Identification and expression analysis of AP2/ERF superfamily in pecan (Carya illinoensis)

AP2/ERF is a large transcription factors superfamily whose members are participated in the control of plant development, metabolism and response to various biotic and abiotic stresses. Nevertheless, few studies have been reported in pecan. In this study, a total of 170 CiAP2/ERF members were identified and divided into 4 main subfamilies, AP2 (16 genes), RAV (6 genes), Soloist (1 gene), as well as ERF (147 genes) families, and ERF subfamily was further classified into group I to VI-L. Gene structures and conserved motifs indicated that individual groups were highly conservative. A large number of cis-elements such as Box 4, ABRE, and MYB were detected in the promoter region of CiAP2/ERF genes. Transcriptional levels in four tissues were analyzed using available transcriptome data. qRT-PCR analysis of the ERF VII group revealed that the subfamily had a positive response to waterlogging stress. The subcellular localization experiments on CiAP2/ERF21, CiAP2/ERF65, and CiAP2/ERF106 manifested that they were localized in nuclear. Additionally, CiAP2/ERF65 and CiAP2/ERF106 had the ability of self-activation in yeast, while the CiAP2/ERF21 gene did not. These results would conduce to understanding the AP2/ERF superfamily and functional roles of CiAP2/ERF TFs under different stresses.

Automated summary

This study investigated the AP2/ERF superfamily in pecan and identified 170 gene members, which were further classified into different subfamilies and groups. Analysis of gene structures and conserved motifs revealed high conservation within each group. Various cis-elements were detected in the promoter region of CiAP2/ERF genes. Transcriptome data and qRT-PCR analysis suggested that certain subfamilies had a positive response to waterlogging stress. Subcellular localization experiments showed that some genes were localized in the nucleus and had self-activation ability.