Abstract
The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TFs) in plants that play a vital role in regulating plant growth, development, and stress response. A total of 202 AP2/ERF genes were identified from the pecan genome and renamed according to the chromosomal distribution of the CiAP2/ERF genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 AP2, 168 ERF, six RAV, and two Soloist gene family members. These genes were distributed randomly across the 16 chromosomes, and we found 19 tandem and 146 segmental duplications which arose from ancient duplication events. The gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of AP2/ERFs. The expression profiling of 202 CiAP2/ERF genes was assessed by using RNA-Seq data and qRT-PCR during development (pistillate flowering development, graft union development, and kernel development) and under abiotic stresses (waterlogging, drought). Moreover, the results suggested that the ERF-VII members may play a critical role in waterlogging stress. These findings provided new insights into AP2/ERF gene evolution and divergence in pecan and can be considered a valuable resource for further functional validation, as well as for utilization in a stress-resistance-variety development program.
Highlights
Transcription factors (TFs), one of the master regulatory proteins types, perform a key role in the plant response to a range of abiotic and biotic stresses [1]
The YRG element is located at the N-terminal of the AP2 domain consisting of about 19–22 amino acid residues, and the RAYD element is located at the C-terminal consisting of about 43 amino acid residues [5]
A total of 202 APETALA2/Ethylene Responsive Factor (AP2/ERF) genes from the pecan genome were identified (Table 1 and Supplementary Table S1), and identified AP2/ERF genes were categorized into four families (ERF, AP2, RAV, and Soloist) depending on the occurrence of conserved AP2 domains
Summary
Transcription factors (TFs), one of the master regulatory proteins types, perform a key role in the plant response to a range of abiotic and biotic stresses [1]. The AP2/ERF transcription factors contain one or two highly conserved AP2 DNA binding domains with 60–70 amino acid residues that consist of three-stranded anti-parallel β-sheets, followed by a parallel α-helix [4]. The AP2 domain contains two conserved elements (YRG and RAYD). The AP2/ERF TFs have been classified into the AP2, ERF, RAV, and Soloist subfamilies [6]. The AP2 subfamily contains either single or double AP2 domains and plays an important role in the plant developmental processes [7]. A small group of TFs containing one AP2 domain, but a different structure, was classified as being in the Soloist subfamily [6]
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