Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in Jatropha curcas L

Abstract

JmjC domain-containing proteins, an important family of histone lysine demethylase, play significant roles in maintaining the homeostasis of histone methylation. In this study, we comprehensively analyzed the JmjC domain-containing gene family in Jatropha curcas and found 20 JmjC domain-containing genes (JcJMJ genes). Phylogenetic analysis revealed that these JcJMJ genes can be classified into five major subgroups, and genes in each subgroup had similar motif and domain composition. Cis-regulatory element analysis showed that the number and types of cis-regulatory elements owned by the promoter of JcJMJ genes in different subgroup were significantly different. Moreover, miRNA target prediction result revealed a complicated miRNA-mediated post-transcriptional regulatory network, in which JcJMJ genes were regulated by different numbers and types of miRNAs. Further analysis of the tissue and stress expression profiles showed that many JcJMJ genes had tissue and stress expression specificity. All these results provided valuable information for understanding the evolution of JcJMJ genes and the complex transcriptional and post transcriptional regulation involved, and laid the foundation for further functional analysis of JcJMJ genes.

Figure 1

Phylogenetic relationship of JMJ genes in J. curcas, Oryza sativa and Arabidopsis thaliana. JMJ genes are clustered into five groups which are marked by different colors. The bootstrap values are marked on the nodes with omitted “%”.

Figure 2

Schematic structure of JmjC domain-containing histone demethylase gene family in J. curcas L. Schematic representation of conserved domains identified among each subfamily of JcJMJs genes. The location and size of domains are shown by different color rectangles as indicated in the key.

Figure 3

Motifs and gene structures of JcJMJ genes in J. curcas. (A) Different kinds of motifs are marked by boxes with different colors. (B) Gene structure of 20 JcJMJ genes. UTRs and CDSs are marked by green and yellow boxes respectively. Grey rounded rectangles represent introns.

Figure 4

Chromosome locations and gene duplication events of JcJMJ genes in J. curcas. Gene names are on the right side of each chromosome according to the locations of JcJMJ genes. Segmentally duplicated genes are connected by pink line. Tandemly duplicated genes are connected by pink line and in the pink box.

Figure 5

Synteny analyses of the JMJ genes among the three species J. curcas, Oryza sativa and Arabidopsis thaliana. The collinear blocks within J. curcas and other specie genomes were displayed by the gray lines. The syntenic JMJ gene pairs between J. curcas and other species were highlighted with the red lines.

Figure 6

Cis-acting elements in the promoters of each JcJMJ gene. The length of the blue bar on the left indicates the number of cis-acting elements; The blue origin on the right indicates the site in the promoter of the gene that does not have the cis-acting element, while the red color indicates the site that does.

Figure 7

Regulatory networks between the conserved miRNAs and their targeted JcJMJ genes. The green and yellow rectangles represent miRNA and JcJMJs, respectively. The direction of the arrow indicates the direction of the target regulation.

Figure 8

Hierarchical clustering of the expression profiles of 20 JcJMJ genes in 6 tissues. The color scale representing log2 signal values is shown on the right. Blue represents a low level and red indicates a high level of transcript abundance. The different tissues and/or organs are noted on the bottom of each lane. Cluster dendrograms by row scale are shown on the left.

Figure 9

Expression patterns of JcJMJ genes under different treatments. Normalized log2 transformed values were used with hierarchical clustering represented by the color scale (− 3 to 3). Blue indicates low expression, and red indicates high expression. Cluster dendrograms by row scale are shown on the left.