Genome-wide identification, phylogeny, duplication, and expression analyses of two-component system genes in Chinese cabbage (Brassica rapa ssp. pekinensis)

Abstract

In plants, a two component system (TCS) composed of sensor histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs) has been employed in cytokinin signal transduction. A TCS exhibits important functions in diverse biological processes, including plant growth, development, and response to environmental stimuli. Conducting an exhaustive search of the Chinese cabbage genome, a total of 20 HK(L) (11 HKs and 9 HKLs), 8 HP (7 authentic and 1 pseudo), and 57 RR (21 Type-A, 17 Type-B, 4 Type-C, and 15 pseudo) proteins were identified. The structures, conserved domains, and phylogenetic relationships of these protein-coding genes were analysed in detail. The duplications, evolutionary patterns, and divergence of the TCS genes were investigated. The transcription levels of TCS genes in various tissues, organs, and developmental stages were further analysed to obtain information of the functions of these genes. Cytokinin-related binding elements were found in the putative promoter regions of Type-A BrRR genes. Furthermore, gene expression patterns to adverse environmental stresses (drought and high salinity) and exogenous phytohormones (tZ and ABA) were investigated. Numerous stress-responsive candidate genes were obtained. Our systematic analyses provided insights into the characterization of the TCS genes in Chinese cabbage and basis for further functional studies of such genes.

Keywords: Chinese cabbage; evolution; expression; phylogeny; two-component system.

Figure 1.

Phylogenetic relationships of HK proteins and related proteins in Chinese cabbage, Arabidopsis, rice, and soybean. The bar indicates the relative divergence of the sequences examined. This figure appears in colour in the online version of DNA Research.

Figure 2.

Phylogenetic relationships of HPt proteins and related proteins in Chinese cabbage, Arabidopsis, rice, and soybean. The bar indicates the relative divergence of the sequences examined.

Figure 3.

Phylogenetic relationships of RR proteins and related proteins in Chinese cabbage, Arabidopsis, rice, and soybean. The bar indicates the relative divergence of the sequences examined. This figure appears in colour in the online version of DNA Research.

Figure 4.

Chromosomal mapping of TCS genes in Chinese cabbage. The arrows next to gene names show the transcription direction.

Figure 5.

The Ks values distribution of the TCS genes in the genome of A. thaliana (At) and B. rapa (Br) viewed through the frequency distribution of Ks modes. Ks value distributions were obtained from duplicated paralogous genes pairs in the At genome (A) and Br genome (B) and duplicated orthologous gene pairs between the Br and At genomes (C). The vertical axis indicates the frequency of paired sequences, whereas the horizontal axis denotes the Ks values with a 0.1 interval. This figure appears in colour in the online version of DNA Research.

Figure 6.

Hierarchical clustering and heat map representation for the tissue- or organ-specific TCS gene expression profiles in Chinese cabbage. R, roots, S, floral stems, L, leaves, LB, little buds, MB, medium-buds, BB, big buds, F, flowers, Se, sepals, Pe, petals, St, stamens, Pi, pistils, LS, little siliques, MS, medium-sized siliques, and BS, big siliques. The expression levels of genes are presented using fold-change values transformed to Log₂ format. This figure appears in colour in the online version of DNA Research.

Figure 7.

Hierarchical clustering and heat map representation for the response patterns to drought and high salinity conditions of TCS genes in Chinese cabbage roots. The expression levels of genes are presented using fold-change values transformed to Log₂ format compared with control. This figure appears in colour in the online version of DNA Research.

Figure 8.

Hierarchical clustering and heat map representation for the response patterns to exogenous tZ of TCS genes in Chinese cabbage leaves. The expression levels of genes are presented using fold-change values transformed to Log₂ format compared with control. This figure appears in colour in the online version of DNA Research.

Figure 9.

Hierarchical clustering and heat map representation for the response patterns to exogenous ABA of TCS genes in Chinese cabbage leaves. The expression levels of genes are presented using fold-change values transformed to Log₂ format compared with the control. This figure appears in colour in the online version of DNA Research.