Genome-wide identification and expression profile analysis of WRKY family genes in the autopolyploid saccharum spontaneum

Zhen Li, Xiuting Hua, Weiming Zhong, Yuan Yuan, Yongjun Wang, Zhengchao Wang, Ray Ming, Jisen Zhang

Research output: Contribution to journalArticle

Abstract

WRKY is one of the largest transcription factor families in plants and plays important roles in the regulation of developmental and physiological processes. To date, the WRKY gene family has not been identified in Saccharum species because of its complex polyploid genome. In this study, a total of 294 sequences for 154 SsWRKY genes were identified in the polyploid Saccharum spontaneum genome and then named on the basis of their chromosome locations, including 13 (8.4%) genes with four alleles, 29 (18.8%) genes with three alleles and 41 (26.6%) genes with two alleles. Among them, 73.8% and 16.0% of the SsWRKY genes originated from segmental duplications and tandem duplications, respectively. The WRKY members exhibited conserved gene structures and amino acid sequences among the allelic haplotypes, which were accompanied by variations in intron sizes. Phylogenetic and collinearity analyses revealed that 27 SsWRKYs originated after the split of sorghum and Saccharum, resulting in a significantly higher number of WRKYs in sugarcane than in the proximal diploid species sorghum. The analysis of RNA-seq data revealed that SsWRKYs' expression profiles in 46 different samples including different developmental stages revealed distinct temporal and spatial patterns with 52 genes expressed in all tissues, four genes not expressed in any tissues and 21 SsWRKY genes likely to be involved in photosynthesis. The comprehensive analysis of SsWRKYs' expression will provide an important and valuable foundation for further investigation of the regulatory mechanisms of WRKYs in physiological roles in sugarcane S. spontaneum.

Original languageEnglish (US)
Pages (from-to)616-630
Number of pages15
JournalPlant and Cell Physiology
Volume61
Issue number3
DOIs
StatePublished - Mar 1 2020

Keywords

  • Expression profiles
  • Genome wide
  • Phylogenetic analysis
  • Saccharum spontaneum
  • WRKY family

ASJC Scopus subject areas

  • Physiology
  • Plant Science
  • Cell Biology

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