Comparative genomic analyses reveal cis-regulatory divergence after polyploidization in cotton

Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty. However, knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited. In this study, we characterized tran-scriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors. We identified 144,827, 99,609, and 219,379 Tn5 transposase-hypersensitive sites (THSs) in Gossypium arbor-eum, G. raimondii, and G. hirsutum, respectively, and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression. This observation was consistent with anal-ysis of transcription-factor binding sites (TFBS) for 262 known motifs: genes with higher TFBS conserva-tion scores (CS) showed less change than those genes with lower TFBS CS in expression levels. TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton. We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development (fiber-related genes). Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidiza-tion and characterizes the regulatory relationships of genes contributing to desirable traits.(c) 2022 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC -ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Automated summary

This study characterizes the regulatory divergence of the transcriptional network in cotton after polyploidization. Conservation of promoter sites and transcription factor binding sites (TFBS) is associated with coordinated gene expression. Genomic variations in TFBS contribute to the formation of novel regulatory networks in tetraploid cotton. The turnover of TFBS is linked to expression pattern divergence of genes involved in fiber development.