Genome-Wide Analysis of the AP2/ERF Transcription Factors Family and the Expression Patterns of DREB Genes in Moso Bamboo (Phyllostachys edulis)

Abstract

The AP2/ERF transcription factor family, one of the largest families unique to plants, performs a significant role in terms of regulation of growth and development, and responses to biotic and abiotic stresses. Moso bamboo (Phyllostachys edulis) is a fast-growing non-timber forest species with the highest ecological, economic and social values of all bamboos in Asia. The draft genome of moso bamboo and the available genomes of other plants provide great opportunities to research global information on the AP2/ERF family in moso bamboo. In total, 116 AP2/ERF transcription factors were identified in moso bamboo. The phylogeny analyses indicated that the 116 AP2/ERF genes could be divided into three subfamilies: AP2, RAV and ERF; and the ERF subfamily genes were divided into 11 groups. The gene structures, exons/introns and conserved motifs of the PeAP2/ERF genes were analyzed. Analysis of the evolutionary patterns and divergence showed the PeAP2/ERF genes underwent a large-scale event around 15 million years ago (MYA) and the division time of AP2/ERF family genes between rice and moso bamboo was 15–23 MYA. We surveyed the putative promoter regions of the PeDREBs and showed that largely stress-related cis-elements existed in these genes. Further analysis of expression patterns of PeDREBs revealed that the most were strongly induced by drought, low-temperature and/or high salinity stresses in roots and, in contrast, most PeDREB genes had negative functions in leaves under the same respective stresses. In this study there were two main interesting points: there were fewer members of the PeDREB subfamily in moso bamboo than in other plants and there were differences in DREB gene expression profiles between leaves and roots triggered in response to abiotic stress. The information produced from this study may be valuable in overcoming challenges in cultivating moso bamboo.

Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses

“…Peng et al (2013) reported a putative recent whole genome duplication at 7-12 MYA based on analyzing whole genome duplication events of P. edulis . Wu et al (2015) found that P. edulis genome underwent a large-scale event around 15 MYA by genome-wide analysis of AP2/ERF transcription factors. Our result is similar to these reports and supported that the expansion of PeTIFYs occurred along with the genome duplication event.…”

Characterization of partial DREB and SOD genes from three Bali local rice cultivars

“…There are two classes of DREB transcription factors, DREB1 and DREB2. DREB1 involved in signal transduction pathways under cold stress, while DREB2 is induced under dehydration [7,8,20]. However, DREB1 and DREB2 genes have sequence similarity at AP2 domain and bind to the same DRE sequence.…”

“…Based on functional validation those genes are grouped into several classes such as transcription, osmolyte biosynthesis, signal transduction, hormone metabolism, and macromolecule protection [5,6]. Among those genes, DREB (dehydration responsive element binding) gene is a well˗studied group of genes in abiotic stress [7,8].DREB has an important role in stress signal transduction since it activates expression of many stress˗inducible target genes [7,8].…”

Transcription Factors-microRNAs regulatory network in response to multiple stresses in Arabidopsis thaliana

“…Interestingly, AT5G43410 encodes members which bind to GCC elements at the promoter of their target genes and are induced by pathogens. The AP2/ERF family is one of the largest of TFs family that are involved in plant development and response to abiotic stresses as well as pathogen attack via ethylene signaling pathway (Wu et al, 2015;Guo and Ecker, 2002). They act as a trans-acting factor interact with drought-responsive elements triggering downstream regulation events to improve stress tolerance in plants.…”