The 3D architecture of the pepper genome and its relationship to function and evolution

Yi Liao, Juntao Wang, Zhangsheng Zhu, Yuanlong Liu, Jinfeng Chen, Yongfeng Zhou, Feng Liu, Jianjun Lei, Brandon S. Gaut, Bihao Cao (), J. J. Emerson () and Changming Chen ()
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Yi Liao: South China Agricultural University
Juntao Wang: South China Agricultural University
Zhangsheng Zhu: South China Agricultural University
Yuanlong Liu: University of Lausanne
Jinfeng Chen: Chinese Academy of Sciences
Yongfeng Zhou: Chinese Academy of Agricultural Sciences
Feng Liu: Hunan Agricultural University
Jianjun Lei: South China Agricultural University
Brandon S. Gaut: University of California
Bihao Cao: South China Agricultural University
J. J. Emerson: University of California
Changming Chen: South China Agricultural University

Nature Communications, 2022, vol. 13, issue 1, 1-18

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-31112-x

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