Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum)

Abstract

Background AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis thaliana ( A. thaliana ) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of tartary buckwheat ( Fagopyum tataricum ), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allowed us to study the tissue and expression profiles of AP2/ERF genes in tartary buckwheat on a genome-wide basis. Results In this study, 134 AP2/ERF genes of tartary buckwheat ( FtAP2/ERF ) were identified and renamed according to the chromosomal distribution of the FtAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic tree analysis, namely, AP2 (15 members), ERF (116 members) and RAV (3 members). A total of 10 motifs were detected in tartary buckwheat AP2/ERF genes, and some of the unique motifs were found to be important for the function of AP2/ERF genes. Conclusion A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and fruit development stages by quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of FtAP2/ERF genes and improvement of tartary buckwheat crops. Electronic supplementary material The online version of this article (10.1186/s12870-019-1681-6) contains supplementary material, which is available to authorized users.

Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour

“…The motif analysis of the DlAP2/ERF superfamily showed that most of the AP2/ERF superfamily members contained motif-1, motif-2, motif-3, and motif-4 related to the AP2 domain. This result is similar to what was found in tartary buckwheat [37]. Motif-6 and motif-10 were detected specifically in the AP2 family, indicating that they may play a unique role in the AP2 family.…”

“…Although some motifs of the AP2/ERF superfamily were highly conserved, the unique motifs in different groups may have important functions in longan; however, these functions require further investigation. Structural analysis of the AP2/ERF superfamily showed that 82% of the DlERF and all of the DlRAV genes had no intron, whereas the AP2 family and Soloist genes had from one to nine introns, which is similar to what was found for AP2/ERF genes in tartary buckwheat [37]. The differences between the structures of ERF, RAV, and AP2 family genes indicated that they had largely differentiated during the evolution of the longan genome, and thus may have great functional differentiation.…”

“…Tissue-specific expression profiles indicated that most of the DlAP2/ERF genes were expressed in almost all organs (96%), and 57.9% of the AP2 family genes were expressed at high levels in root, which is similar to what was found in Chinese cabbage and tartary buckwheat [29,37]. The phylogenetic analysis showed that two AP2 genes, Dlo_009234.2 (RAP2.7) and Dlo_007774.3 (RAP2.7) that were highly expressed in young fruit, flower bud, and flower clustered together.…”

Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana)

“…Previous studies found that intron number and distribution are related to plant evolution, and introns of the ERF family genes were probably lost during evolution in higher plants [27,28]. In total, 215 of the 301 members (70%) of the ERF family had no introns, which was a little less than that of tartary buckwheat [24] and also consistent with previous findings.…”

“…S1). For example, the WLG element (58th-60th amino acids; 58-60AA) was highly conserved in in the ERF and RAV families; alternatively, in the AP2 family, the conserved sequences from 58-60AA were converted into YLG elements [24]. In many species, these conserved amino acid profiles contribute to convincing classification of AP2/ERF genes.…”