Evidence map›Paper›PMID 41649387›Full record

ArticleJournal of experimental botany2026

Red-light-responsive metabolome reveals the crucial role of phytochrome A- and B-dependent secondary metabolism in Arabidopsis seed germination.

Cong Li, Yuxuan Zhu, Di Zhang, Wenjuan Qian, Suting Ma, Huiru Tang, Hongyan Yao

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of experimental botany, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Cong LiState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, China.
Yuxuan ZhuState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, China.
Di ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, China.
Wenjuan QianState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, China.
Suting MaState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, China.
Huiru TangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, China.ORCID 0000-0002-7139-2756
Hongyan YaoState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Zhongshan Hospital, Fudan University, Shanghai, China.ORCID 0000-0001-8688-3737

Funding

National Science Foundation of China 31870280Startup Foundation of Fudan University JIH1322014Y
6 · The paper itself

Abstract

Phytochrome A (phyA) and phyB are red and far-red photoreceptors that play essential roles in modulating seed germination. Despite extensive research on the roles of hormones and light signaling, the metabolic characteristics of phytochromes during red-light-mediated seed germination remain largely unknown. Using high-throughput non-targeted metabolomics, this study profiled Arabidopsis seeds including the wild-type (Col-0), single mutants (phyA-211 and phyB-9), the double mutant phyAB, and the pifq quadruple mutant during red-light-induced germination, and identified a total of 164 metabolites linked to primary and secondary metabolism. Comparative analysis of the metabolome revealed that the levels of flavonols including quercetin, kaempferol, and relevant glycosides were increased in phyA-211, decreased in Col-0 and phyB-9, and exhibited less change in phyAB, demonstrating that phyA and phyB antagonistically regulate flavonoid biosynthesis. Flavonoid biosynthesis was up-regulated in pifq under red light. Exogenous quercetin and kaempferol treatment modestly inhibited Col-0 and pifq seed germination. Taken together, these results reveal the comprehensive metabolic networks, highlight flavonoid metabolism under red light, and elucidate the synergistic and antagonistic roles of phyA and phyB in regulating seed metabolism. This study provides novel insight into the functional mechanisms of flavonoid metabolism and light signaling in plant development.

Indexed as

ArabidopsisArabidopsis ProteinsGerminationMetabolomePhytochrome APhytochrome BSeedsFlavonoidsRed LightSecondary MetabolismArabidopsis ProteinsFlavonoidsPHYB protein, ArabidopsisPhytochrome APhytochrome BArabidopsisflavonoid biosynthesismetabolomicsphytochromered lightsecondary metabolismseed germination

Identifiers

PMID41649387
PMCPMC13187680

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.