Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton

文献类型： 外文期刊

第一作者： Hu, Guanjing

作者： Hu, Guanjing;Hu, Guanjing;Xiong, Xianpeng;Zhu, De;Li, Dongming;Grover, Corrinne E.;Miller, Emma R.;Conover, Justin L.;Wendel, Jonathan F.;Vera, Daniel L.;Bass, Hank W.;Lung, Pei-Yau;Sui, Xin;Zhang, Jinfeng;Girimurugan, Senthil B.;Conover, Justin L.;Conover, Justin L.;Ou, Shujun;Li, Dongming;Gallagher, Joseph P.;Udall, Joshua A.

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关键词： allopolyploidy; chromatin accessibility; nucleosome organization; cotton; genome dominance; homoeolog expression bias

期刊名称：MOLECULAR BIOLOGY AND EVOLUTION （ 影响因子：10.7； 五年影响因子：15.1 ）

ISSN： 0737-4038

年卷期： 2024 年 41 卷 5 期

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收录情况： SCI

摘要： Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.

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