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

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成果类型：

期刊论文

作者：

Liao, Yi;Wang, Juntao;Zhu, Zhangsheng;Liu, Yuanlong;Chen, Jinfeng;...

通讯作者：

Emerson, J.J.;Cao, B.;Chen, C.

作者机构：

[Liao, Yi; Wang, Juntao; Lei, Jianjun; Zhu, Zhangsheng] Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China

[Liao, Yi; Gaut, Brandon S.] Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA

[Wang, Juntao; Lei, Jianjun; Zhu, Zhangsheng] Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China

[Liu, Yuanlong] Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

[Liu, Yuanlong] Swiss Cancer Center Leman, Lausanne, Switzerland

通讯机构：

[Cao, Bihao; Chen, Changming] K

[Emerson, J. J.] D

Department of Ecology and Evolutionary Biology, University of California, Irvine, USA<&wdkj&>Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, China<&wdkj&>Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China

语种：

英文

期刊：

Nature Communications

ISSN：

2041-1723

年：

2022

卷：

期：

页码：

3479

DOI：

10.1038/s41467-022-31112-x

基金类别：

This work was funded by the National Natural Science Foundation of China (32070331, U21A20230, 32102380, and 32072580), the Guangdong Basic and Applied Basic Research Foundation (2020A1515011396), the National Key Research and Development Program (2018YFD1000800), and Strategic Priority Research Program of Chinese Academy of Sciences (XDPB16). This work was jointly funded by National Institutes of Health (R01GM123303), National Science Foundation (IOS-1656260), and start-up funding from the University of California, Irvine to J.J.E. We are grateful to Dr. Shujun Ou (Johns Hopkins University, USA) and Hongru Wang (University of California Berkeley, USA) for discussions and advice on the project. We also thank Frasergen Bioinformatics Co., Ltd (Wuhan, China) and Shanghai Jiayin Biotechnology Co., Ltd for Tech & Expert Services.

机构署名：

本校为其他机构

院系归属：

园艺园林学院

摘要：

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 loo...

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

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