Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton

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: Abiotic stress; Early maturity; Expression patterns; Gossypium; Histone deacetylases.

Fig. 1

Neighbor-joining phylogenetic tree of RPD3 gene family. The 108 predicted RPD3 proteins from G. hirsutum, G. arboreum, G. barbadense, G. raimondii, A. thaliana, P. trichocarpa, T. cacao, Oryza sativa, and Zea mays were aligned using ClustalW, and the neighbor-joining (NJ) method was used to construct this unrooted phylogenetic tree using MEGA 7.0 program with 1000 bootstrap repetitions. Four subfamilies are represented by the different colored lines

Fig. 2

Phylogenetic relationships, exon-intron structure, and conversed motif analysis of cotton RPD3 genes. a A neighbor-joining phylogenetic tree of 54 cotton RPD3 genes was generated using the MEGA7.0 program; (b) Exon-intron structure analysis of 54 cotton RPD3 genes. The UTRs, exons, and introns are represented with yellow boxes, green boxes, and black lines, respectively; (c) The 10 conversed protein motifs of RPD3 genes are indicated by different colored boxes

Fig. 3

Chromosomal distribution of cotton RPD3 genes. a, b, c and d represent the chromosomal location of RPD3 genes from G. hirsutum (a), G. barbadense (b), G. arboreum (c), and G. raimondii (d), respectively. The chromosome number is shown on the top of each chromosome. The scale bars represent the length in mega bases (Mb)

Fig. 4

RPD3 homologous gene pairs among G. arboreum, G. raimondii and G. hirsutum. Orange, blue and red represent chromosomes of G. arboreum, G. raimondii and G. hirsutum, respectively

Fig. 5

Cis-elements of GhRPD3 genes in promoter regions. The numbers of different cis-elements are presented in the form of bar graphs, and similar cis-elements are exhibited with the same colors

Fig. 6

Expression patterns of RPD3 genes in G. hirsutum. a and b represent the expression patterns of GhRPD3 genes in different tissues (a) and under four different abiotic stresses (b), respectively. Gene names are shown on the right. Scale bars on the right represent the log2-transformed FPKM values of each gene

Fig. 7

Expression levels of 9 GhRPD3 genes between CCRI50 and GX11. Blue and orange bar graphs indicate the expression of early-maturity cotton (CCRI 50) and late-maturity cotton (GX11), respectively. The error bars show the standard deviation of three biological replicates

Fig. 8

Expression profiles of 13 GhRPD3 genes under MeJA treatment. Orange boxes represent the MeJA-responsive elements of 13 GhRPD3 genes in the promoter regions (left). The expression changes of 13 GhRPD3 genes under MeJA treatment are shown using a heatmap (right). qRT-PCR was carried out with three technical and three biological replicates. Relative expression levels of each gene were calculated after normalizing the expression level in CK (water) to 1.0

Fig. 9

Expression patterns of 11 GhRPD3 genes under ABA treatment. Green boxes represent the ABRE of 11 GhRPD3 genes in the promoter regions (left). The expression changes of 11 GhRPD3 genes under ABA treatment are shown using a heatmap (right). qRT-PCR was conducted with three technical and three biological replicates. Relative expression levels of each gene were calculated after normalizing the expression level in CK (water) to 1.0