Evidence map›Paper›PMID 40308064›Full record

ArticlePlant communications2025

An integrative 3D-genome database for plants.

Qihang Yang, Tong Wu, Mengyang Liu, Xiaomeng Zhang, Xiaoxue Sun, Daling Feng, Yin Lu, Xueping Chen, Yiguo Hong, Wei Ma and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. 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

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

11 authors.

Qihang YangState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
Tong WuState Key Laboratory of North China Crop Improvement and Regulation, College of Resources and Environmental Sciences, Hebei Agricultural University, Baoding 071000, Hebei, China.
Mengyang LiuState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
Xiaomeng ZhangState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
Xiaoxue SunState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
Daling FengState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
Yin LuState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
Xueping ChenKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
Yiguo HongState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
Wei MaState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China. Electronic address: mawei0720@163.com.
Jianjun ZhaoState Key Laboratory of North China Crop Improvement and Regulation, Hebei International Research Center of Vegetable Functional Genomics, College of Horticulture, Hebei Agricultural University, Baoding 071000, China. Electronic address: jjz1971@aliyun.com.

Funding

Non-US Government Research Support type
6 · The paper itself

Abstract

High-throughput sequencing technologies have revolutionized studies of 3D genome structures, revealing unprecedented insights into the complexity of genome-wide gene regulation in eukaryotes. To analyze and compare 3D genome structures, we developed a plant 3D-genome database, 3D-GDP, for interspecies comparative functional genomics (http://www.3d-gdp.com/). 3D-GDP includes all publicly available plant 3D genome sequences. It offers detailed analyses and comparisons of 3D genome structures among 26 plant species, with comprehensive information on topologically associating domains (TADs), loops, and compartments, as well as gene annotations. 3D-GDP also provides a range of bioinformatic tools such as a genome browser, TAD function prediction, and specialized modules for prediction and systematic comparison of chromatin structures across species to identify conserved TADs and loop structures. 3D-GDP thus constitutes a resource-rich, integrated database and innovative platform that can be used to reveal the evolutionary conservation of 3D genome structures and their relevance for genome-wide gene regulation in plants and beyond.

Indexed as

Databases, GeneticGenome, PlantPlantsChromatinComputational BiologyGenomicsChromatin3D genome sequenceschromatin structuredatabaseHi-Cplant comparative genomicsplatform

Identifiers

PMID40308064
PMCPMC12177499

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.