Genome-wide identification and analysis of MAPK and MAPKK gene family in Chinese jujube (Ziziphus jujuba Mill.)

Abstract

Background: Chinese jujube (Ziziphus jujuba Mill.) is one of the most important members in the Rhamnaceae family. The whole genome sequence and more than 30,000 proteins of Chinese jujube have been obtained in 2014. Mitogen-activated protein kinase cascades are universal signal transduction modules in plants, which is rapidly activated under various biotic and abiotic stresses. To date, there has been no comprehensive analysis of the MAPK and MAPKK gene family in Chinese jujube at the whole genome level.

Results: By performing a series of bioinformatics analysis, ten MAPK and five MAPKK genes were identified from the genome database of Chinese jujube, and then compared with the homologous genes from Arabidopsis. Phylogenetic analysis showed that ZjMAPKs was classified into four known groups, including A, B, C and D. ZjMAPKs contains five members of the TEY phosphorylation site and five members with the TDY motif. The ZjMAPKK family was subsequently divided into three groups, A, B and D. The gene structure, conserved motifs, functional annotation and chromosome distribution of ZjMAPKs and ZjMAPKKs were also predicted. ZjMAPKs and ZjMAPKKs were distributed on nine pseudo-chromosomes of Chinese jujube. Subsequently, expression analysis of ZjMAPK and ZjMAPKK genes using reverse transcription PCR and quantitative real-time PCR was carried out. The majority of ZjMAPK and ZjMAPKK genes were expressed in all tested organs/tissues with considerable differences in transcript levels indicating that they might be constitutively expressed. Moreover, ZjMKK5 was specific expressed in early development stage of jujube flower bud, indicating it plays some roles in reproductive organs development. The transcript expression of most ZjMAPK and ZjMAPKK genes was down-regulated in response to plant growth regulators, darkness treatment and phytoplasma infection.

Conclusions: We identified ten ZjMAPK and five ZjMAPKK genes from the genome database of Chinese jujube, the research results shown that ZjMPKs and ZjMKKs have the different expression patterns, indicating that they might play different roles in response to various treatments. The results provide valuable information for the further elucidation of physiological functions and biological roles of jujube MAPKs and MAPKKs.

Keywords: Bioinformatics analysis; Chinese jujube; Gene expression; MAPKKs; MAPKs.

Fig. 1

Positions of ZjMPK and ZjMKK genes on the jujube chromosomes. Genes were mapped to the jujube chromosomes via the Circos tool. The jujube chromosomes were arranged in a circle

Fig. 2

Multiple sequence alignment of the kinase domains of ZjMPK and ZjMKK proteins

Fig. 3

The exon/intron structure of 9 ZjMPK genes in Chinese jujube. Introns and exons are represented by black lines and green boxes respectively. The length in base pairs of each intron and exon is also indicated

Fig. 4

The exon/intron structure of 5 ZjMKK genes in Chinese jujube. Introns and exons are represented by black lines and blue boxes respectively. Introns and exons are represented by black lines and green boxes respectively. The length in base pairs of each intron and exon is also indicated. Numbers correspond to the length of the intron and exon

Fig. 5

Phylogenetic relationships of MPK genes from Chinese jujube and Arabidopsis

Fig. 6

Phylogenetic relationships of MKK genes from Chinese jujube and Arabidopsis

Fig. 7

Tissue-specific expression patterns for ZjMPKs. ZjACT was used as an internal control. From left to right: root, bearing shoot, secondary shoot, leaf, flower bud, flower, and fruit

Fig. 8

Tissue-specific expression patterns for ZjMKKs. ZjACT was used as an internal control. From left to right: root, bearing shoot, secondary shoot, leaf, flower bud, flower, and fruit

Fig. 9

Relative expression of ZjMPK and ZjMKK genes analyzed by qRT-PCR upon plant growth regulators treatment. ZjACT primers were used as the internal standard for each gene. The mean expression value was calculated from 3 independent replicates. The vertical bars indicate the standard deviation. Significant and highly significant difference are shown as * (P < 0.05) and ** (P < 0.01), respectively

Fig. 10

Relative expression of ZjMPK and ZjMKK genes analyzed by qRT-PCR upon darkness treatment. ZjACT primers were used as the internal standard for each gene. The mean expression value was calculated from 3 independent replicates. The vertical bars indicate the standard deviation. Significant and highly significant difference are shown as * (P < 0.05) and ** (P < 0.01), respectively

Fig. 11

Relative expression of ZjMPK and ZjMKK genes analyzed by qRT-PCR under phytoplasma infection. ZjACT primers were used as the internal standard for each gene. The mean expression value was calculated from 3 independent replicates. The vertical bars indicate the standard deviation. Significant and highly significant difference are shown as * (P < 0.05) and ** (P < 0.01), respectively