The 3D Architecture of the Pepper Genome and Its Relationship to Function and Evolution

Overview

Journal Nat Commun

Specialty Biology

Date 2022 Jun 17

PMID 35710823

Authors

Yi Liao

Juntao Wang

Zhangsheng Zhu

Yuanlong Liu

Jinfeng Chen

Yongfeng Zhou

Feng Liu

Jianjun Lei

Brandon S Gaut

Bihao Cao

J J Emerson

Changming Chen

Affiliations

Soon will be listed here.

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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