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.

Aerial bulbils are important vegetative reproductive organs in Lilium. They are often perpetually dormant in most Lilium species, and little is known about the induction of these vegetative structures. The world-famous Oriental hybrid lily cultivar ‘Sorbonne’, which blooms naturally devoid of aerial bulbils, is known for its lovely appearance and sweet fragrance. We found that decapitation stimulated the outgrowth of aerial bulbils at lower stems (LSs) and then application of low and high concentrations of IAA promoted aerial bulbils emergence around the wound at upper stems (USs) of ‘Sorbonne’. However, the genetic basis of aerial bulbil induction is still unclear. Herein, ‘Sorbonne’ transcriptome has been sequenced for the first time using the combination of third-generation long-read and next-generation short-read technology. A total of 46,557 high-quality non-redundant full-length transcripts were generated. Transcriptomic profiling was performed on seven tissues and stems with treatments of decapitation and application of low and high concentrations of IAA, respectively. Functional annotation of 1918 DEGs within stem samples of different treatments showed that hormone signaling, sugar metabolism and wound-induced genes were crucial to bulbils outgrowth. The expression pattern of auxin-, shoot branching hormone-, plant defense hormone- and wound-inducing-related genes indicated their crucial roles in bulbil induction. Then we established five hormone- and wounding-regulated co-expression modules and identified some candidate transcriptional factors, such as MYB, bZIP, and bHLH, that may function in inducing bulbils. High connectivity was observed among hormone signaling genes, wound-induced genes, and some transcriptional factors, suggesting wound- and hormone-invoked signals exhibit extensive cross-talk and regulate bulbil initiation-associated genes via multilayered regulatory cascades. We propose that the induction of aerial bulbils at LSs after decapitation can be explained as the release of apical dominance. In contrast, the induction of aerial bulbils at the cut surface of USs after IAA application occurs via a process similar to callus formation. This study provides abundant candidate genes that will deepen our understanding of the regulation of bulbil outgrowth, paving the way for further molecular breeding of lily.

Traditional breeding objectives focusing on flower type and colour have resulted in the lack of floral fragrances in modern daylilies. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) was used to determine the contributions of floral volatiles to floral fragrances in 46 daylilies (seven species, one variety, and 38 cultivars). Thirty-seven floral volatiles were identified, including 30 terpenoids, five benzenoids, and two nitrogenous compounds. Sensory evaluation and HS-SPME-GC-MS revealed that variations in the relative emission rates and proportions of (E)-β-ocimene and linalool were mainly responsible for different fragrance patterns in Hemerocallis. The studied daylilies were grouped to six fragrance patterns: (1) intense herbaceous and pungent scent, having the highest (E)-β-ocimene emission level; (2) intense flowery and pungent scent, having medium (E)-β-ocimene and low linalool emission levels; (3) medium flowery and sweet scent, having very low (E)-β-ocimene and the highest linalool emission levels; (4) low flowery and fresh scent, having low (E)-β-ocimene and no linalool emission levels; (5) very low herbaceous and fresh scent, having very low (E)-β-ocimene and linalool emission levels; and (6) no scent, having trace amounts of floral volatiles.

Leaf color change of variegated leaves from chimera species is regulated by fine-tuned molecular mechanisms. Hosta “Gold Standard” is a typical chimera Hosta species with golden-green variegated leaves, which is an ideal material to investigate the molecular mechanisms of leaf variegation. In this study, the margin and center regions of young and mature leaves from Hosta “Gold Standard”, as well as the leaves from plants after excess nitrogen fertilization were studied using physiological and comparative proteomic approaches. We identified 31 differentially expressed proteins in various regions and development stages of variegated leaves. Some of them may be related to the leaf color regulation in Hosta “Gold Standard”. For example, cytosolic glutamine synthetase (GS1), heat shock protein 70 (Hsp70), and chloroplastic elongation factor G (cpEF-G) were involved in pigment-related nitrogen synthesis as well as protein synthesis and processing. By integrating the proteomics data with physiological results, we revealed the metabolic patterns of nitrogen metabolism, photosynthesis, energy supply, as well as chloroplast protein synthesis, import and processing in various leaf regions at different development stages. Additionally, chloroplast-localized proteoforms involved in nitrogen metabolism, photosynthesis and protein processing implied that post-translational modifications were crucial for leaf color regulation. These results provide new clues toward understanding the mechanisms of leaf color regulation in variegated leaves.

Thyme essential oils (EOs) have antioxidant, antiviral, antifungal, antibacterial, anti-inflammatory, and immunological properties and are used in medicine, food, feed additives, and cosmetics. Here, we made use of a multidimensional analytical method to analyze the differences in the chemical components, chemotypes, and antioxidant and antibacterial activities of EOs from 24 Chinese native thymes. These Chinese native thymes comprised 10 species (Thymus quinquecostatus, T. mongolicus, T. inaequalis, T. mandschuricus, T. curtus, T. amurensis, T. roseus, T. proximu, T. marschallianus, and T. altaicus) and two varieties (T. quinquecostatus var. asiaticus and T. quinquecostatus var. przewalskii). Four primary chemotype groups were identified, namely carvacrol, thymol, geraniol, and α-terpineol. The maximum carvacrol, thymol, geraniol, and α-terpineol contents were 72.4, 58.6, 59.5, and 65.4%, respectively. The antioxidant capacities of the thymol and carvacrol chemotype EOs were found to be significantly superior to the other chemotypes using three antioxidant assays: DPPH, ABTS, and FRAP. Moreover, the thymol and carvacrol EO chemotypes could significantly inhibit the growths of the common food-borne pathogenic bacteria Staphylococcus aureus and Escherichia coli. A correlation analysis between the EO components and the bacteria showed that thymol significantly positively correlated with the bacteria. In summary, we analyzed the thyme EOs’ antioxidant and antibacterial activities, which laid a foundation for their use in medicines, foods, feed additives, and cosmetics. The results will also be very useful for the selection of wild thymes for functional research on carvacrol-, thymol-, geraniol-, and α-terpineol-rich essential oil chemotypes and the product development of feed additives, cosmetics, etc.