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

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.

Comparative Analysis of MicroRNA Expression in Three Paulownia Species with Phytoplasma Infection

“…In PaWB seedlings, miR160a-5p, miR172a-3p, and miR172d were down-regulated and their targets RAV, AP2, and EREBP were up-regulated. AP2 and EREBP are members of the AP2/ERF superfamily, which plays vital roles in regulating various developmental and physiological processes in plants [40]. In Arabidopsis, overabundance of the AP2/ERF transcription factor (WIND1) increased the B-type ARR-mediated cytokinin response, which also promoted cell dedifferentiation [41].…”

Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta

“…This TF family is associated with a few other pleiotropic roles, like regulating stress tolerance via expression of genes involved in abiotic stress response, disease resistance and ethylene/jasmonic acid/salicylic acid response (Cui et al, 2016; Guo et al, 2016). Based on the number of AP2/ERF DNA binding domains they possess, the AP2/ERF family is further classified into four subfamilies, namely ERF, DREB (one AP2/ERF domain); AP2 (two AP2/ERF domains) and RAV (one AP2 and an additional B3 DNA binding domain; Licausi et al, 2013; Guo et al, 2016; Huang Z. et al, 2016).…”

Besides and beyond Flowering: Other Roles of EuAP2 Genes in Plant Development

“…It is usually the largest subfamily within the ERF/AP2 superfamily in most plant species whose genomes have been studied. It is subdivided into ten groups, broadly divided into dehydration-responsive element binding-proteins (DREB) comprising groups I-IV and ethylene response factor made up of groups V-X [9,10,14]. • RAV (RAV for related to AB13/VP1): This subfamily is characterized by the possession of a B3 domain in addition to a single AP2 domain [9,14,15].…”

“…It is subdivided into ten groups, broadly divided into dehydration-responsive element binding-proteins (DREB) comprising groups I-IV and ethylene response factor made up of groups V-X [9,10,14]. • RAV (RAV for related to AB13/VP1): This subfamily is characterized by the possession of a B3 domain in addition to a single AP2 domain [9,14,15]. • Soloist: This subfamily is comprised of genes with domain sequences that closely resemble the AP2 domain but are too diverged and lack other features that can qualify them to be classified into any of the other subfamilies [11].…”