ArticleNature communications2022
The 3D architecture of the pepper genome and its relationship to function and evolution.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 88 citations in OpenAlex.
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Evolution and domestication-trait associations of ultra-long centromere haplotypes in pepper plants.Nature ecology & evolution · 2026Article
- TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement.Journal of integrative plant biology · 2026Review
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- 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
- A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity.Horticulture research · 2026Article
- Comparative centromere genomics reveals evolutionary divergence in Solanaceae genomes.Genome biology · 2026Article
- Centromere organization and epigenetic regulation in Aristolochia fimbriata.Genome biology · 2026Article
- Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant.Nature communications · 2026Article
- Article
- An Integrative Small RNA-Degradome-Transcriptome Analysis Reveals Mechanisms of Heat-Induced Anther Indehiscence in Pepper.Biology · 2026Article
- Features of DNA methylome in Capsicum spp.Epigenetics & chromatin · 2025Article
- Three Novel Genomes Broaden the Wild Side of thePlant direct · 2025Article
- A heat stress-responsive epigenome defines the dynamic 3D chromatin structure in Chinese cabbage.Plant physiology · 2025Article
- Review
- Chromosome-level genome assembly of the autotetraploid yellow pitaya provides novel insights into evolution of trait patterning in pitaya species with different ploidy.Genome biology · 2025Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).Nature communications · 2025Article
- An integrative 3D-genome database for plants.Plant communications · 2025Article
Corrections and comments
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Authors and funding
12 authors at 6 institutions in 4 countries.
Funding
Abstract
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints.
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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.