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- Title
Comparative genomic analyses reveal cis-regulatory divergence after polyploidization in cotton.
- Authors
Jiaqi You; Min Lin; Zhenping Liu; Liuling Pei; Yuexuan Long; Lili Tu; Xianlong Zhang; Maojun Wanga
- Abstract
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 transcriptional 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 arboreum, 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 analysis of transcription-factor binding sites (TFBS) for 262 known motifs: genes with higher TFBS conservation 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 polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.
- Subjects
COTTON genetics; POLYPLOIDY; COMPARATIVE genomics; GENE expression in plants; TRANSCRIPTION factors; PLANT physiology
- Publication
Crop Journal (2095-5421), 2022, Vol 10, Issue 6, p1545
- ISSN
2095-5421
- Publication type
Article
- DOI
10.1016/j.cj.2022.03.002