Multiomics analyses of two Leonurus species illuminate leonurine biosynthesis and its evolution

Molecular Plant, Journal Year: 2023, Volume and Issue: 17(1), P. 158 - 177

Published: Nov. 10, 2023

Language: Английский

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Application of third-generation sequencing to herbal genomics

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 7, 2023

There is a long history of traditional medicine use. However, little genetic information available for the plants used in medicine, which limits exploitation these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology Oxford Nanopore technology, compare against Illumina, predominant next-generation technique. addition, summarize nuclear organelle genome assemblies commonly medicinal plants, choose several examples from genomics, transcriptomics, molecular identification studies dissect specific processes advantages disadvantages when applied organisms. Finally, describe how expect that will be widely utilized assemble telomere-to-telomere (T2T) genomes epigenomics research involving plants.

Language: Английский

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Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 4, 2023

The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such tanshinones and carnosic acids, are specific to exhibit taxonomic diversity among lineages. To elucidate how ATD evolved, we carried out large-scale metabolic phylogenetic analyses 71 species, combined enzyme function, ancestral sequence trait reconstruction, comparative genomics experiments. This integrated approach showed that the lineage-wide diversities in were induced by differences oxidation terpenoid skeleton at C-20, which was caused functional divergence cytochrome P450 subfamily CYP76AK. These findings present a unique pattern plants shaped loss activity associated catalytic pathways.

Language: Английский

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Multi‐omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(10), P. 2320 - 2335

Published: Sept. 9, 2023

Diterpenoid alkaloids (DAs) have been often utilized in clinical practice due to their analgesic and anti-inflammatory properties. Natural DAs are prevalent the family Ranunculaceae, notably Aconitum genus. Nevertheless, evolutionary origin of biosynthesis pathway responsible for DA production remains unknown. In this study, we successfully assembled a high-quality, pseudochromosome-level genome DA-rich species vilmorinianum (A. vilmorinianum) (5.76 Gb). An A. vilmorinianum-specific whole-genome duplication event was discovered using comparative genomic analysis, which may aid evolution pathway. We identified several genes involved via integrated genomic, transcriptomic, metabolomic analyses. These included enzymes encoding target ent-kaurene oxidases aminotransferases, facilitated activation diterpenes insertion nitrogen atoms into diterpene skeletons, thereby mediating transformation DAs. The divergence periods these were further assessed, it shown that two major types establishment Our analysis offers fresh insights as well suggestions engineering biosynthetic pathways obtain desired

Language: Английский

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De novo chromosome-level genome assembly of Chinese motherwort (Leonurus japonicus)

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Jan. 9, 2024

Chinese motherwort (Leonurus japonicus), a member of Lamiaceae family, is commonly used medicinal herb for treating obstetrical and gynecological diseases, producing over 280 officinal natural products. Due to limited genomic resources, little progress has been made in deciphering the biosynthetic pathway valuable products L. japonicus. Here, we de novo assembled japonicus genome using high-coverage ONT long reads Hi-C reads. The chromosome-level assembly contained ten chromosomes representing 99.29% 489.34 Mb sequence with contig scaffold N50 7.27 50.86 Mb, respectively. Genome validations revealed BUSCO LAI score 99.2% 21.99, respectively, suggesting high quality assembly. Using transcriptomic data from various tissues, 22,531 protein-coding genes were annotated. Phylogenomic analysis 13 angiosperm plants suggested had 58 expanded gene families functionally enriched specialized metabolism such as diterpenoid biosynthesis. assembly, annotation, sequencing provide resources elucidation pathways behind pharmaceutical applications

Language: Английский

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

The Plant Journal, Journal Year: 2022, Volume and Issue: 113(4), P. 819 - 832

Published: Dec. 29, 2022

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

Language: Английский

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Whole-genome resequencing identifies exonic single-nucleotide variations in terpenoid biosynthesis genes of the medicinal and aromatic plant common sage (Salvia officinalis L.)

Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: 71(8), P. 4171 - 4181

Published: Feb. 18, 2024

Abstract Common sage ( Salvia officinalis L.), the type species of genus , is a historically acknowledged medicinal and aromatic plant that utilized in several different industries for manufacturing diverse end products, including food, pharmaceuticals, cosmetics, personal hygiene products insect repellants. The medical uses essential oil terpenoids have made these secondary metabolites focus medical/pharmaceutical chemistry research. In present work, common genome was resequenced assembled, protein-encoding gene content annotated. terpenoid biosynthesis repertoire, which includes 75 terpene synthase 67 backbone pathway genes, predicted located on assembly scaffolds, revealing tandem duplication blocks chromosomes. Variant analysis identified 188 variable single-nucleotide loci coding sequences genes. A total 24,570 polymorphisms were exome, representing database potential targeted genotyping Given activity highly prone to modulation by point mutations genotype plays an important role complex traits composition, constitute candidate functional markers can be associated with compositional future

Language: Английский

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Biodiversity and Breeding in Salvia officinalis L.

Published: Jan. 1, 2025

Language: Английский

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Integrated metabolite profiling and transcriptome analysis identify candidate genes involved in diterpenoid alkaloid biosynthesis in Aconitum pendulum

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: March 24, 2025

Introduction Aconitum pendulum is a well-known Tibetan medicine that possesses abundant diterpenoid alkaloids (DAs) with high medicinal value. However, due to the complicated structures of DAs and associated challenges in vitro synthesis presents, plants like remain primary source for DAs. Methods Given underutilization A. , thorough metabolomic transcriptomic analysis was conducted on its flowers, leaves, stems elucidate regulatory network underlying DA biosynthesis. Results Metabolomic profiling (utilizing UPLC-QQQ-MS/MS) identified 198 alkaloids, which 61 were relative abundance different among tissues. Without reference genome, we performed de novo assembly transcriptome . We generated 181,422 unigenes, 411 candidate enzyme genes related pathway identified, including 34 differentially expressed (DEGs). Through joint metabolome data, found correlation between detected metabolite levels various tissues expression genes. Specifically, it ApCYP1, ApCYP72, ApCYP256 may be turupellin accumulation, while ApBAHD9, ApBAHD10, ApBAHD12 positively accumulation aconitine. Furthermore, our study also revealed involved diterpene skeleton tend highly whereas their subsequent modifications are more likely leaf stem Functional gene families 77 BAHD acyltransferases, 12 O -methyltransferases, 270 CYP450 potentially biosynthesis The co-expression metabolites 116 significant correlations involving 30 58 Discussion This provides valuable resources in-depth research secondary metabolism not only deepening understanding mechanisms but providing genetic improvement metabolic engineering strategies.

Language: Английский

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The chromosome‐scale assembly of the Salvia plebeia genome provides insight into the biosynthesis and regulation of rosmarinic acid

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 13, 2025

Summary Salvia plebeia is an important traditional Chinese medicinal herb, with flavonoids and phenolic acids as its primary bioactive components. However, the absence of a reference genome hinders our understanding genetic basis underlying synthesis these Here, we present high‐quality, chromosome‐scale assembly S. , spanning 1.22 Gb, contig N50 91.72 Mb 36 861 annotated protein‐coding genes. Leveraging data, identified four catalytic enzymes—one rosmarinic acid synthase (RAS) three cytochrome P450 monooxygenases (CYP450s) —in which are involved in biosynthesis. We demonstrate that SpRAS catalyses conjugation various acyl donors acceptors, resulting formation precursor compounds. SpCYP98A75, SpCYP98A77 SpCYP98A78 catalyse from precursors at either C‐3 or C‐3′ position. Notably, SpCYP98A75 exhibited stronger hydroxylation capacity position, whereas greater efficiency Furthermore, hydroxylated both positions simultaneously, promoting conversion 4‐coumaroyl‐4′‐hydroxyphenyllactic to acid. Next, using hairy root transformation system for basic helix–loop–helix protein type transcription factor, SpbHLH54 positively regulates biosynthesis homoplantaginin . These findings provide valuable genomic resource elucidating mechanisms regulation improve evolutionary patterns within Lamiaceae family.

Language: Английский

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