Evidence map›Paper›PMID 39833155›Full record

ArticleNature communications2025

Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos.

Xiaoyang Ge, Xiaole Yu, Zhixin Liu, Jiachen Yuan, Aizhi Qin, Ye Wang, Yanli Chen, Wenqiang Qin, Yumeng Liu, Xingxing Liu and 12 more

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 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

15 citing papers in PubMed.

  1. Review
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  3. Article
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  6. Genome-Wide Identification and Expression Analysis of theInternational journal of molecular sciences · 2026
    Article
  7. Article
  8. Frontiers in pharmacology · 2026
    Article
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  10. Article
  11. Article
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  15. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Xiaoyang Ge *Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China.
Xiaole Yu *State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Zhixin Liu *State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Jiachen Yuan *Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China.
Aizhi Qin *State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Ye Wang *State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
Yanli Chen *State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
Wenqiang Qin *State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
Yumeng LiuState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Xingxing LiuZhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China.
Yaping ZhouState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Peng WangState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
Jincheng YangState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Hao LiuState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Zihao ZhaoState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Mengke HuState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Yixin ZhangState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Susu SunState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China.
Luis Herrera-EstrellaInstitute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.ORCID http://orcid.org/0000-0001-7936-3856
Lam-Son Phan TranInstitute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
Xuwu SunState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China. sunxuwu@henu.edu.cn.ORCID http://orcid.org/0000-0001-8462-6948
Fuguang LiZhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China. aylifug@caas.cn.ORCID http://orcid.org/0000-0002-9057-0554

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Somatic embryogenesis (SE) is a developmental process related to the regeneration of tissue-cultured plants, which serves as a useful technique for crop breeding and improvement. However, SE in cotton is difficult and elusive due to the lack of precise cellular level information on the reprogramming of gene expression patterns involved in somatic embryogenesis. Here, we investigate the spatial and single-cell expression profiles of key genes and the metabolic patterns of key metabolites by integrated single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics (ST), and spatial metabolomics (SM). To evaluate the results of these analyses, we functionally characterized the potential roles of two representative marker genes, AATP1 and DOX2, in the regulation of cotton somatic embryo development. A publicly available web-based resource database ( https://cotton.cricaas.com.cn/somaticembryo/ ) in this study provides convenience for future studies of the expression patterns of marker genes at specific developmental stages during the process of SE in cotton.

Indexed as

GossypiumMetabolomeSeedsTranscriptomeGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Expression Regulation, PlantMetabolomicsPlant ProteinsPlant Somatic Embryogenesis TechniquesSingle-Cell AnalysisPlant Proteins

Identifiers

PMID39833155
PMCPMC11747644

What OpenQuestion holds

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Registered trials

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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.