Abstract
BackgroundIn 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.ResultsHere, 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.ConclusionsThis 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.
Highlights
One of the largest gene families in plants is the AP2/ERF transcription factor (TF) superfamily, which includes at least one APETALA2 (AP2) domain comprising approximately 60 amino acid residues and is significant to the regulation of plant development and the response to various types of stress [1, 2]
The BLASTP programme with an e-value of 1e− 5 and identity of 50% as the threshold was used to search against the sweet potato protein dataset by using the AP2/ERF protein sequences of rice and Arabidopsis obtained from the plant transcription factor database as the query
The chromosome distribution results showed that these IbAP2/ERF genes were located on all 15 chromosomes in the sweet potato
Summary
One of the largest gene families in plants is the AP2/ERF transcription factor (TF) superfamily, which includes at least one APETALA2 (AP2) domain comprising approximately 60 amino acid residues and is significant to the regulation of plant development and the response to various types of stress [1, 2]. By the rule of the components of conserved domains, AP2/ERF TFs can be separated into ERF, AP2 and RAV gene subfamilies [3,4,5]. With the exception of one single AP2 domain, the RAV subfamily includes a B3 DNA binding domain that is conserved in other plant-specific transcription factors [6]. The sequences of the AP2 domain are highly conserved, the DNA binding elements of each subfamily are totally different. A comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato
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