Metabolomics Combined with Transcriptomics Analysis Reveals the Regulation of Flavonoids in the Leaf Color Change of Acer truncatum Bunge DOI Open Access

Yinglun Sun,

Ranbo Yu, Yushan Liu

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(24), P. 13325 - 13325

Published: Dec. 12, 2024

The color variation of the leaves in autumn is a significant ornamental feature Acer truncatum Bunge, especially when gradually become redder. Many studies focused on leaf changes; however, less research has been conducted mechanism by which A. truncatum’s turn red. Red, middle and green were used as study materials to evaluate their flavonoid-related metabolites infer gene metabolite expression patterns conjunction with transcriptome expression. For start, phenotypic parameters analyses showed that red had highest redness greenness (a*). In addition, total 23 identified through metabolome, including five anthocyanins. Of them, cyanidin 3-O-β-D-sambubioside, 3-O rutinoside, pelargonidin 3-O-3″,6″-O-dimalonylglucoside, delphinidin 3,7-di-O-β-D-glucoside 3-O-β-D-sambubioside would help truncatum. Similarly, combined transcriptomics metabolomics most genes flavonoid anthocyanin biosynthetic pathways differentially expressed both types leaves. Chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR) (ANS) could affect synthesis during change. This provide data for genetic improvement maple plants exploring valuable synthesis, enhance understanding different developmental stages.

Language: Английский

Technology-enabled great leap in deciphering plant genomes DOI
Lingjuan Xie, Xiaojiao Gong, Kun Yang

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: 10(4), P. 551 - 566

Published: March 20, 2024

Language: Английский

Citations

34
Unraveling the specialized metabolic pathways in medicinal plant genomes: a review DOI Creative Commons
Mingcheng Wang, Shuqiao Zhang, Rui Li

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 24, 2024

Medicinal plants are important sources of bioactive specialized metabolites with significant therapeutic potential. Advances in multi-omics have accelerated the understanding metabolite biosynthesis and regulation. Genomics, transcriptomics, proteomics, metabolomics each contributed new insights into biosynthetic gene clusters (BGCs), metabolic pathways, stress responses. However, single-omics approaches often fail to fully address these complex processes. Integrated provides a holistic perspective on key regulatory networks. High-throughput sequencing emerging technologies like single-cell spatial omics deepened our cell-specific spatially resolved dynamics. Despite advancements, challenges remain managing large datasets, standardizing protocols, accounting for dynamic nature metabolism, effectively applying synthetic biology sustainable production. This review highlights recent progress omics-based research medicinal plants, discusses available bioinformatics tools, explores future trends aimed at leveraging integrated improve quality utilization plant resources.

Language: Английский

Citations

11
A long road ahead to reliable and complete medicinal plant genomes DOI Creative Commons

L. Cheng,

Zilong Wang, Qian‐Hao Zhu

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 4, 2025

Language: Английский

Citations

1
Unlocking plant genetics with telomere-to-telomere genome assemblies DOI
Vanika Garg, Abhishek Bohra, Martin Mascher

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(9), P. 1788 - 1799

Published: July 24, 2024

Language: Английский

Citations

7
The gap-free genome of Forsythia suspensa illuminates the intricate landscape of centromeres DOI Creative Commons
Jian Cui,

Congle Zhu,

Lisha Shen

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(9)

Published: July 10, 2024

, commonly known as weeping forsythia, holds significance in traditional medicine and horticulture. Despite its ecological cultural importance, the existing reference genome presents challenges with duplications gaps, hindering in-depth genomic analyses. Here, we present a Telomere-to-Telomere (T2T) assembly of

Language: Английский

Citations

6
CentIER: accurate centromere identification for plant genome DOI Creative Commons
Dong Xu,

Jinbao Yang,

Huaming Wen

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(10), P. 101046 - 101046

Published: Aug. 8, 2024

This paper introduces CentIER, the first bioinformatic tool designed to detect complete centromeric regions without additional wet experiments. The accuracy of CentIER was validated on diverse plant genomes such as Arabidopsis, rice, maize and mulberry, results show that can perform significantly more accurate detection than existing tool.

Language: Английский

Citations

6
Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus DOI Creative Commons

Hanwen Yu,

Haixia Wang, Xiao Liang

et al.

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(5)

Published: Feb. 1, 2025

Abstract Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory hepatoprotective properties. P. important clinical value the active triterpenoid saponins roots. However, biosynthetic pathway remains unclear, related genes remain unknown. Therefore, this study, we assembled high-quality integrated telomere-to-telomere reference genome combined time-specific transcriptome metabolome profiling to identify cytochrome P450s (CYPs) responsible for hydroxylation processes involved saponin biosynthesis. Nine chromosomes were without gaps or mismatches, nine centromeres 18 telomere regions identified. This eliminated redundant sequences from previous versions incorporated structural variation information. Comparative analysis revealed that underwent core eudicot γ-WGT event. We screened 211 CYPs found tandem proximal duplications may be crucial expansion CYP families. outlined proposed steps, likely catalyzed by CYP716A/72A/749A families, platycodin biosynthesis identified three PgCYP716A, seven PgCYP72A, PgCYP749A showed positive correlation with By establishing T2T assembly genome, transcriptome, resource grandiflorus, provide foundation complete elucidation platycodins pathway, which consequently leads heterologous bioproduction, serves fundamental genetic molecular-assisted breeding improvement grandiflorus.

Language: Английский

Citations

0
CYP98A monooxygenases: a key enzyme family in plant phenolic compound biosynthesis DOI Creative Commons

Zheng Zhou,

Yonghao Duan,

Yajing Li

et al.

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(6)

Published: March 10, 2025

Abstract Phenolic compounds are derived from the phenylpropanoid metabolic pathways of plants and include phenylpropionic acids, lignins, coumarins, flavonoids. These among most abundant diverse classes secondary metabolites found throughout plant kingdom. play critical roles in growth, development, stress resistance horticultural plants. Moreover, some phenolic exhibit substantial biological activities, they widely utilized across various sectors, such as pharmaceutical food industries. The cytochrome P450 monooxygenase 98A subfamily (CYP98A) is involved mainly biosynthesis compounds, mediating meta-hydroxylation aromatic rings common phenylpropane compounds. However, research on this family oxidases currently fragmented, a systematic comprehensive review has not yet been conducted. This offers an exhaustive summary molecular features CYP98A functions monooxygenases different types In addition, study provides reference for exploration functional enzymes. An enhanced understanding can help cultivation high-quality with increased to biotic abiotic stresses accumulation natural bioactive via engineering strategies. structural optimization modification provide additional potential targets synthetic biology, enabling efficient vitro production important address supply conflicts.

Language: Английский

Citations

0
The high-quality chromosome-level genome assembly of Dracocephalum rupestre Hance DOI Creative Commons
Qian Zhao, Zhiyong Fan,

Hui Yu

et al.

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: March 21, 2025

Dracocephalum rupestre Hance is China's traditional herbal medicine in the family Labiatae with numerous health benefits, including anti-inflammatory, antiviral and anti-tumor activities. However, genus has no reference genome currently, which restricts research on breeding, cultivation exploration of medicinal properties D. rupestre. Thus, we present high-quality chromosome-level assembly using a combination Pacbio HiFi sequencing Hi-C scaffolding technologies. The final was 435.45 Mb contig N50 49.83 scaffold 59.06 Mb. assembled sequences were anchored to 7 chromosomes an integration efficiency 96.96%. Furthermore, predicted 25,865 protein-coding genes, 98.23% functionally annotated. These results offer valuable resources for understanding genetic basis unique phenotypes will facilitate further study functional genomics this species.

Language: Английский

Citations

0
Research Progress of Genomics Applications in Secondary Metabolites of Medicinal Plants: A Case Study in Safflower DOI Open Access
Zhihua Wu,

Yan Na Hu,

Rui Hao

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3867 - 3867

Published: April 19, 2025

Medicinal plants, recognized as significant natural resources, have gained prominence in response to the increasing global demand for herbal medicines, necessitating large-scale production of these plants and their derivatives. are exposed a variety internal external factors that interact influence biosynthesis accumulation secondary metabolites. With rapid development omics technologies such genomics, transcriptomics, proteomics, metabolomics, multi-omics become important tools revealing complexity functionality organisms. They conducive further uncovering biological activities metabolites medicinal clarifying molecular mechanisms underlying Also, artificial intelligence (AI) technology accelerates comprehensive utilization high-dimensional datasets offers transformative potential analysis. However, there is currently no systematic review summarizing genomic metabolite plants. Safflower (Carthamus tinctorius L.) has rich diverse bioactive flavonoids, among which Hydroxysafflor yellow A (HSYA) specific safflower emerging medication treating wide range diseases. Hence, progress been made study an excellent example regulation recent years. Here, we on understanding main at level, summarize various types contents, with particular focus flavonoids. This aims provide insight into regulatory from perspective genomics.

Language: Английский

Citations

0