Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube.

Ji Qing,Zhou Fan,Xu Yulan,Shen Bingqi,Zhou Jun,Wang Dawei

doi:10.7717/peerj.6353

Ji Qing, Zhou Fan + Show 4 more

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https://doi.org/10.7717/peerj.6353

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Abstract

The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analysis of MYB genes between jujube and Arabidopsis to predict that the functions of the ZjMYBs involve flavonoid/phenylpropanoid metabolism, the light signaling pathway, auxin signal transduction, and responses to various abiotic stresses (cold, drought, and salt stresses). Additionally, we speculate that ZjMYB108 is an important TF involved in the flavonoid metabolic pathway. This comprehensive analysis of MYB superfamily genes in jujube lay a solid foundation for future comprehensive analyses of ZjMYB gene functions.

Highlights

Transcription factors (TFs) play essential roles in plants by controlling the expression of genes, activating or inhibiting the transcription of other genes, or interacting with other transcription factor (TF) to regulate gene transcription (Singh, Foley & Onate-Sanchez, 2002; Liu, White & MacRae, 1999)
We performed the first genome-wide detailed analysis of jujube MYB superfamily genes, including 171 MYB genes. These 99 R2R3-MYB genes in jujube were divided into 35 groups, C1–C35, and 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups
A total of 93 expressed genes were identified from the RNA-sequencing data of jujube fruit, and 56 ZjMYB members presented a significant correlation with the total flavonoid contents by correlation analysis

Summary

Introduction

Transcription factors (TFs) play essential roles in plants by controlling the expression of genes, activating or inhibiting the transcription of other genes, or interacting with other TFs to regulate gene transcription (Singh, Foley & Onate-Sanchez, 2002; Liu, White & MacRae, 1999). As the Arabidopsis MYB gene family has gradually been identified (Stracke, Werber & Weisshaar, 2001; Yanhui et al, 2006), more MYB genes have been identified in many other plants (Zhang et al, 2018b; Li et al, 2016b; Hou et al, 2014; Zhou et al, 2015); these genes are identified by the family-specific feature of a highly conserved MYB domain at the N-terminus (Lipsick, 1996; Mmadi et al, 2017; Dubos et al, 2010). MYB genes are classified into the following subfamilies according to the number of MYB imperfect tandem repeats (Rs) of the proteins: MYB-related (or 1R-MYB, one R), R2R3-MYB (two Rs), R1R2R3-MYB (three Rs), and 4R-MYB (four Rs) (Dubos et al, 2010; Zhang et al, 2018b)

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