Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

BMC Plant Biol. 2021 Nov 25;21(1):561. doi: 10.1186/s12870-021-03329-3.

Abstract

Background: AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis.

Results: A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger.

Conclusion: A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

Keywords: Abiotic stress; Expression patterns; Ginger; Inflorescence/rhizome development; ZoAP2/ERF.

MeSH terms

  • Adaptation, Physiological / genetics*
  • Crops, Agricultural / genetics
  • Crops, Agricultural / growth & development
  • Evolution, Molecular
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genes, Plant
  • Genome, Plant
  • Genome-Wide Association Study
  • Ginger / genetics*
  • Ginger / growth & development*
  • Multigene Family*
  • Phylogeny
  • Stress, Physiological / genetics*
  • Transcription Factor AP-2 / genetics*

Substances

  • Transcription Factor AP-2