Abstract
BackgroundThe AP2/ERF transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses. Although AP2/ERFs have been thoroughly characterized in many plant species, little is known about this family in the model plant Brachypodium distachyon, especially those involved in the regulatory network of stress processes.ResultsIn this study, a comprehensive genome-wide search was performed to identify AP2/ERF gene family in Brachypodium and a total of 141 BdAP2/ERFs were obtained. Phylogenetic analysis classified them into four subfamilies, of which 112 belonged to ERF, four to RAV and 24 to AP2 as well as one to soloist subfamily respectively, which was in accordance with the number of AP2 domains and gene structure analysis. Chromosomal localization, gene structure, conserved protein motif and cis-regulatory elements as well as gene duplication events analysis were further performed to systematically investigate the evolutionary features of these BdAP2/ERF genes. Furthermore, the regulatory network between BdAP2/ERF and other genes were constructed using the orthology-based method, and 39 BdAP2/ERFs were found to be involved in the regulatory network and 517 network branches were identified. The expression profiles of BdAP2/ERF during development and under diverse stresses were investigated using the available RNA-seq and microarray data and ten tissue-specific and several stress-responsive BdAP2/ERF genes were identified. Finally, 11 AP2/ERF genes were selected to validate their expressions in different tissues and under different stress treatments using RT-PCR method and results verified that these AP2/ERFs were involved in various developmental and physiological processes.ConclusionsThis study for the first time reported the characteristics of the BdAP2/ERF family, which will provide the invaluable information for further evolutionary and functional studies of AP2/ERF in Brachypodium, and also contribute to better understanding the molecular basis for development and stresses tolerance in this model species and beyond.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2968-8) contains supplementary material, which is available to authorized users.
Highlights
The APETALA2/Ethylene responsive factor (AP2/ERF) transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses
The difference between them were further compared and results found that previous study considered the alternative splices transcripts encoded by the same gene into different AP2/ERF members, which resulted in the increase of the gene number
Since there is no standard nomenclature, the predicted BdAP2/ERF genes were designated as BdAP2/ERF001 to BdAP2/ERF141 based on their chromosome location and family classification (Table 1)
Summary
The AP2/ERF transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses. The AP2 subfamily members were the main factors involving in regulating organ architecture and development, such as leaf epidermal cell determinacy, spikelet meristem differentiation and floral organ patterning [12] as well as seed mass and seed yield [13, 14], while the RAV subfamily showed the important functions in plant hormone signal transduction, such as ethylene [15], Brassinosteroid [16], and involved in response to biotic and aboitic stresses [17, 18]. The DREB, together with other members in ERF subfamily mainly involved in response to biotic and abiotic stresses, such as water deficit [19], low and high temperature [20, 21] and high salinity [22]
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