Evidence map›Paper›PMID 41402284›Full record

ArticleNature communications2025

A cis-regulatory element of the PHYTOCHROME A gene confers the submergence escape capacity for amphibious plants.

Chuanwei Yang, Wenbo Liu, Meiquan Qiu, Chenshu Xie, Huanhuan Lu, Wenjing Liang, Ruiyi Qiu, Dongming Li, Lin Li, Ji Yang

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Chuanwei YangState Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China. yangchuanwei@fudan.edu.cn.ORCID http://orcid.org/0000-0001-6076-8554
Wenbo LiuState Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
Meiquan QiuState Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
Chenshu XieState Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
Huanhuan LuState Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai, China.
Wenjing LiangState Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai, China.
Ruiyi QiuState Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
Dongming LiKey Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
Lin LiState Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai, China. linli@fudan.edu.cn.ORCID http://orcid.org/0000-0003-4840-5245
Ji YangState Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China. jiyang@fudan.edu.cn.ORCID http://orcid.org/0000-0002-4308-211X

Funding

Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission) 14DZ2260400
6 · The paper itself

Abstract

Amphibious plants escape submergence by plastically accelerating shoot growth, yet the mechanism underlying this convergent strategy remains unclear. Here, we demonstrate that PHYTOCHROME A (PHYA), a light photoreceptor, acts as a central regulator of the contrasting submergence escape capacities between amphibious Alternanthera philoxeroides and its terrestrial congener A. pungens. PHYA is distinctively regulated upon submergence in two congeners and negatively regulates submergence-induced elongation. Crucially, we find a cis-regulatory element (CRE) variant in the PHYA promoter between two congeners, which governs EIN3-dependent transcriptional repression and drives species-specific PHYA expression. Expanded investigation unveils phyletic retention of this CRE in other amphibious species, providing preliminary evidence for convergent evolution in the submergence escape capacity through independent co-option of the same CREs. Our findings demonstrate a role of PHYA in mediating submergence responses, deepen the understanding of the molecular basis for plant secondary aquatic adaptation, and inform flood-resilient crops engineering via cis-regulatory manipulation.

Indexed as

AmaranthaceaePhytochrome AAdaptation, PhysiologicalFloodsGene Expression Regulation, PlantPhylogenyPromoter Regions, GeneticPhytochrome A

Identifiers

PMID41402284
PMCPMC12708772

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.