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

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.

Genome-wide identification and characterization of AP2/ERF gene superfamily during flower development in Actinidia eriantha

“…AtDDF2 most abundantly expressed in rosette leaves and stems, conversely, AeAP2/ERF081 did not express, which suggested that the functions gradually appeared divergence during evolution. The similar pattern was found in ginger ( Zingiber officinale ) [ 53 ]. Additionally, partial genes have high transcription abundance.…”

Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

“…The reason for this phenomenon may be due to the ftsH gene duplication or gene loss during the evolution of the tobacco plant, resulting in the absence of the ftsH gene on some chromosomes and the appearance of multiple genes on others. In addition, the frequency of gene occurrence was not related to chromosome length and gene density [26].…”

“…From tobacco's whole genome sequence data, we identified 20 members of the ftsH gene family (Additional file 1: Table S1). The genes were renamed according to their order and position on the chromosome, from NtftsH1 to NtftsH20 [26]. At the same time, the physicochemical properties and subcellular localization of gene sequences were analyzed.…”

Genome-Wide Identification of AP2/ERF Transcription Factor Family and Functional Analysis of DcAP2/ERF#96 Associated with Abiotic Stress in Dendrobium catenatum

“…Members of the AP2/ERF family have been identified and scaled in many species, including 146 in Arabidopsis thaliana [ 11 ], 163 in Oryza sativa [ 11 ], 134 in Fagopyum Tataricum [ 14 ], 364 in Salix matsudana [ 15 ], 163 in Zingiber officinale [ 16 ], 322 in Triticum aestivum [ 17 ], 189 in Panax ginseng [ 18 ] and 531 in Brassica campestris [ 19 ]. AP2/ERF transcription factor family has been confirmed to be involved in a variety of abiotic stress responses; for example, AtCBF1/2/3 control low temperature responses in Arabidopsis [ 20 , 21 ], ZmDREB2a participates in heat response in maize [ 22 ], and GmERF4/7 mediate salt stress response in soybean [ 23 ].…”