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Article|10 Mar 2021|OPEN
Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication
Le Zhang1,2, Jingtian Zhao1, Hao Bi1, Xiangyu Yang1, Zhiyang Zhang1, Yutao Su1, Zhenghao Li1, Brian J. Sanderson3, Jianquan Liu1,4, Tao Ma1, & Lei Zhang1,
1College of Computer Science & Medical Big Data Center of Sichuan University & Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, 610065 Chengdu, China
2Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 310024 Hangzhou, China
3Department of Biology, West Virginia University, Morgantown, WV 26506, USA
4State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, 730000 Lanzhou, China

Horticulture Research 8,
Article number: 62 (2021)
doi: 10.1038/hortres.2021.62
Views: 347

Received: 16 Jun 2020
Revised: 07 Dec 2020
Accepted: 03 Jan 2021
Published online: 10 Mar 2021

Abstract

The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.