High-quality chromosome-level genome assembly and multi-omics analysis of rosemary (Salvia rosmarinus) reveals new insights into the environmental and genome adaptation.

High-quality genome of rosemary (Salvia rosmarinus) represents a valuable resource and tool for understanding genome evolution and environmental adaptation as well as its genetic improvement. However, the existing rosemary genome did not provide insights into the relationship between antioxidant components and environmental adaptability. In this study, by employing Nanopore sequencing and Hi-C technologies, a total of 1.17 Gb (97.96%) genome sequences were mapped to 12 chromosomes with 46 121 protein-coding genes and 1265 non-coding RNA genes. Comparative genome analysis reveals that rosemary had a closely genetic relationship with Salvia splendens and Salvia miltiorrhiza, and it diverged from them approximately 33.7 million years ago (MYA), and one whole-genome duplication occurred around 28.3 MYA in rosemary genome. Among all identified rosemary genes, 1918 gene families were expanded, 35 of which are involved in the biosynthesis of antioxidant components. These expanded gene families enhance the ability of rosemary adaptation to adverse environments. Multi-omics (integrated transcriptome and metabolome) analysis showed the tissue-specific distribution of antioxidant components related to environmental adaptation. During the drought, heat and salt stress treatments, 36 genes in the biosynthesis pathways of carnosic acid, rosmarinic acid and flavonoids were up-regulated, illustrating the important role of these antioxidant components in responding to abiotic stresses by adjusting ROS homeostasis. Moreover, cooperating with the photosynthesis, substance and energy metabolism, protein and ion balance, the collaborative system maintained cell stability and improved the ability of rosemary against harsh environment. This study provides a genomic data platform for gene discovery and precision breeding in rosemary. Our results also provide new insights into the adaptive evolution of rosemary and the contribution of antioxidant components in resistance to harsh environments.

The chromosome-scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis.

Rosemary (Salvia rosmarinus) is considered a sacred plant because of its special fragrance and is commonly used in cooking and traditional medicine. Here, we report a high-quality chromosome-level assembly of the S. rosmarinus genome of 1.11 Gb in size; the genome has a scaffold N50 value of 95.5 Mb and contains 40 701 protein-coding genes. In contrast to other diploid Labiataceae, an independent whole-genome duplication event occurred in S. rosmarinus at approximately 15 million years ago. Transcriptomic comparison of two S. rosmarinus cultivars with contrasting carnosic acid (CA) content revealed 842 genes significantly positively associated with CA biosynthesis in S. rosmarinus. Many of these genes have been reported to be involved in CA biosynthesis previously, such as genes involved in the mevalonate/methylerythritol phosphate pathways and CYP71-coding genes. Based on the genomes and these genes, we propose a model of CA biosynthesis in S. rosmarinus. Further, comparative genome analysis of the congeneric species revealed the species-specific evolution of CA biosynthesis genes. The genes encoding diterpene synthase and the cytochrome P450 (CYP450) family of CA synthesis-associated genes form a biosynthetic gene cluster (CPSs-KSLs-CYP76AHs) responsible for the synthesis of leaf and root diterpenoids, which are located on S. rosmarinus chromosomes 1 and 2, respectively. Such clustering is also observed in other sage (Salvia) plants, thus suggesting that genes involved in diterpenoid synthesis are conserved in the Labiataceae family. These findings provide new insights into the synthesis of aromatic terpenoids and their regulation.

Carnosol, a diterpene present in rosemary, increases ELP1 levels in familial dysautonomia patient-derived cells and healthy adults: a possible therapy for FD.

Recent research on familial dysautonomia (FD) has focused on the development of therapeutics that facilitate the production of the correctly spliced, exon 20-containing, transcript in cells and individuals bearing the splice-altering, FD-causing mutation in the elongator acetyltransferase complex subunit I (ELP1) gene. We report here the ability of carnosol, a diterpene present in plant species of the Lamiaceae family, including rosemary, to enhance the cellular presence of the correctly spliced ELP1 transcript in FD patient-derived fibroblasts by upregulating transcription of the ELP1 gene and correcting the aberrant splicing of the ELP1 transcript. Carnosol treatment also elevates the level of the RNA binding motif protein 24 (RBM24) and RNA binding motif protein 38 (RBM38) proteins, two multifunctional RNA-binding proteins. Transfection-mediated expression of either of these RNA binding motif (RBMs) facilitates the inclusion of exon 20 sequence into the transcript generated from a minigene-bearing ELP1 genomic sequence containing the FD-causing mutation. Suppression of the carnosol-mediated induction of either of these RBMs, using targeting siRNAs, limited the carnosol-mediated inclusion of the ELP1 exon 20 sequence. Carnosol treatment of FD patient peripheral blood mononuclear cells facilitates the inclusion of exon 20 into the ELP1 transcript. The increased levels of the ELP1 and RBM38 transcripts and the alternative splicing of the sirtuin 2 (SIRT2) transcript, a sentinel for exon 20 inclusion in the FD-derived ELP1 transcript, are observed in RNA isolated from whole blood of healthy adults following the ingestion of carnosol-containing rosemary extract. These findings and the excellent safety profile of rosemary together justify an expedited clinical study of the impact of carnosol on the FD patient population.

Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Biosynthesis of the Active Compounds with Methyl Jasmonate in Rosemary Suspension Cells.

To study the effects of Methyl jasmonates (MeJA) on rosemary suspension cells, the antioxidant enzymes' change of activities under different concentrations of MeJA, including 0 (CK), 10 (M10), 50 (M50) and 100 µM MeJA (M100). The results demonstrated that MeJA treatments increased the activities of phenylalanine ammonla-lyase (PAL), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and polyphenol oxidase (PPO) and reduced the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA), thus accelerating the ROS scavenging. Comparative transcriptome analysis of different concentrations of MeJA showed that a total of 7836, 6797 and 8310 genes were differentially expressed in the comparisons of CKvsM10, CKvsM50, CKvsM100, respectively. The analysis of differentially expressed genes (DEGs) showed phenylpropanoid biosynthesis, vitamin B6, ascorbate and aldarate metabolism-related genes were significantly enriched. The transcripts of flavonoid and terpenoid metabolism pathways and plant hormone signal transduction, especially the jasmonic acid (JA) signal-related genes, were differentially expressed in CKvsM50 and CKvsM100 comparisons. In addition, the transcription factors (TFs), e.g., MYC2, DELLA, MYB111 played a key role in rosemary suspension cells under MeJA treatments. qRT-PCR of eleven DEGs showed a high correlation between the RNA-seq and the qRT-PCR result. Taken together, MeJA alleviated peroxidative damage of the rosemary suspension cells in a wide concentration range via concentration-dependent differential expression patterns. This study provided a transcriptome sequence resource responding to MeJA and a valuable resource for the genetic and genomic studies of the active compounds engineering in rosemary.

Characterization of Sicilian rosemary (Rosmarinus officinalis L.) germplasm through a multidisciplinary approach.

In Sicily, small differences exist between wild and cultivated rosemary biotypes; VOCs and genetic profiles may be a useful tool to distinguish them. A germplasm collection of Rosmarinus officinalis L. was harvested from 15 locations in Sicily. Eleven wild and four cultivated populations were collected and, due to the surveyed area covered, they can be considered as a representative panel of Sicilian genetic background of the species. Ex situ plant collection was transferred to the field cultivation in homogeneous conditions for characterizing through a multidisciplinary approach. The study included morphological traits observations (growth habitus, flower color, number and size of leaves, length and number of internodes), VOC profiles using HS-SPME, genome size by flow cytometry analysis, and genetic characterization by means of DNA and nuclear microsatellite (nSSR) investigation. To detect any pattern within- and among-populations variability, all morphological and chemical data were submitted to ANOVA, while clustering and structure population analysis were carried out using genetic profiles. The present work allowed us to distinguish rather well between wild and cultivated genotypes and to underline the biodiversity richness among rosemary Sicilian germplasm, never highlighted, useful for future breeding programs addressed to exploit this important resource.

Identification of RoCYP01 (CYP716A155) enables construction of engineered yeast for high-yield production of betulinic acid.

Betulinic acid (BA) and its derivatives possess potent pharmacological activity against cancer and HIV. As with many phytochemicals, access to BA is limited by the requirement for laborious extraction from plant biomass where it is found in low amounts. This might be alleviated by metabolically engineering production of BA into an industrially relevant microbe such as Saccharomyces cerevisiae (yeast), which requires complete elucidation of the corresponding biosynthetic pathway. However, while cytochrome P450 enzymes (CYPs) that can oxidize lupeol into BA have been previously identified from the CYP716A subfamily, these generally do not seem to be specific to such biosynthesis and, in any case, have not been shown to enable high-yielding metabolic engineering. Here RoCYP01 (CYP716A155) was identified from the BA-producing plant Rosmarinus officinalis (rosemary) and demonstrated to effectively convert lupeol into BA, with strong correlation of its expression and BA accumulation. This was further utilized to construct a yeast strain that yields > 1 g/L of BA, providing a viable route for biotechnological production of this valuable triterpenoid.

Carnosic acid biosynthesis elucidated by a synthetic biology platform.

Synthetic biology approaches achieving the reconstruction of specific plant natural product biosynthetic pathways in dedicated microbial "chassis" have provided access to important industrial compounds (e.g., artemisinin, resveratrol, vanillin). However, the potential of such production systems to facilitate elucidation of plant biosynthetic pathways has been underexplored. Here we report on the application of a modular terpene production platform in the characterization of the biosynthetic pathway leading to the potent antioxidant carnosic acid and related diterpenes in Salvia pomifera and Rosmarinus officinalis.Four cytochrome P450 enzymes are identified (CYP76AH24, CYP71BE52, CYP76AK6, and CYP76AK8), the combined activities of which account for all of the oxidation events leading to the biosynthesis of the major diterpenes produced in these plants. This approach develops yeast as an efficient tool to harness the biotechnological potential of the numerous sequencing datasets that are increasingly becoming available through transcriptomic or genomic studies.

Secondary compounds enhance flammability in a Mediterranean plant.

Some plant secondary compounds, such as terpenes, are very flammable; however, their role in enhancing plant flammability is poorly understood and often neglected in reviews on plant chemical ecology. This is relevant as there is growing evidence that flammability-enhancing traits are adaptive in fire-prone ecosystems. We analyzed the content of monoterpenes and sesquiterpenes, performed flammability tests and genotyped microsatellite markers, all in the same individuals of Rosmarinus officinalis, to evaluate the link between the content of terpenes, flammability and the genetic similarity among individuals. The results suggest that terpenes enhance flammability in R. officinalis, and that variability in flammability among individuals is likely to have a genetic basis. Overall our results suggest that the capacity to produce and store terpenes can be considered a flammability-enhancing trait and could have an adaptive value in fire-prone ecosystems.

Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Functional Characterization of the Three First Steps of the Pathway in Salvia fruticosa and Rosmarinus officinalis.

Carnosic acid (CA) is a phenolic diterpene with anti-tumour, anti-diabetic, antibacterial and neuroprotective properties that is produced by a number of species from several genera of the Lamiaceae family, including Salvia fruticosa (Cretan sage) and Rosmarinus officinalis (Rosemary). To elucidate CA biosynthesis, glandular trichome transcriptome data of S. fruticosa were mined for terpene synthase genes. Two putative diterpene synthase genes, namely SfCPS and SfKSL, showing similarities to copalyl diphosphate synthase and kaurene synthase-like genes, respectively, were isolated and functionally characterized. Recombinant expression in Escherichia coli followed by in vitro enzyme activity assays confirmed that SfCPS is a copalyl diphosphate synthase. Coupling of SfCPS with SfKSL, both in vitro and in yeast, resulted in the synthesis miltiradiene, as confirmed by 1D and 2D NMR analyses (1H, 13C, DEPT, COSY H-H, HMQC and HMBC). Coupled transient in vivo assays of SfCPS and SfKSL in Nicotiana benthamiana further confirmed production of miltiradiene in planta. To elucidate the subsequent biosynthetic step, RNA-Seq data of S. fruticosa and R. officinalis were searched for cytochrome P450 (CYP) encoding genes potentially involved in the synthesis of the first phenolic compound in the CA pathway, ferruginol. Three candidate genes were selected, SfFS, RoFS1 and RoFS2. Using yeast and N. benthamiana expression systems, all three where confirmed to be coding for ferruginol synthases, thus revealing the enzymatic activities responsible for the first three steps leading to CA in two Lamiaceae genera.

Characterization of two genes for the biosynthesis of abietane-type diterpenes in rosemary (Rosmarinus officinalis) glandular trichomes.

Rosemary (Rosmarinus officinalis) produces the phenolic diterpenes carnosic acid and carnosol, which, in addition to their general antioxidant activities, have recently been suggested as potential ingredients for the prevention and treatment of neurodegenerative diseases. Little is known about the biosynthesis of these diterpenes. Here we show that the biosynthesis of phenolic diterpenes in rosemary predominantly takes place in the glandular trichomes of young leaves, and used this feature to identify the first committed steps. Thus, a copalyl diphosphate synthase (RoCPS1) and two kaurene synthase-like (RoKSL1 and RoKSL2) encoding genes were identified and characterized. Expression in yeast (Saccharomyces cerevisiae) and Nicotiana benthamiana demonstrate that RoCPS1 converts geranylgeranyl diphosphate (GGDP) to copalyl diphosphate (CDP) of normal stereochemistry and that both RoKSL1 and RoKSL2 use normal CDP to produce an abietane diterpene. Comparison to the already characterized diterpene synthase from Salvia miltiorrhiza (SmKSL) demonstrates that the product of RoKSL1 and RoKSL2 is miltiradiene. Expression analysis supports a major contributing role for RoKSL2. Like SmKSL and the sclareol synthase from Salvia sclarea, RoKSL1/2 are diterpene synthases of the TPS-e group which have lost the internal gamma-domain. Furthermore, phylogenetic analysis indicates that RoKSL1 and RoKSL2 belong to a distinct group of KSL enzymes involved in specialized metabolism which most likely emerged before the dicot-monocot split.

New microsatellite markers for Salvia officinalis (Lamiaceae) and cross-amplification in closely related species.

PREMISE OF THE STUDY: Microsatellite primers were identified to study the genetic diversity, population genetic structure, and relationships of common sage and closely related species. METHODS AND RESULTS: Nine novel polymorphic trinucleotide microsatellite loci were identified for Salvia officinalis. A total of 127 alleles were observed. The observed and expected heterozygosity values ranged from 0.375 to 0.880 and from 0.624 to 0.931, respectively. Nine new and 11 previously published microsatellite primers were tested for cross-amplification. The species with the most successful cross-amplification was S. fruticosa. CONCLUSIONS: The nine new microsatellite markers will be useful in genetic studies of wild and cultivated populations of common sage and are potentially useful in genetic studies of closely related species.

Produção de mudas de dois genótipos de alecrim-de-tabuleiro (Lippia gracilis Schauer) em função de fertilizante mineral, calcário, substratos e recipientes / Seedling production of two "alecrim-de-tabuleiro" (Lippia gracilis Schauer) genotypes under mineral fertilizer, limestone, substrates and containers

Lippia gracilis Schauer popularmente conhecida como alecrim-de-tabuleiro possui moderada atividade antibacteriana, antimicrobiana e antiséptica. Objetivando avaliar o efeito de doses de fertilizante mineral, calcário, substratos e recipientes na produção de mudas de dois genótipos de alecrim-de-tabuleiro realizou-se experimentos com estacas de dois genótipos de L. gracilis. No experimento 1, foram utilizadas estacas apicais distribuídas em bandejas de poliestireno expandido de 128 células com o substrato pó-de-coco + areia (1:1), três repetições e oito estacas por repetição. O delineamento experimental foi em blocos ao acaso, em esquema fatorial 4x2x2, sendo quatro doses do fertilizante (6-24-12+micronutrientes) (1, 2, 3 e 4 g L-1), duas doses de calcário (0 e 1 g L-1) e dois genótipos (LGRA106 e LGRA201). Aos 35 após plantio, foram avaliadas a sobrevivência ( por cento), enraizamento ( por cento), comprimento de raiz (cm) e massa seca de raiz (mg). No experimento 2, foram utilizadas três repetições com oito estacas por repetição. O delineamento experimental foi em blocos ao acaso, em esquema de parcelas subdivididas onde foram testados nas parcelas dois recipientes (bandeja de poliestireno expandido de 128 alvéolos e tubetes de 110 cm³, na sub parcela foram testadas as combinações de quatro substratos (PC - pó de coco; PCA (1:1) - pó de coco + areia (1:1); PCA (2:1) - pó de coco + areia (2:1) e PCA (3:1) - pó de coco + areia (3:1) e dois genótipos (LGRA106 e LGRA201). Aos 35 dias após o plantio foram analisadas as mesmas variáveis do experimento 1, além de altura de parte aérea (cm) e massa seca de parte aérea (mg). A utilização de 1 g L-1 do fertilizante na ausência de calcário foi efetivo para sobrevivência de plantas e enraizamento de estacas de alecrim-de-tabuleiro. Com base nesses experimentos, concluiu-se que o genótipo LGRA106 é superior ao LGRA201 nas variáveis analisadas e recomenda-se a bandeja de poliestireno expandido para produção de mudas de L. gracilis via estaquia.

Commonly known as "alecrim-de-tabuleiro", Lippia gracilis Schauer (Verbenaceae) has moderate antibacterial, antimicrobial and antiseptic activity. This study aimed to evaluate the effect of doses of mineral fertilizer, limestone, substrates and containers on seedling production of two "alecrim-de-tabuleiro" genotypes, using cuttings. In experiment 1, apical cuttings were distributed on expanded polystyrene trays of 128 cells containing coir + sand (1:1), using three replicates of eight cuttings each. Experimental design was in randomized blocks, in a 4x2x2 factorial arrangement, i.e. four doses of fertilizer (6-24-12 + micronutrients) (1, 2, 3 and 4 g L-1), two doses of limestone (0 and 1 g L-1) and two genotypes (LGRA106 and LGRA201). At 35 days after planting, we evaluated survival ( percent), rooting ( percent), root length (cm) and root dry matter (mg). In experiment 2, three replicates of eight cuttings each were used. Experimental design was in randomized blocks, in a split-plot scheme. In the plots, we tested two containers (expanded polystyrene tray of 128 cells and 110 cm³ tubets). In the subplots, we tested four substrate combinations [coir, coir + sand (1:1), coir + sand (2:1) and coir + sand (3:1)] and two genotypes (LGRA106 and LGRA201). At 35 days after planting, the same variables of experiment 1 were evaluated, besides shoot length (cm) and shoot dry matter (mg). The use of 1 g L-1 fertilizer without limestone was effective for plant survival and cutting rooting. Based on these experiments, the genotype LGRA106 is superior to LGRA201 as to the evaluated variables and the expanded polystyrene tray is recommended for the production of L. gracilis seedlings through cuttings.

chemical composition, plant genetic differences, antimicrobial and antifungal activity investigation of the essential oil of Rosmarinus officinalis L.

The chemical composition of the essential oil of the Sardinian Rosmarinus officinalis L. obtained by hydro distillation and steam\hydro distillation was studied using GC-FID and MS. Samples were collected at different latitude and longitude of Sardinia (Italy). The yields ranged between 1.75 and 0.48% (v/w, volume/dry-weight). A total of 30 components were identified. The major compounds in the essential oil were alpha-pinene, borneol, (-) camphene, camphor, verbenone, and bornyl-acetate. Multivariate analysis carried out on chemical molecular markers, with the appraisal of chemical, pedological, and random amplified polymorphic DNA data, allows four different clusters to be distinguished. The antimicrobial and antifungal tests showed a weak activity of Sardinian rosemary. On the other hand, an inductive effect on fungal growth, especially toward Fusarium graminearum was observed.