Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance surging drug prices etc., harnessing healing power plants gifted from mother nature is more urgent than ever helping us survive future sustainable way. PNP research efforts pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- inter-disciplinary approaches integrating interrogating all accessible data genomics, metabolomics, structural biology, chemical informatics necessary to accelerate full characterization biosynthetic regulatory circuitry producing PNPs plants. In this review, attempt provide brief update current focusing how different state-of-the-art biotechnologies facilitate their discovery, molecular basis biosynthesis, as well synthetic biology. Finally, humbly foresight trend understanding biology coming decades.

Language: Английский

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Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement

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

Published: Oct. 17, 2023

Assembly of a high-quality genome is important for downstream comparative and functional genomic studies. However, most tools assembly assessment only give qualitative reports, which do not pinpoint errors at specific regions. Here, we develop new reference-free tool, Clipping information Revealing Quality (CRAQ), maps raw reads back to assembled sequences identify regional structural based on effective clipped alignment information. Error counts are transformed into corresponding evaluation indexes reflect the quality single-nucleotide resolution. Notably, CRAQ distinguishes from heterozygous sites or differences between haplotypes. This tool can clearly indicate low-quality regions potential error breakpoints; thus, it misjoined that should be split further scaffold building improvement assembly. We have benchmarked multiple genomes using different strategies, demonstrated misjoin correction improving constructed pseudomolecules.

Language: Английский

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Beyond genome: Advanced omics progress of Panax ginseng

Plant Science, Journal Year: 2024, Volume and Issue: 341, P. 112022 - 112022

Published: Feb. 3, 2024

Language: Английский

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Genome sequencing of three Polyscias species reveals common features in terpene synthase gene family evolution in these species

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: Feb. 19, 2025

Abstract The genus Polyscias , part of the Araliaceae family, is known for its significant ornamental and medicinal value, as well rich variety metabolites. These plants are primarily found in tropical regions, particularly Southeast Asia Pacific islands. diverse geographical environments have led to emergence many unique endangered species, although there limited genomic information available about them. In this study, we generated high‐quality reference genomes three species: two that endemic Hawaiʻi, cf. bisattenuata lallanii one more widespread macgillivrayi . We identified a total 51,083, 60,881, 29,060 genes these respectively. Whole‐genome duplication analysis indicated all species underwent common event. By examining phylogenetic structural characteristics terpene synthase gene family closely related several clusters play crucial roles metabolite synthesis. A mono‐ sesquiterpenoids were detected, with compounds having been validated previous studies. Our findings provide foundation further genetic biochemical investigations which may aid conservation species.

Language: Английский

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From single- to multi-omics: future research trends in medicinal plants

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 24(1)

Published: Nov. 22, 2022

Abstract Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies medicinal performed to identify molecular markers species functional genes controlling key biological traits, as well understand biosynthetic pathways bioactive regulatory mechanisms environmental responses. Omics technologies applied plants, including taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics mutagenomics. However, because complex regulation network, single usually fail explain specific phenomena. In recent years, reports integrated multi-omics increased. Until now, there few assessments developments upcoming trends in plants. We highlight research summarise typical bioinformatics resources available for analysing datasets, discuss related future directions challenges. This information facilitates further refinement current approaches leads new ideas.

Language: Английский

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Chromosome‐level genome assembly of Prunella vulgaris L. provides insights into pentacyclic triterpenoid biosynthesis

The Plant Journal, Journal Year: 2024, Volume and Issue: 118(3), P. 731 - 752

Published: Jan. 16, 2024

SUMMARY Prunella vulgaris is one of the bestselling and widely used medicinal herbs. It recorded as an ace medicine for cleansing protecting liver in Chinese Pharmacopoeia has been main constitutions many herbal tea formulas China centuries. also a traditional folk Europe other countries Asia. Pentacyclic triterpenoids are major class bioactive compounds produced P. . However, their biosynthetic mechanism remains to be elucidated. Here, we report chromosome‐level reference genome using approach combining Illumina, ONT, Hi‐C technologies. 671.95 Mb size with scaffold N50 49.10 complete BUSCO 98.45%. About 98.31% sequence was anchored into 14 pseudochromosomes. Comparative analysis revealed recent WGD Genome‐wide identified 35 932 protein‐coding genes (PCGs), which 59 encode enzymes involved 2,3‐oxidosqualene biosynthesis. In addition, 10 PvOSC , 358 PvCYP 177 PvUGT were identified, five PvOSCs 25 PvCYPs 9 PvUGTs predicted biosynthesis pentacyclic triterpenoids. Biochemical activity assay PvOSC2, PvOSC4, PvOSC6 recombinant proteins showed that they mixed amyrin synthase (MAS), lupeol (LUS), β‐amyrin (BAS), respectively. The results provide solid foundation further elucidating

Language: Английский

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Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(6)

Published: April 9, 2024

Ginseng (Panax ginseng) is a representative of Chinese traditional medicine, also used worldwide, while the triterpene saponin ginsenoside most important effective compound within it. an allotetraploid, with complex genetic background, making study its metabolic evolution challenging. In this study, we assembled telomere-to-telomere ginseng reference genome, constructed 3.45 Gb 24 chromosomes and 77 266 protein-coding genes. Additionally, genome was divided into two subgenomes, designated as subgenome A B. Subgenome contains larger number genes, whereas B has general expression advantage, suggesting that subgenomes experienced asymmetric gene loss biased expression. The separated approximately 6.07 million years ago, shows closest relation to Panax vietnamensis var. fuscidiscus. Comparative genomics revealed expansion families associated biosynthesis in both subgenomes. Furthermore, tandem duplications proximal play crucial roles biosynthesis. We screened functional genes identified previous research found some these located colinear regions between have divergence functions, revealing unbalanced pathway ginseng. Our work provides resources for future studies breeding programs ginseng, well ginsenosides.

Language: Английский

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Genome-wide analysis of the C2H2 zinc finger protein gene family and its response to salt stress in ginseng, Panax ginseng Meyer

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: June 17, 2022

Abstract The C2H2 zinc finger protein (C2H2-ZFP) gene family plays important roles in response to environmental stresses and several other biological processes plants. Ginseng is a precious medicinal herb cultivated Asia North America. However, little known about the C2H2-ZFP its functions ginseng. Here, we identified 115 genes from ginseng, defined as PgZFP family. It was clustered into five groups featured with eight conserved motifs, each containing one six of them. are categorized 17 ontology subcategories have numerous regulatory elements responsive variety process, suggesting their functional differentiation. were spliced 228 transcripts at seed setting stage varied dramatically expression across tissues, developmental stages, genotypes, but they form co-expression network, correlation. Furthermore, four genes, PgZFP31 , PgZFP78-01 PgZFP38 PgZFP39-01 that actively involved plant salt stress. These results provide new knowledge on origin, differentiation, evolution, function resources for research application ginseng species.

Language: Английский

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Integrated analysis of nutritional quality changes and molecular regulation in ‘Qingcui’ plum fruit treated with 1-MCP during storage

Postharvest Biology and Technology, Journal Year: 2023, Volume and Issue: 207, P. 112591 - 112591

Published: Oct. 5, 2023

Language: Английский

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Genome-wide analysis of Panax MADS-box genes reveals role of PgMADS41 and PgMADS44 in modulation of root development and ginsenoside synthesis

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 233, P. 123648 - 123648

Published: Feb. 11, 2023

Language: Английский

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