LAUSR

Significance Polyploidization may cause reshuffling of gene expression accompanied by changes in chromatin-structure dynamic. In eukaryotes, gene expression is regulated via the complex interplay between transcription factors and cis-regulatory DNA elements (CREs) in regions of open chromatin. We reveal that chromatin accessibility, displaying distinct distributions in diploid progenitors, shows a convergent change during polyploidization in cotton. We propose that this convergent change might be a common feature in polyploids, and not a consequence of domestication after polyploidization. Moreover, we show that the coordinated interplay among histone modifications, transposable elements, and CREs drove open chromatin dynamics under polyploidization. This study presents a holistic view of the regulatory landscape changes during polyploidization.