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

文献类型： 外文期刊

第一作者： Liao, Yi

作者： Liao, Yi;Wang, Juntao;Zhu, Zhangsheng;Lei, Jianjun;Cao, Bihao;Chen, Changming;Liao, Yi;Gaut, Brandon S.;Emerson, J. J.;Wang, Juntao;Zhu, Zhangsheng;Lei, Jianjun;Cao, Bihao;Chen, Changming;Liu, Yuanlong;Liu, Yuanlong;Liu, Yuanlong;Chen, Jinfeng;Zhou, Yongfeng;Liu, Feng

作者机构：

期刊名称：NATURE COMMUNICATIONS （ 影响因子：17.694； 五年影响因子：17.763 ）

ISSN：

年卷期： 2022 年 13 卷 1 期

页码：

收录情况： SCI

摘要： The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression. 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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