Genome-wide investigation of AP2/ERF gene family in the desert legume Eremosparton songoricum: Identification, classification, evolution, and expression profiling under drought stress

Abstract

Eremosparton songoricum (Litv.) Vass. is a rare leafless legume shrub endemic to central Asia which grows on bare sand. It shows extreme drought tolerance and is being developed as a model organism for investigating morphological, physiological, and molecular adaptations to harsh desert environments. APETALA2/Ethylene Responsive Factor (AP2/ERF) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, our knowledge on the AP2/ERF family in legume species is limited, and no respective study was conducted so far on the desert shrubby legume E. songoricum. Here, 153 AP2/ERF genes were identified based on the E. songoricum genome data. EsAP2/ERFs covered AP2 (24 genes), DREB (59 genes), ERF (68 genes), and Soloist (2 genes) subfamilies, and lacked canonical RAV subfamily genes based on the widely used classification method. The DREB and ERF subfamilies were further divided into A1–A6 and B1–B6 groups, respectively. Protein motifs and exon-intron structures of EsAP2/ERFs were also examined, which matched the subfamily/group classification. Cis-acting element analysis suggested that EsAP2/ERF genes shared many stress- and hormone-related cis-regulatory elements. Moreover, the gene numbers and the ratio of each subfamily and the intron-exon structures were systematically compared with other model plants ranging from algae to angiosperms, including ten legumes. Our results supported the view that AP2 and ERF evolved early and already existed in algae, whereas RAV and DREB began to appear in moss species. Almost all plant AP2 and Soloist genes contained introns, whereas most DREB and ERF genes did not. The majority of EsAP2/ERFs were induced by drought stress based on RNA-seq data, EsDREBs were highly induced and had the largest number of differentially expressed genes in response to drought. Eight out of twelve representative EsAP2/ERFs were significantly up-regulated as assessed by RT-qPCR. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of AP2/ERF genes in E. songoricum and lays a foundation for better understanding of drought stress tolerance mechanisms in legume plants. Moreover, candidate genes for drought-resistant plant breeding are proposed.

Functional characterization of MdERF113 in apple

“…Consistent with AtRAP2.6L (Gao et al, 2020), MdERF113 is also localized in the nucleus when transiently expressed in epidermal cells of N. benthamiana . According to our findings and the results of previous articles, MdERF113 functions as a member of the ERF/AP2 TF family (Han et al, 2022; Xie et al, 2019; M. Zhao et al, 2022). Further bioinformatic analysis revealed that MdERF113 and AtRAP2.6L share a conserved AP2 structural domain (Figure 2B), which belonged to the AP2/ERF family.…”

“…MdERF113 is also localized in the nucleus when transiently expressed in epidermal cells of N. benthamiana. According to our findings and the results of previous articles, MdERF113 functions as a member of the ERF/AP2 TF family (Han et al, 2022;Xie et al, 2019;M. Zhao et al, 2022).…”

Genome-Wide Identification and Expression of the AP2/ERF Gene Family in Morus notabilis

“…Further division of the ERF family can be performed based on the DNAbinding domain, resulting in the ERF and DREB subfamilies [23]. The Soloist subfamily stands out due to substantial differences in its protein sequence characteristics and specific gene structures, warranting its classification as a distinct subfamily within the AP2/ERF family [24].…”

Genome-Wide Identification of the ERF Transcription Factor Family for Structure Analysis, Expression Pattern, and Response to Drought Stress in Populus alba × Populus glandulosa

“…The ERF family is divided into ERF and Dehydration-Responsive Element Binding (DREB) subfamilies according to cis-acting elements associated with ERF binding; ERF subfamily members bind to the ethylene response element GCC-box, while DREB subfamily members bind to the drought and low temperature response element DRE [ 11 ]. The RAV family is characterized by a conserved AP2/ERF domain at the N-terminus and a B3 domain at the C-terminus [ 12 ], while the soloist family contains an AP2/ERF conserved domain, but its gene structure is significantly different from that of other subfamilies [ 13 ]. AP2/ERF family members are important transcription factors in plants, and their functions cannot be replaced.…”