Integrated metabolome and transcriptome analysis of Magnolia champaca identifies biosynthetic pathways for floral volatile organic compounds

Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis

Magnolia lotungensis is an extremely endangered endemic tree in China. To elucidate the genetic basis of M. lotungensis, we performed a comprehensive transcriptome analysis using a sample integrating the plant's bark, leaves, and flowers. De novo transcriptome assembly yielded 177,046 transcripts and 42,518 coding sequences. Notably, we identified 796 species-specific genes enriched in organelle gene regulation and defense responses. A codon usage bias analysis revealed that mutation bias appears to be the primary driver of selection in shaping the species' genetic architecture. An evolutionary analysis based on dN/dS values of paralogous and orthologous gene pairs indicated a predominance of purifying selection, suggesting strong evolutionary constraints on most genes. A comparative transcriptomic analysis with Magnolia sinica identified approximately 1000 ultra-conserved genes, enriched in essential cellular processes such as transcriptional regulation, protein synthesis, and genome stability. Interestingly, only a limited number of 511 rapidly evolving genes under positive selection were detected compared to M. sinica and Magnolia kuangsiensis. These genes were enriched in metabolic processes associated with adaptation to specific environments, potentially limiting the species' ability to expand its range. Our findings contribute to understanding the genetic architecture of M. lotungensis and suggest that an insufficient number of adaptive genes contribute to its endangered status.

Physiological and Biochemical Analysis Revealing the Key Factors Influencing 2-Phenylethanol and Benzyl Alcohol Production in Crabapple Flowers

Floral scent (FS) plays a crucial role in the ecological functions and industrial applications of plants. However, the physiological and metabolic mechanisms underlying FS formation remain inadequately explored. Our investigation focused on elucidating the differential formation mechanisms of 2-phenylethanol (2-PE) and benzyl alcohol (BA) by examining seven related enzyme concentrations and the content of soluble sugar, soluble proteins, carbon (C) and nitrogen (N), as well as the C/N ratio. The findings revealed that the peak content of 2-PE in M. 'Praire Rose' and BA in M. 'Lollipop' occurred during the end flowering stage (S4) and flowering stage (S3) periods, respectively. The enzyme concentration change trends of phenylpyruvate decarboxylase (PDL), phenylacetaldehyde reductase (PAR), soluble protein, C, N, and C/N ratio changes during the S3-S4 period in M. 'Praire Rose' and M. 'Lollipop' were entirely opposite. Correlation and PCA analysis demonstrated that the content of CYP79D73 (a P450) and N, and the C/N ratio were key factors in 2-PE production in M. 'Praire Rose'. The production of BA in M. 'Lollipop' was more influenced by the content of phenylacetaldehyde synthase (PAAS), CYP79D73, and soluble sugar. As CYP79D73 exits oppositely in correlation to 2-PE (M. 'Praire Rose') and BA (M. 'Lollipop'), it is hypothesized that CYP79D73 was postulated as the primary factor contributing to the observed differences of 2-PE (M. 'Praire Rose') and BA (M. 'Lollipop') formation. These results carry significant implications for crabapple aromatic flower breeding and the essential oil industry etc.

Transcriptome and volatile compounds analyses of floral development provide insight into floral scent formation in Paeonia lactiflora 'Wu Hua Long Yu'

Herbaceous peony (Paeonia lactiflora) is a well-known ornamental plant in China, celebrated for its beautiful flowers that can emit fragrances. However, exact molecular mechanisms governing synthesis of floral volatiles within herbaceous peony remain unclear. To address this gap in knowledge, our study focused on analyzing the transcriptome and the levels of floral volatile compounds in P. lactiflora 'Wu Hua Long Yu' at different stages of flower development. Using gas chromatography-mass spectrometry (GC-MS), we obtained eighteen major volatile compounds, with monoterpenes being the dominant components among them. Our transcriptome analysis, based on pooled sequencing data, revealed the most differentially expressed genes (DEGs) existed between stages S1 and S3 of flower development. Among these DEGs, we identified 89 functional genes associated with the synthesis of volatile monoterpenes, with 28 of these genes showing a positive correlation with the release of monoterpenes. Specifically, key regulators of monoterpene synthesis in herbaceous peony appear to be 1-deoxy-D-xylulose 5-phosphate synthase (DXS), geranyl pyrophosphate synthase (GPPS), and terpene synthase (TPS). Additionally, our study identified some transcription factors (TFs) that may be involved in the biosynthesis of monoterpenes. These discoveries offer invaluable illumination into the intricate molecular underpinnings orchestrating the generation of floral fragrances in herbaceous peonies, and they offer a foundation for further research to identify and utilize candidate gene resources for this purpose.

Identification of Floral Volatile Components and Expression Analysis of Controlling Gene in Paeonia ostii 'Fengdan' under Different Cultivation Conditions

In order to explore the release rule of floral volatile substances and the diurnal variation of different flower development stages of Paeonia ostii 'Fengdan' in potted and ground-planted conditions, dynamic headspace adsorption combined with gas chromatography-mass spectrometry(GC-MS) was used to analyze the dynamic changes in floral volatile components and contents. Quantitative real-time PCR (qRT-PCR) was used to analyze changes in flower fragrance-regulating genes PsPAL, PsTPSs, and PsbHLH at different flower development stages and a daily change process at the full-blooming stage. The results show that there were differences in aroma components and contents of Paeonia ostii 'Fengdan' at different flower development stages and different time quantum of every day. There were 25 and 28 aroma components identified in 7 flower development stages of tree peonies planted in pots and in the field, respectively, and 23 and 22 aroma components identified at different time quantum of the day, of which the largest and highest content was alkanes. The main characteristic aroma substances were (E)-β-ocimene, 1,3,5-trimethoxybenzene, 2,4-di-tert-butylphenol, methyl jasmonate, nerol, and cinnamyl alcohol; released amounts of the abovementioned substances varied depending on the development stage and the time of the day. The expression of flower fragrance-controlling genes (PsPAL, PsTPSs, and PsbHLH) in tree peonies varied greatly in different conditions. The results of this study provide a valuable resource to investigate floral fragrance formation in tree peonies.

Volatile metabolome and floral transcriptome analyses reveal the volatile components of strongly fragrant progeny of Malus × robusta

Floral fragrance is an important trait that contributes to the ornamental properties and pollination of crabapple. However, research on the physiological and molecular biology of the floral volatile compounds of crabapple is rarely reported. In this study, metabolomic and transcriptomic analyses of the floral volatile compounds of standard Malus robusta flowers (Mr), and progeny with strongly and weakly fragrant flowers (SF and WF, respectively), were conducted. Fifty-six floral volatile compounds were detected in the plant materials, mainly comprising phenylpropane/benzene ring-type compounds, fatty acid derivatives, and terpene compounds. The volatile contents were significantly increased before the early flowering stage (ES), and the contents of SF flowers were twice those of WF and Mr flowers. Odor activity values were determined for known fragrant volatiles and 10-11 key fragrant volatiles were identified at the ES. The predominant fragrant volatiles were methyl benzoate, linalool, leaf acetate, and methyl anthranilate. In the petals, stamens, pistil, and calyx of SF flowers, 26 volatiles were detected at the ES, among which phenylpropane/benzene ring-type compounds were the main components accounting for more than 75% of the total volatile content. Functional analysis of transcriptome data revealed that the phenylpropanoid biosynthesis pathway was significantly enriched in SF flowers. By conducting combined analyses between volatiles and differentially expressed genes, transcripts of six floral scent-related genes were identified and were associated with the contents of the key fragrant volatiles, and other 23 genes were potentially correlated with the key volatile compounds. The results reveal possible mechanisms for the emission of strong fragrance by SF flowers, and provide a foundation for improvement of the floral fragrance and development of new crabapple cultivars.

Transcriptomic and metabolomic data reveal key genes that are involved in the phenylpropanoid pathway and regulate the floral fragrance of Rhododendron fortunei

BACKGROUND

To reveal the key genes involved in the phenylpropanoid pathway, which ultimately governs the fragrance of Rhododendron fortunei, we performed a comprehensive transcriptome and metabolomic analysis of the petals of two different varieties of two alpine rhododendrons: the scented R. fortunei and the unscented Rhododendron 'Nova Zembla'.

RESULTS

Our transcriptomic and qRT-PCR data showed that nine candidate genes were highly expressed in R. fortunei but were downregulated in Rhododendron 'Nova Zembla'. Among these genes, EGS expression was significantly positively correlated with various volatile benzene/phenylpropanoid compounds and significantly negatively correlated with the contents of various nonvolatile compounds, whereas CCoAOMT, PAL, C4H, and BALDH expression was significantly negatively correlated with the contents of various volatile benzene/phenylpropanoid compounds and significantly positively correlated with the contents of various nonvolatile compounds. CCR, CAD, 4CL, and SAMT expression was significantly negatively correlated with the contents of various benzene/phenylpropanoid compounds. The validation of RfSAMT showed that the RfSAMT gene regulates the synthesis of aromatic metabolites in R. fortunei.

CONCLUSION

The findings of this study indicated that key candidate genes and metabolites involved in the phenylpropanoid biosynthesis pathway may govern the fragrance of R. fortunei. This lays a foundation for further research on the molecular mechanism underlying fragrance in the genus Rhododendron.

Transcriptomic analysis of deceptively pollinated Arum maculatum (Araceae) reveals association between terpene synthase expression in floral trap chamber and species-specific pollinator attraction

Deceptive pollination often involves volatile organic compound emissions that mislead insects into performing nonrewarding pollination. Among deceptively pollinated plants, Arum maculatum is particularly well-known for its potent dung-like volatile organic compound emissions and specialized floral chamber, which traps pollinators-mainly Psychoda phalaenoides and Psychoda grisescens-overnight. However, little is known about the genes underlying the production of many Arum maculatum volatile organic compounds, and their influence on variation in pollinator attraction rates. Therefore, we performed de novo transcriptome sequencing of Arum maculatum appendix and male floret tissue collected during anthesis and postanthesis, from 10 natural populations across Europe. These RNA-seq data were paired with gas chromatography-mass spectrometry analyses of floral scent composition and pollinator data collected from the same inflorescences. Differential expression analyses revealed candidate transcripts in appendix tissue linked to malodourous volatile organic compounds including indole, p-cresol, and 2-heptanone. In addition, we found that terpene synthase expression in male floret tissue during anthesis significantly covaried with sex- and species-specific attraction of Psychoda phalaenoides and Psychoda grisescens. Taken together, our results provide the first insights into molecular mechanisms underlying pollinator attraction patterns in Arum maculatum and highlight floral chamber sesquiterpene (e.g. bicyclogermacrene) synthases as interesting candidate genes for further study.

Comparative Transcriptome Analysis Reveals Coordinated Transcriptional Regulation of Central and Secondary Metabolism in the Trichomes of Cannabis Cultivars

Cannabis is one of the few plant genera capable of producing cannabinoids, the effects of which are synergized by terpene interactions. As the biosynthesis of both metabolite classes requires the same intracellular feedstocks, this work describes the coordinated regulation of global metabolic pathways that allows for their joint copious production in vivo. To this end, a transcriptomics-based approach to characterize the glandular trichomes of five Cannabis cultivars was pursued. Besides revealing metabolic traits that enhanced and proportionated the supply of critical carbon precursors, in-depth analysis showed significantly increased gene expression of two particular enzymes to meet the huge nicotinamide adenine dinucleotide phosphate (NADPH) demand of secondary metabolite production. Furthermore, it led to a hypothesis that the methyl-d-erythritol 4-phosphate pathway might be utilized more than the mevalonic acid pathway in Cannabis trichomes. While both pathways were found to be activated in a modular and calibrated way that reflected their broad participation in physiological processes, the genes for hexanoate, cannabinoid, and terpene biosynthesis were, in contrast, up-regulated in an en bloc and multi-loci manner due to their specific roles in secondary metabolite production. In addition, three new terpene synthases were characterized based on both in silico and experimental assays. Altogether, the study enhances the current understanding of secondary metabolite production in Cannabis cultivars, which may assist in their characterization and development.

Comprehensive Flavor Analysis of Volatile Components During the Vase Period of Cut Lily (Lilium spp. 'Manissa') Flowers by HS-SPME/GC-MS Combined With E-Nose Technology

Volatile compounds could affect the flavor and ornamental quality of cut flowers, but the flavor change occurring during the vase period of the cut flower is unclear. To clarify the dynamic changes during the vase period of cut lily (Lilium spp. 'Manissa') flowers, comprehensive flavor profiles were characterized by the electronic nose (E-nose) and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-MS). The response value of sensor W2W was significantly higher than other sensors, and its response value reached the highest on day 4. A total of 59 volatiles were detected in cut lilies by HS-SPME/GC-MS, mainly including aldehydes, alcohols, and esters. There were 19 volatiles with odor activity values (OAVs) greater than 1. Floral and fruity aromas were stronger, followed by a pungent scent. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) could effectively discriminate lily samples derived from different vase times on the basis of E-nose and HS-SPME-GC-MS. In summary, our study investigates the flavor change profile and the diversity of volatile compounds during the vase period of cut lilies, and lilies on day 4 after harvest exhibited excellent aroma and flavor taking into consideration of the flavor intensity and diversity. This provided theoretical guidance for the assessment of scent volatiles and flavor quality during the vase period of cut lily flowers and will be helpful for the application of cut lilies during the postharvest process.

Integration of Transcriptome and Methylome Analyses Provides Insight Into the Pathway of Floral Scent Biosynthesis in Prunus mume

DNA methylation is a common epigenetic modification involved in regulating many biological processes. However, the epigenetic mechanisms involved in the formation of floral scent have rarely been reported within a famous traditional ornamental plant Prunus mume emitting pleasant fragrance in China. By combining whole-genome bisulfite sequencing and RNA-seq, we determined the global change in DNA methylation and expression levels of genes involved in the biosynthesis of floral scent in four different flowering stages of P. mume. During flowering, the methylation status in the “CHH” sequence context (with H representing A, T, or C) in the promoter regions of genes showed the most significant change. Enrichment analysis showed that the differentially methylated genes (DMGs) were widely involved in eight pathways known to be related to floral scent biosynthesis. As the key biosynthesis pathway of the dominant volatile fragrance of P. mume, the phenylpropane biosynthesis pathway contained the most differentially expressed genes (DEGs) and DMGs. We detected 97 DMGs participated in the most biosynthetic steps of the phenylpropane biosynthesis pathway. Furthermore, among the previously identified genes encoding key enzymes in the biosynthesis of the floral scent of P. mume, 47 candidate genes showed an expression pattern matching the release of floral fragrances and 22 of them were differentially methylated during flowering. Some of these DMGs may or have already been proven to play an important role in biosynthesis of the key floral scent components of P. mume, such as PmCFAT1a/1c, PmBEAT36/37, PmPAL2, PmPAAS3, PmBAR8/9/10, and PmCNL1/3/5/6/14/17/20. In conclusion, our results for the first time revealed that DNA methylation is widely involved in the biosynthesis of floral scent and may play critical roles in regulating the floral scent biosynthesis of P. mume. This study provided insights into floral scent metabolism for molecular breeding.

The chromosome-scale genome of Magnolia officinalis provides insight into the evolutionary position of magnoliids

Magnolia officinalis, a representative tall aromatic tree of the Magnoliaceae family, is a medicinal plant that is widely used in diverse industries from medicine to cosmetics. We report a chromosome-scale draft genome of M. officinalis, in which ∼99.66% of the sequences were anchored onto 19 chromosomes with the scaffold N50 of 76.62 Mb. We found that a high proportion of repetitive sequences was a common feature of three Magnoliaceae with known genomic data. Magnoliids were a sister clade to eudicots-monocots, which provided more support for understanding the phylogenetic position among angiosperms. An ancient duplication event occurred in the genome of M. officinalis and was shared with Lauraceae. Based on RNA-seq analysis, we identified several key enzyme-coding gene families associated with the biosynthesis of lignans in the genome. The construction of the M. officinalis genome sequence will serve as a reference for further studies of Magnolia, as well as other Magnoliaceae.

Functional characterization of an Indian sandalwood (Santalum album L.) dual-localized bifunctional nerolidol/linalool synthase gene involved in stress response

Essential oils extracted from the heartwood of Indian sandalwood (Santalum album L.) contain linalool and nerolidol as minor components. However, nerolidol/linalool synthase (NES/LIS), which produce linalool and nerolidol, have yet to be characterized in sandalwood. Using a transcriptomic-based approach, a terpene synthase gene was screened from unigenes of transcriptome data derived from S. album seedlings exposed to low temperature (4 °C). The enzyme encoded by these complementary DNAs belongs to the TPS-b clade. Recombinant SaNES/LIS is a bifunctional enzyme that can catalyze the formation of (E)-nerolidol from farnesyl diphosphate and linalool from geranyl diphosphate, respectively. Whereas SaNES/LIS was primarily localized in chloroplastids, both as granular fluorescence and as diffuse fluorescence, it was also detected in the cytosol of a limited number of cells. Agrobacterium tumefaciens-mediated transient gene expression in planta produced the same terpene products as those obtained in vitro. Real-time PCR analysis showed the highest expression of SaNES/LIS in fruits, with about a three-fold higher level than in leaves, followed by flowers, heartwood and roots. SaNES/LIS transcripts were differentially activated in different tissues in response to methyl jasmonate, cold, high temperature, strong illumination, and drought stress. Our results provide novel insight into the role of sandalwood terpenoids in response to various environmental stresses.

Identification of VOCs in essential oils extracted using ultrasound- and microwave-assisted methods from sweet cherry flower

The floral fragrance of plants is an important indicator in their evaluation. The aroma of sweet cherry flowers is mainly derived from their essential oil. In this study, based on the results of a single-factor experiment, a Box-Behnken design was adopted for ultrasound- and microwave-assisted extraction of essential oil from sweet cherry flowers of the Brooks cultivar. With the objective of extracting the maximum essential oil yield (w/w), the optimal extraction process conditions were a liquid-solid ratio of 52 mL g^-1, an extraction time of 27 min, and a microwave power of 435 W. The essential oil yield was 1.23%, which was close to the theoretical prediction. The volatile organic compounds (VOCs) of the sweet cherry flowers of four cultivars (Brooks, Black Pearl, Tieton and Summit) were identified via headspace solid phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). The results showed that a total of 155 VOCs were identified and classified in the essential oil from sweet cherry flowers of four cultivars, 65 of which were shared among the cultivars. The highest contents of VOCs were aldehydes, alcohols, ketones and esters. Ethanol, linalool, lilac alcohol, acetaldehyde, (E)-2-hexenal, benzaldehyde and dimethyl sulfide were the major volatiles, which were mainly responsible for the characteristic aroma of sweet cherry flowers. It was concluded that the VOCs of sweet cherry flowers were qualitatively similar; however, relative content differences were observed in the four cultivars. This study provides a theoretical basis for the metabolism and regulation of the VOCs of sweet cherry flowers.

Integrated Analysis of the Transcriptome and Metabolome Reveals Genes Involved in Terpenoid and Flavonoid Biosynthesis in the Loblolly Pine (Pinus taeda L.)

Loblolly pine (Pinus taeda L.) is an important tree for afforestation with substantial economic and ecological value. Many metabolites with pharmacological activities are present in the tissues of P. taeda. However, the biosynthesis regulatory mechanisms of these metabolites are poorly understood. In the present study, transcriptome and metabolome analyses were performed on five tissues of P. taeda. A total of 40.4 million clean reads were obtained and assembled into 108,663 unigenes. These were compared with five databases, revealing 39,576 annotated unigenes. A total of 13,491 differentially expressed genes (DEGs) were observed in 10 comparison groups. Of these, 487 unigenes exhibited significantly different expressions in specific tissues of P. taeda. The DEGs were explored using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis. We identified 343 and 173 candidate unigenes related to the biosynthesis of terpenoids and flavonoids, respectively. These included 62 R2R3-MYB, 30 MYB, 15 WRKY, seven bHLH, seven ERF, six ZIP, five AP2, and one WD40 genes that acted as regulators in flavonoid and/or terpenoid biosynthesis. Additionally, metabolomics analysis detected 528 metabolites, among which 168 were flavonoids. A total of 493 differentially accumulated metabolites (DAMs) were obtained in 10 comparison groups. The 3,7-Di-O-methyl quercetin was differentially accumulated in all the comparison groups. The combined transcriptome and metabolome analyses revealed 219 DEGs that were significantly correlated with 45 DAMs. Our study provides valuable genomic and metabolome information for understanding P. taeda at the molecular level, providing a foundation for the further development of P. taeda-related pharmaceutical industry.

Co-expression network analysis uncovers key candidate genes related to the regulation of volatile esters accumulation in Woodland strawberry

FveERF (FvH4_5g04470.1), FveAP2 (FvH4_1g16370.1) and FveWRKY (FvH4_6g42870.1) might be involved in fruit maturation of strawberry. Overexpression of FveERF could activate the expression of AAT gene and ester accumulation. Volatile esters play an important role in the aroma of strawberry fruits, whose flavor is the result of a complex mixture of various esters. The accumulation of these volatiles is closely tied to changes in metabolism during fruit ripening. Acyltransferase (AAT) is recognized as having a significant effect in ester formation. However, there is little knowledge about the regulation network of AAT. Here, we collected the data of RNA-seq and headspace GC-MS at five time points during fruit maturation of Hawaii4 and Ruegen strawberry varieties. A total of 106 volatile compounds were identified in the fruit of woodland strawberries, including 58 esters, which occupied 41.09% (Hawaii4) or 33.40% (Ruegen) of total volatile concentration. Transcriptome analysis revealed eight transcription factors highly associated with AAT genes. Through the changes in esters and the weight co-expression network analysis (WGCNA), a detailed gene network was established. This demonstrated that ERF gene (FvH4_5g04470.1), AP2 gene (FvH4_1g16370.1) and one WRKY gene (FvH4_6g42870.1) might be involved in expression of AAT genes, especially ERF genes. Overexpression of FveERF (FvH4_5g04470.1) does activate expression of AAT genes and ester accumulation in fruits of strawberry. Our findings provide valuable clues to gain better insight into the ester formation process of numerous fruits.

Production of multiple terpenes of different chain lengths by subcellular targeting of multi-substrate terpene synthase in plants

Multi-substrate terpene synthases (TPSs) are distinct from typical TPSs that react with a single substrate. Although in vitro activity of few multi-substrate TPSs have been reported, in vivo characterization has not been well investigated for most of them. Here, a new TPS from Cananga odorata, CoTPS5, belonging to TPS-f subfamily was functionally characterized in vitro as well as in vivo. CoTPS5 reacted with multiple prenyl-pyrophosphate substrates of various chain lengths as a multi-substrate TPS. It catalyzed the formation of (E)-β-ocimene, (E,E)-α-farnesene and α-springene from geranyl pyrophosphate, (E,E)-farnesyl pyrophosphate and geranylgeranyl pyrophosphate, respectively. Upon transient expression in Nicotiana benthamiana, CoTPS5 localized to cytosol and produced only (E,E)-α-farnesene. However, expression of plastid-targeted CoTPS5 in N. benthamiana resulted in biosynthesis of all three compounds, (E)-β-ocimene, (E,E)-α-farnesene and α-springene. Similarly, transgenic Arabidopsis plants overexpressing plastid-targeted CoTPS5 showed stable and sustainable production of (E)-β-ocimene, (E,E)-α-farnesene and α-springene. Moreover, their production did not affect the growth and development of transgenic Arabidopsis plants. Our results demonstrate that redirecting multi-substrate TPS to a different intracellular compartment could be an effective way to prove in vivo activity of multi-substrate TPSs and thereby allowing for the production of multiple terpenoids simultaneously in plants.

Composition and Biosynthesis of Scent Compounds from Sterile Flowers of an Ornamental Plant Clematis florida cv. 'Kaiser'

Clematisflorida is a popular ornamental vine species known for diverse colors and shapes of its flowers but not for scent. Here we investigated the composition and biosynthesis of floral scent in ‘Kaiser’, a fragrant cultivar of C. florida that has sterile flowers. Volatile profiling revealed that flowers of ‘Kaiser’ emit more than 20 compounds, with monoterpenes being most abundant. Among the three floral organs, namely sepals, transformed-petals, and ovaries, ovaries had the highest rates of total volatile emission. To determine the molecular mechanism underlying floral scent biosynthesis in ‘Kaiser’, we sequenced a flower transcriptome and searched the transcriptome for terpene synthase genes (TPSs), which are key genes for terpene biosynthesis. Among the TPS genes identified, three were putative intact full-length genes and were designated CfTPS1, CfTPS2, and CfTPS3. Phylogenetic analysis placed CfTPS1, CfTPS2, and CfTPS3 to the TPS-g, TPS-b, and TPS-a subfamily, respectively. Through in vitro enzyme assays with Escherichia coli-expressed recombinant proteins, both CfTPS1 and CfTPS2 were demonstrated to catalyze the conversion of geranyl diphosphate to linalool, the most abundant constituent of C. florida floral scent. In addition, CfTPS1 and CfTPS2 produced the sesquiterpene nerolidol from (E,E)-farnesyl diphosphate. CfTPS3 showed sesquiterpene synthase activity and produced multiple products in vitro. All three CfTPS genes showed higher levels of expression in sepals than those in transformed-petals and ovaries. Our results show that despite being sterile, the flowers of ‘Kaiser’ have normal mechanisms for floral scent biosynthesis that make the flowers fragrant.

Experimental Design and Sample Preparation in Forest Tree Metabolomics

Appropriate experimental design and sample preparation are key steps in metabolomics experiments, highly influencing the biological interpretation of the results. The sample preparation workflow for plant metabolomics studies includes several steps before metabolite extraction and analysis. These include the optimization of laboratory procedures, which should be optimized for different plants and tissues. This is particularly the case for trees, whose tissues are complex matrices to work with due to the presence of several interferents, such as oleoresins, cellulose. A good experimental design, tree tissue harvest conditions, and sample preparation are crucial to ensure consistency and reproducibility of the metadata among datasets. In this review, we discuss the main challenges when setting up a forest tree metabolomics experiment for mass spectrometry (MS)-based analysis covering all technical aspects from the biological question formulation and experimental design to sample processing and metabolite extraction and data acquisition. We also highlight the importance of forest tree metadata standardization in metabolomics studies.

Transcriptomic and proteomic approaches to explore the differences in monoterpene and benzenoid biosynthesis between scented and unscented genotypes of wintersweet

Wintersweet (Chimonanthus praecox L.) is an important ornamental plant in China with a pleasant floral scent. To explore the potential mechanisms underlying differences in the fragrances among genotypes of this plant, we analyzed floral volatile organic compounds (VOCs) from two different genotypes: SW001, which has little to no fragrance, and the scented genotype H29. The major VOCs in H29 were linalool, trans-β-ocimene, benzyl acetate, methyl salicylate, benzyl alcohol (BAlc) and methyl benzoate. The most important aroma-active compound in H29, linalool, was emitted at a low concentration in SW001, which had markedly higher levels of trans-β-ocimene than H29. Next, to investigate scent biosynthesis, we analyzed the transcriptome and proteome of fully open flowers of the two genotypes. A total of 14 443 differentially expressed unigenes and 196 differentially expressed proteins were identified. Further analyses indicated that 56 differentially expressed genes involved in the terpenoid and benzenoid biosynthesis pathways might play critical roles in regulating floral fragrance difference. Disequilibrium expression of four terpene synthase genes resulted in diverse emission of linalool and trans-β-ocimene in both genotypes. In addition, the expressions of two CpMYC2 transcription factors were both upregulated in H29, implying that they may regulate linalool production. Notably, 16 of 20 genes in the benzenoid biosynthesis pathway were downregulated, corresponding to the relatively low level of benzenoid production in SW001. The lack of benzyl acetate might indicate that SW001 may lack substrate BAlc or functional acetyl-CoA:benzylalcohol acetyltransferase.

CYP79D73 Participates in Biosynthesis of Floral Scent Compound 2-Phenylethanol in Plumeria rubra

Plumeria (Plumeria rubra), well known for its brightly colored and fragrant flowers, emits a number of floral volatile organic compounds (VOCs). Plumeria flowers emit a total of 43 VOCs including nine phenylpropanoids/benzenoids, such as 2-phenylethanol (2PE), benzaldehyde, 2-phenylacetaldehyde (PAld), (E/Z)-phenylacetaldoxime (PAOx), benzyl nitrile (BN), and 2-phenylnitroethane (PN). To identify genes and pathways involved in the production of the major compound 2PE, we analyzed the plumeria floral transcriptome and found a highly expressed, flower-specific gene encoding a cytochrome P450 family 79D protein (PrCYP79D73), which catalyzed the formation of (E/Z)-PAOx. Feeding experiments with deuterated phenylalanine or deuterated (E/Z)-PAOx showed that (E/Z)-PAOx is an intermediate in the biosynthesis of 2PE, as are two nitrogen-containing volatiles, BN and PN, in plumeria flowers. Crude enzyme extracts from plumeria flowers converted l-phenylalanine to (E/Z)-PAOx, PAld, 2PE, BN, and PN. The biosynthesis of these compounds increased with addition of PrCYP79D73-enriched microsomes but was blocked by pretreatment with 4-phenylimidazole, an inhibitor of cytochrome P450 enzymes. Moreover, overexpression of PrCYP79D73 in Nicotiana benthamiana resulted in the emission of (E/Z)-PAOx as well as PAld, 2PE, BN, and PN, all of which were also found among plumeria floral VOCs. Taken together, our results demonstrate that PrCYP79D73 is a crucial player in the biosynthesis of the major floral VOC 2PE and other nitrogen-containing volatiles. These volatiles may be required for plant defense as well as to attract pollinators for the successful reproduction of plumeria.

Transcriptomic profiling of the flower scent biosynthesis pathway of Cymbidium faberi Rolfe and functional characterization of its jasmonic acid carboxyl methyltransferase gene

Background

Cymbidium faberi, one of the most famous oriental orchids, has a distinct flower scent, which increases its economic value. However, the molecular mechanism of the flower scent biosynthesis was unclear prior to this study. Methyl jasmonate (MeJA) is one of the main volatile organic compounds (VOC) produced by the flowers of C. faberi. In this study, unigene 79,363 from comparative transcriptome analysis was selected for further investigation.

Results

A transcriptome comparison between blooming and withered flowers of C. faberi yielded a total of 9409 differentially expressed genes (DEGs), 558 of which were assigned to 258 pathways. The top ten pathways included α-linolenic acid metabolism, pyruvate metabolism and fatty acid degradation, which contributed to the conversion of α-linolenic acid to MeJA. One of the DEGs, jasmonic acid carboxyl methyltransferase (CfJMT, Unigene 79,363) was highly expressed in the blooming flower of C. faberi, but was barely detected in leaves and roots. Although the ectopic expression of CfJMT in tomato could not increase the MeJA content, the expression levels of endogenous MeJA biosynthesis genes were influenced, especially in the wound treatment, indicating that CfJMT may participate in the response to abiotic stresses.

Conclusion

This study provides a basis for elucidating the molecular mechanism of flower scent biosynthesis in C. faberi, which is beneficial for the genetically informed breeding of new cultivars of the economically valuable oriental orchids.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5501-z) contains supplementary material, which is available to authorized users.

Transcriptomic Analysis of Flower Bud Differentiation in Magnolia sinostellata

Magnolias are widely cultivated for their beautiful flowers, but despite their popularity, the molecular mechanisms regulating flower bud differentiation have not been elucidated. Here, we used paraffin sections and RNA-seq to study the process of flower bud differentiation in Magnolia sinostellata. Flower bud development occurred between 28 April and 30 May 2017 and was divided into five stages: undifferentiated, early flower bud differentiation, petal primordium differentiation, stamen primordium differentiation, and pistil primordium differentiation. A total of 52,441 expressed genes were identified, of which 11,592 were significantly differentially expressed in the five bud development stages. Of these, 82 genes were involved in the flowering. In addition, MADS-box and AP2 family genes play critical roles in the formation of flower organs and 20 differentially expressed genes associated with flower bud differentiation were identified in M. sinostellata. A qRT-PCR analysis verified that the MADS-box and AP2 family genes were expressed at high levels during flower bud differentiation. Consequently, this study provides a theoretical basis for the genetic regulation of flowering in M. sinostellata, which lays a foundation for further research into flowering genes and may facilitate the development of new cultivars.