JmjC domain-containing histone demethylase gene family in Chinese cabbage: Genome-wide identification and expressional profiling

Abstract

The Jumonji C (JmjC) structural domain-containing gene family plays essential roles in stress responses. However, descriptions of this family in Brassica rapa ssp. pekinensis (Chinese cabbage) are still scarce. In this study, we identified 29 members of the BrJMJ gene family, with cis-acting elements related to light, low temperature, anaerobic conditions, and phytohormone responses. Most BrJMJs were highly expressed in the siliques and flowers, suggesting that histone demethylation may play a crucial role in reproductive organ development. The expression of BrJMJ1, BrJMJ2, BrJMJ5, BrJMJ13, BrJMJ21 and BrJMJ24 gradually increased with higher Cd concentration under Cd stress, while BrJMJ4 and BrJMJ29 could be induced by osmotic, salt, cold, and heat stress. These results demonstrate that BrJMJs are responsive to abiotic stress and support future analysis of their biological functions.

Fig 1. Phylogenetic relationships of JmjC family members in Brassica rapa (Br), Arabidopsis thaliana (At), Zea mays (Zm), Oryza sativa (Os), Betula platyphylla (Bp), and Glycine max (Gm).

Using MEGA11.0, a phylogenetic tree was constructed for 158 JmjC protein sequences from the six species. Red stars, pink circles, orange stars, yellow triangles, pink triangles, and blue starts: Br, At, Zm, Os, Bp, and Gm, respectively.

Fig 2. Conserved structural domains of BrJMJ proteins in Chinese cabbage.

JmjC, Jumonji C domain; JmjN, Jumonji N domain; DEXDc, DEAD-like helicases superfamily; HELICc, Helicase superfamily c-terminal domain; PHD, plant homeobox domain; ARID, AT-rich interaction domain; FYRC, “FY-rich” domain C-terminal; FYRN, “FY-rich” domain N-terminal; F-box FBOX a receptor for ubiquitination targets; ZnF_C2H2, zinc-finger of C2H2-type; AT_hook, DNA binding domain with preference for A/T rich regions; DM, Dsx and Mab-3; RING, really interesting new gene (A). Gene structure analysis of BrJMJs in Chinese cabbage, green boxes, exons; black lines, introns. The sizes of exons and introns can be estimated using the scale at the bottom (B).

Fig 3. Cis-acting elements of BrJMJs in Brassica rapa.

Different color blocks represent different components. Relative frequencies in BrJMJs of promoter cis-regulatory elements (CREs), including environment and stress-responsive CREs, phytohormone response CREs, and growth and biological process-responsive CREs.

Fig 4

Chromosome distribution (A) and schematic representation of inter-chromosomal relationships (B) of the BrJMJs in Brassica rapa. Repeated BrJMJ pairs are highlighted with red lines.

Fig 5. Tissue-specific BrJMJ expression.

The heatmap was constructed using TBtools, based on the fragments per kilobase of transcripts per million mapped reads (FPKM) values of BrJMJs in the tissue-specific transcriptome data.

Fig 6. Profiling of BrJMJ expression under Cd stress.

Variation in BrJMJ gene expression with Cd stress, via qRT–PCR, with BrACTIN7 as an internal reference gene. BrJMJ relative expression was calculated using the 2^−ΔΔCt method. The results were visualized as a heatmap using TBtools (A). Growth status of Chinese cabbage under Cd stress. Scale bar, 4 cm (B). Using the same RT-qPCR results as in Fig 6A, a histogram of representative genes were generated to analyze significance. Brassica rapa growth varied significantly under Cd stress, with different lowercase letters indicating significant differences (p<0.05). The x axis represents different concentrations of Cd stress treatment, and the y axis represents relative expression (C).

Fig 7. Profiling of BrJMJ expression under other abiotic stresses.

Expression under drought, salt, cold, and heat stress of the 29 BrJMJs, via qRT–PCR. BrACTIN7 was an internal reference gene. BrJMJ relative expression was calculated using the 2^−ΔΔCt method. The results were visualized as a heatmap using TBtools (A). The significant changes of representative genes under four abiotic stresses are indicated by the length of vertical lines (p<0.05). Red polyline, green polyline, blue polyline and purple polyline are respectively represented Expression under osmotic, salt, cold, and heat stress of the 29 BrJMJs. The x axis represents the different treatment times of the four abiotic stresses (osmotic, salt, cold, and heat stress), and the y axis represents the relative expression (B).