Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton
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RESEARCH ARTICLE
Open Access
Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton Jingjing Zhang, Aimin Wu, Hengling Wei, Pengbo Hao, Qi Zhang, Miaomiao Tian, Xu Yang, Shuaishuai Cheng, Xiaokang Fu, Liang Ma, Hantao Wang* and Shuxun Yu*
Abstract Background: Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. Results: In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. Conclusions: Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future. Keywords: Gossypium, Histone deacetylases, Expression patterns, Abiotic stress, Early maturity
Background DNA combines with nuclear proteins to constitute the chromatin, which is responsible for storing genetic and directive information in eukaryotic cells. Chromatin is highly arranged and mainly composed of nucleosomes, which are formed by approximately 147 bp of DNA and an octamer organized by the four core histone proteins_ * Correspondence: [email protected]; [email protected] State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
H3, H4, H2A, and H2B [1]. Gene expression in eukaryotes involves a complicated interaction, which is controlled not only by the DNA sequence but also by epigenetic events. Epigenetic mechanisms mainly consist of histone modification and DNA methylation, and play an important role in the regulatio
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