ArticleGenome biology2023
Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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.
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.
Who cites it
38 citing papers in PubMed.
- Chromosome-level phylogenomics and genome evolution of the grape family.Nature plants · 2026Article
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement.Journal of integrative plant biology · 2026Review
- Turbocharging crop breeding with integrated biotechnology for a climate-resilient future.Journal of integrative plant biology · 2026Review
- Pan-genomic and transcriptomic analyses reveal subfunctionalization of CBP/p300-like histone acetyltransferases in soybean seed development.BMC plant biology · 2026Article
- 3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Post-polyploid chromosomal diploidization in plants is affected by clade divergence and constrained by shared genomic features.Nature communications · 2026Article
- Dynamic reorganization of three-dimensional genome architecture during Populus diversification.Nature ecology & evolution · 2026Article
- A telomere-to-telomere gap-free genome of the new cultivar 'Zhongtian No. 5', combined with pan-genome analysis, aids in exploration and genetic enhancement of red clover (Horticulture research · 2026Article
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genome-wide dissection ofHorticulture research · 2026Article
- Structural Variation and 3D Genome-Driven DNA/RNA Methylation Divergence Contributing to Cotton Fiber Domestication.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Natural genetic variation in calcium sensor genes as a novel resource for abiotic stress tolerance in crops.Frontiers in plant science · 2026Review
- Integrating Hi-C data and RNA-seq data to reveal the 3D genome in sheep.BMC genomics · 2025Article
- Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes.bioRxiv : the preprint server for biology · 2025Article
- Combination of 3D chromatin architecture and omics analysis provides insight into anthocyanin regulation inHorticulture research · 2025Article
- Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.Journal of integrative plant biology · 2025Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.
resultsHere, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site (TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation (PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication.
conclusionOur study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.