Genome-wide Chromatin Accessibility Analysis Unveils Open Chromatin Convergent Evolution During Polyploidization in Cotton

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2022 Oct 24

PMID 36279429

Authors

Jinlei Han

Damar Lopez-Arredondo

Guangrun Yu

Yankun Wang

Baohua Wang

Sarah Brooke Wall

Xin Zhang

Hui Fang

Alfonso Carlos Barragan-Rosillo

Xiaoping Pan

Yanqin Jiang

Jingbo Chen

Hui Zhang

Bao-Liang Zhou

Luis Herrera-Estrella

Baohong Zhang

Kai Wang

Affiliations

Soon will be listed here.

Abstract

Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a "genome shock", leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton ( and , AADD) and its extant AA () and DD () progenitors. We observed distinct DHS distributions between and . In contrast, the DHSs of the two subgenomes of and showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids and var. , but absent from a resynthesized hybrid of and , suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative -regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.

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