segregation data.

System network analysis of Rosmarinus officinalis transcriptome and metabolome-Key genes in biosynthesis of secondary metabolites

Medicinal plants contain valuable compounds that have attracted worldwide interest for their use in the production of natural drugs. The presence of compounds such as rosmarinic acid, carnosic acid, and carnosol in Rosmarinus officinalis has made it a plant with unique therapeutic effects. The identification and regulation of the biosynthetic pathways and genes will enable the large-scale production of these compounds. Hence, we studied the correlation between the genes involved in biosynthesis of the secondary metabolites in R. officinalis using proteomics and metabolomics data by WGCNA. We identified three modules as having the highest potential for the metabolite engineering. Moreover, the hub genes highly connected to particular modules, TFs, PKs, and transporters were identified. The TFs of MYB, C3H, HB, and C2H2 were the most likely candidates associated with the target metabolic pathways. The results indicated that the hub genes including Copalyl diphosphate synthase (CDS), Phenylalanine ammonia lyase (PAL), Cineole synthase (CIN), Rosmarinic acid synthase (RAS), Tyrosine aminotransferase (TAT), Cinnamate 4-hydroxylase (C4H), and MYB58 are responsible for biosynthesis of important secondary metabolites. Thus, we confirmed these results using qRT-PCR after treating R. officinalis seedlings with methyl jasmonate. These candidate genes may be employed for genetic and metabolic engineering research to increase R. officinalis metabolite production.

Draft genome of the medicinal tea tree Melaleuca alternifolia

BACKGROUND

Melaleuca alternifolia is a commercially important medicinal tea tree native to Australia. Tea tree oil, the essential oil distilled from its branches and leaves, has broad-spectrum germicidal activity and is highly valued in the pharmaceutical and cosmetic industries. Thus, the study of genome, which can provide reference for the investigation of genes involved in terpinen-4-ol biosynthesis, is quite crucial for improving the productivity of Tea tree oil.

METHODS AND RESULTS

In our study, the next-generation sequencing was used to investigate the whole genome of Melaleuca alternifolia. About 114 Gb high quality sequence data were obtained and assembled into 1,838,159 scafolds with an N50 length of 1021 bp. The assembled genome size is about 595 Mb, twice of that predicted by flow cytometer (300 Mb) and k-mer analysis (345 Mb). Benchmarking Universal Single-Copy Orthologs analyses indicated that only 11.3% of the conserved single-copy genes were miss. Repetitive regions cover over 40.43% of the genome. A total of 44,369 protein-coding genes were predicted and annotated against Nr, Swissprot, Refseq, COG, KOG, and KEGG database. Among these genes, 32,909 and 16,241 genes were functionally annotated in Nr and KEGG, respectively. Moreover, 29,411 and 14,435 genes were functionally annotated in COG and KOG. Additionally, 457,661 simple sequence repeats and 1109 transcription factors (TFs) form 67 TF families were identified in the assembled genome.

CONCLUSION

Our findings provide a draft genome sequencing of M. alternifolia which can act as a reference for the deep sequencing strategies, and are useful for future functional and comparative genomics analyses.

Essential Oils of Aromatic Plant Species from the Atlantic Rainforest Exhibit Extensive Chemical Diversity and Antimicrobial Activity

Microbial resistance, caused by the overuse or inadequate application of antibiotics, is a worldwide crisis, increasing the risk of treatment failure and healthcare costs. Plant essential oils (EOs) consist of hydrophobic metabolites with antimicrobial activity. The antimicrobial potential of the chemical diversity of plants from the Atlantic Rainforest remains scarcely characterized. In the current work, we determined the metabolite profile of the EOs from aromatic plants from nine locations and accessed their antimicrobial and biocidal activity by agar diffusion assays, minimum inhibitory concentration, time-kill and cell-component leakage assays. The pharmacokinetic properties of the EO compounds were investigated by in silico tools. More than a hundred metabolites were identified, mainly consisting of sesqui and monoterpenes. Individual plants and botanical families exhibited extensive chemical variations in their EO composition. Probabilistic models demonstrated that qualitative and quantitative differences contribute to chemical diversity, depending on the botanical family. The EOs exhibited antimicrobial biocidal activity against pathogenic bacteria, fungi and multiple predicted pharmacological targets. Our results demonstrate the antimicrobial potential of EOs from rainforest plants, indicate novel macromolecular targets, and contribute to highlighting the chemical diversity of native species.

Implications of the foliar phytochemical diversity of the avocado crop Persea americana cv. Hass in its susceptibility to pests and pathogens

Phytochemical diversity (PD) can be considered as a defensive trait; it can operate through single plant secondary metabolites or usually as complex mixtures of them. We tested the more diversity-better defense hypothesis correlating the leaf plant secondary metabolites (PSMs) with the incidence of plant enemies on Hass avocado trees. We expected a negative correlation between the occurrence of plant enemies and PD metrics. Also, as intraspecific PSMs polymorphisms in plant populations are common, we studied the incidence of plant enemies on Hass avocado trees representing chemical variants (chemotypes). We expected a differential incidence of plant enemies among trees grouped by their mono and sesquiterpene + phenylpropanoid chemotypes. We analyzed foliar hexane extracts from 236 trees in 17 orchards by gas chromatography and for the incidence of red mite, thrips, whitefly, avocado branch borer, fruit rot, scab, and peduncle collar blight. The predicted negative correlation between the plant enemies’ incidence and the phytochemical metrics did not occur. To determine the relationship between enemy incidence and chemotypes we grouped the trees by cluster analysis using a matrix of PSMs in each tree. Most trees were grouped under four out of 23 chemotypes. Branch borers attacked trees of low-frequency chemotypes more frequently than trees with common chemotypes. The incidence of five plant enemies was different among the predominant chemotypes. The hypothesis of more diversity-better defense was not supported by the correlations between the phytochemical diversity and the incidence of pests and pathogens in Hass avocado orchards. Based on our results, we hypothesize that phytochemical diversity function as a defensive trait relies more on differentiation among individuals in a population than on the sole increase of chemical diversity. Also, the differential incidence of pests and pathogens on trees classified by their foliar chemotypes implies that these susceptibility or resistance markers represent potential useful tools for Hass avocado orchard pest management.

Bioactive (Poly)phenols, Volatile Compounds from Vegetables, Medicinal and Aromatic Plants

Polyphenols, as well as volatile compounds responsible for aromatic features, play a critical role in the quality of vegetables and medicinal, and aromatic plants (MAPs). The research conducted in recent years has shown that these plants contain biologically active compounds, mainly polyphenols, that relate to the prevention of inflammatory processes, neurodegenerative diseases, cancers, and cardiovascular disorders as well as to antimicrobial, antioxidant, and antiparasitic properties. Throughout the years, many researchers have deeply studied polyphenols and volatile compounds in medicinal and aromatic plants, particularly those associated with consumer's choices or with their beneficial properties. In this context, the purpose of this review is to provide an overview of the presence of volatile and nonvolatile compounds in some of the most economically relevant and consumed vegetables and medicinal and aromatic plants, with an emphasis on bioactive polyphenols, polyphenols as prebiotics, and, also, the most important factors that affect the contents and profiles of the volatile and nonvolatile compounds responsible for the aromatic features of vegetables and MAPs. Additionally, the new challenges for science in terms of improving polyphenol composition and intensifying volatile compounds responsible for the positive characteristics of vegetables and medicinal and aromatic plants are reported.

Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes

Background

Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol.

Results

Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Finally, quantitative real-time PCR was conducted to detect the actual expression level of those candidate genes related to the D-borneol biosynthesis pathway, and the result showed that the expression patterns of the candidate genes related to D-borneol biosynthesis were basically consistent with those revealed by transcriptome analysis.

Conclusions

We used transcriptome sequencing to analyze three different chemotypes of C. burmannii, identifying three candidate structural genes (one DXS, two monoterpene synthases) and seven potential transcription factor candidates (one WRKY, two BHLH, one AP2/ERF and three MYB) involved in D-borneol biosynthesis. These results provide new insight into our understanding of the production and accumulation of D-borneol in C. burmannii.

Transcriptome Landscape Variation in the Genus Thymus

Among the Lamiaceae family, the genus Thymus is an economically important genera due to its medicinal and aromatic properties. Most Thymus molecular research has focused on the determining the phylogenetic relationships between different species, but no published work has focused on the evolution of the transcriptome across the genus to elucidate genes involved in terpenoid biosynthesis. Hence, in this study, the transcriptomes of five different Thymus species were generated and analyzed to mine putative genes involved in thymol and carvacrol biosynthesis. High-throughput sequencing produced ~43 million high-quality reads per sample, which were assembled de novo using several tools, then further subjected to a quality evaluation. The best assembly for each species was used as queries to search within the UniProt, KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (Clusters of Orthologous Groups) and TF (Transcription Factors) databases. Mining the transcriptomes resulted in the identification of 592 single-copy orthogroups used for phylogenetic analysis. The data showed strongly support a close genetic relationship between Thymus vulgaris and Thymus daenensis. Additionally, this study dates the speciation events between 1.5–2.1 and 9–10.2 MYA according to different methodologies. Our study provides a global overview of genes related to the terpenoid pathway in Thymus, and can help establish an understanding of the relationship that exists among Thymus species.

Metabotype variation in a field population of tansy plants influences aphid host selection

It is well known that plant volatiles influence herbivores in their selection of a host plant; however, less is known about how the nonvolatile metabolome affects herbivore host selection. Metabolic diversity between intraspecific plants can be characterized using non-targeted mass spectrometry that gives us a snapshot overview of all metabolic processes occurring within a plant at a particular time. Here, we show that non-targeted metabolomics can be used to reveal links between intraspecific chemical diversity and ecological processes in tansy (Tanacetum vulgare). First, we show that tansy plants can be categorized into five subgroups based up on their metabolic profiles, and that these "metabotypes" influenced natural aphid colonization in the field. Second, this grouping was not due to induced metabolomic changes within the plant due to aphid feeding but rather resulted from constitutive differences in chemical diversity between plants. These findings highlight the importance of intraspecific chemical diversity within one plant population and provide the first report of a non-targeted metabolomic field study in chemical ecology.

Transcriptome Analysis of Oleoresin-Producing Tree Sindora Glabra and Characterization of Sesquiterpene Synthases

Terpenes serve important physiological and ecological functions in plants. Sindora glabra trees accumulate copious amounts of sesquiterpene-rich oleoresin in the stem. A transcriptome approach was used to determine the unique terpene biosynthesis pathway and to explore the different regulatory mechanisms responsible for the variation of terpene content among individuals. Analysis of de novo-assembled contigs revealed a complete set of genes for terpene biosynthesis. A total of 23,261 differentially expressed unigenes (DEGs) were discovered between high and low oil-yielding plants. DEG enrichment analysis suggested that the terpene biosynthesis process and the plant hormone signal transduction pathway may exert a major role in determining terpene variation in S. glabra. The expression patterns of candidate genes were further verified by quantitative RT-PCR experiments. Key genes involved in the terpene biosynthesis pathway were predominantly expressed in phloem and root tissues. Phylogenetic analysis and subcellular localization implied that S. glabra terpene synthases may evolve from a common ancestor. Furthermore, two sesquiterpene synthase genes, SgSTPS1 and SgSTPS2, were functionally characterized. SgSTPS1 mainly generated β-caryophyllene from farnesyl pyrophosphate. SgSTPS2 is a versatile enzyme that catalyzes the formation of 12 sequiterpenes from farnesyl pyrophosphate and synthesis of three monoterpenes using geranyl pyrophosphate. Together, these results provide large reservoir for elucidating the molecular mechanism of terpene biosynthesis and for exploring the ecological function of sesquiterpenes in S. glabra.

In depth investigation of the metabolism of Nectandra megapotamica chemotypes

Plants produce a wide range of secondary metabolites. Within a single species, chemotypes can be distinguished by the differences in the composition of the secondary metabolites. Herein, we evaluated Nectandra megapotamica (Spreng.) chemotypes and the balance of different classes of metabolites to verify how significant differences in plant metabolism are regarding chemotypes. We collected N. megapotamica leaves from eight adult plants in two Brazilian states. The essential oils and ethanol/water extracts were analyzed by GC-MS and LC-DAD-MS, respectively. Histochemical tests were performed, as well as chemical analyses of leaves from adaxial and abaxial foliar surfaces of N. megapotamica, and the stereochemistry of α-bisabolol was determined. Two different chemotypes, based on volatile compounds, were identified, distinguished by the presence of isospathulenol, α-bisabolol, β-bisabolene, and (E)-nerolidol for chemotype A, and bicyclogermacrene and elemicin for chemotype B. A stereochemical analysis of chemotype A extract revealed (+)-α-bisabolol enantiomer. Histochemical tests of chemotypes showed similar results and suggested the presence of essential oil in idioblasts stained with the dye NADI. The analyses of chemotype A leaves by GC-MS revealed similar compositions for abaxial and adaxial surfaces, such pattern was also observed for chemotype B. Medium and high polarity metabolites showed high chemical similarities between the chemotypes, highlighting the presence of proanthocyanidins and glycosylated flavonoids (O- and C-glycosides). Thus, N. megapotamica produced distinct volatile chemotypes with highly conserved medium to high polarity compounds. Such results suggest that phenolic derivatives have a basal physiological function, while genetic or environmental differences lead to differentiation in volatile profiles of N. megapotamica.

Foliar Terpene Chemotypes and Herbivory Determine Variation in Plant Volatile Emissions

Plants that synthesize and store terpenes in specialized cells accumulate large concentrations of these compounds while avoiding autotoxicity. Stored terpenes may influence the quantity and profile of volatile compounds that are emitted into the environment and the subsequent role of those volatiles in mediating the activity of herbivores. The Australian medicinal tea tree, Melaleuca alternifolia, occurs as several distinct terpene chemotypes. We studied the profile of its terpene emissions to understand how variations in stored foliar terpenes influenced emissions, both constitutive and when damaged either by herbivores or mechanically. We found that foliar chemistry influenced differences in the composition of terpene emissions, but those emissions were minimal in intact plants. When plants were damaged by herbivores or mechanically, the emissions were greatly increased and the composition corresponded to the constitutive terpenes and the volatility of each compound, suggesting the main origin of emissions is the stored terpenes and not de novo biosynthesized volatiles. However, herbivores modified the composition of the volatile emissions in only one chemotype, probably due to the oxidative metabolism of 1,8-cineole by the beetles. We also tested whether the foliar terpene blend acted as an attractant for the specialized leaf beetles Paropsisterna tigrina and Faex sp. and a parasitoid fly, Anagonia zentae. None of these species responded to extracts of young leaves in an olfactometer, so we found no evidence that these species use plant odor cues for host location in laboratory conditions.