Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

Abstract

Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

Genome-Wide Analysis of AP2/ERF Superfamily Genes in Contrasting Wheat Genotypes Reveals Heat Stress-Related Candidate Genes

“…It is also supported by the presence of a larger number of intronless genes in these sub-families, leading to functional evolution and stress adaptation ( Shu et al, 2015 ; Faraji et al, 2020 ). Similar nature of AP2/ERF gene structure has also been reported in Arabidopsis , tartary buckwheat ( Lata et al, 2014 ), sweet potato ( He et al, 2021 ), dark jute ( Kabir et al, 2021 ). Thus, structural features of genes are directly associated with the expression pattern of genes, which determines their functional characters and makes TaERF and TaDREB sub-family genes more heat-responsive as compared to TaAP2 and TaRAV family genes under HS.…”

“…This shows that some TaAP2/ERF genes are more important than others in response to abiotic stresses. The regulatory role of AP2/ERF family genes under various abiotic stress has also been reported in a diverse range of plant species ( Faraji et al, 2020 ; Hao et al, 2020 ; He et al, 2021 ; Kabir et al, 2021 ; Riaz et al, 2021 ; Xing et al, 2021 ; Zhou and Yarra, 2021 ).…”

“…In this study, we identified 517 AP2/ERF genes with at least one AP2-domain in the wheat genome, which is four times higher than in jute (119 genes; Kabir et al, 2021 ), more than three times higher than in buckwheat (134 genes), Arabidopsis (147 genes), rice (164 genes), foxtail millet (171 genes), and oil palm (172 genes; Nakano et al, 2006 ; Lata et al, 2014 ; Liu et al, 2019 ; Zhou and Yarra, 2021 ) and more than double as in sweet potato (198 genes) and durum wheat (271; Faraji et al, 2020 ; He et al, 2021 ). This larger number of genes signifies the hexaploid nature of the wheat genome.…”

ERF subfamily transcription factors and their function in plant responses to abiotic stresses

“… Phylogenetic relationships of ERF family members. The phylogenetic analysis of the ERF subfamily of Nicotiana tabacum , Arabidopsis thaliana , Glycine max , Oryza sativa , Triticum aestivum , and Zea mays by MEGA7.0 ( Kumar et al., 2016 ), constructed the tree using the neighbor joining method and 1000 bootstrap replicates and used iTOL ( ) to visualize the tree ( He et al., 2021 ; Magar et al., 2022 ). The category of functional annotated ERFs mentioned in this review which are listed in Supplementary Table S2 are labeled with black star markers.…”

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 the largest family in the AP2/ERF superfamily and has been widely reported in Manihot esculenta Crantz [ 33 ] and Ipomoea batatas (L.) Lam [ 34 ]; for example, 170 ERFs have been identified in P. trichocarpa [ 35 ] and 147 ERFs have been identified in Manihot esculenta [ 36 ]. Although ERF transcription factors in Populus trichocarpa were identified [ 37 ] and shown to respond to abiotic stresses such as salt stress [ 11 ], the molecular mechanism of ERF transcription factors in response to drought stress in poplar remains unknown.…”