Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube

Zhong Zhang, Xingang Li
2018 Scientific Reports  
The Ethylene response factor (ERF) belongs to the APETALA2/ethylene response factor (AP2/ERF) superfamily, located at the end of the ethylene signalling pathway, and has important roles in regulating the ethylene-related response genes. Thus, identifying and charactering this transcription factor would be helpful to elucidate ethylene related fruit ripening regulation in Chinese jujube (Ziziphus jujuba Mill.). In the present study, 119 AP2/ERF genes, including 5 Related to ABI3/VPs (RAV), 17
more » ... I3/VPs (RAV), 17 AP2s, 57 ERFs, 39 dehydration-responsive element-binding (DREB) factors and 1 soloist gene, were identified from the jujube genome sequences. Genome localization, gene duplication, phylogenetic relationships and conserved motifs were simultaneously analysed. Using available transcriptomic data, 85 genes with differential transcripts in the flower, leaf and fruit were detected, suggesting a broad regulation of AP2/ERF genes in the growth and development of jujube. Among them, 44 genes were expressed in the fruit. As assessed by quantitative PCR, 15 up-and 23 downregulated genes corresponding to fruit full maturity were found, while in response to 100 μl l −1 ethylene, 6 up-and 16 downregulated genes were generated. By comparing the output, ZjERF54 and DREB39 were found to be the best candidate genes that positively participated in jujube fruit ripening, while ZjERF25 and ZjERF36, which had an ERFassociated amphiphilic repression (EAR) motif, were ripening repressors. These findings help to gain insights into AP2/ERF gene evolution and provide a useful resource to further understand the ethylene regulatory mechanisms underlying Chinese jujube fruit ripening. Chinese jujube (Ziziphus jujuba Mill.) belongs to the Rhamnacease family and is a traditionally popular fruit crop that is native to China 1 . The fruit has been introduced worldwide due to its immensely nutritional and economic benefits 2,3 . However, the fresh fruit has a short shelf life; the harvested fruit rots easily, with substantial water loss within 2-3 days under normal ambient conditions 4 . Knowledge of fruit ripening characterization and its molecular regulation is limited but is urgently required for the development of the jujube industry. Recently, increasing expression levels of ethylene metabolism pathway genes at fruit full maturity have been characterized, suggesting that ethylene-dependent pathways are involved in the ripening of this non-climacteric fruit 5 . Ethylene response factor (ERF), located at the end of the ethylene signalling pathway, has been found to mediate ethylene-regulated gene expression 6 . Thus, identification and characterization of the ERF genes in jujube would help understand the ethylene-related ripening regulation, and would also help to improve fruit storage and quality in the long term. The ERF genes belong to the large superfamily of APETALA2/ethylene response factor (AP2/ERF), which are some of the most important plant transcription factors (TFs). The genes involved in this superfamily commonly share a conserved AP2 domain that consists of approximately 60 amino acid residues and binds to specific DNA sites located in gene promoters, such as the GCC box and the dehydration-responsive element (DRE) 7 . According to the differences in domain sequence, this superfamily is classified into four families, including Related to ABI3/ VP (RAV), AP2, ERF and soloist 8 . RAV family genes contain an AP2 and a B3 domain, and AP2 family genes usually have multiple repeated AP2 domains, while ERF family genes have a single AP2 domain and are further
doi:10.1038/s41598-018-33744-w fatcat:cu44ihooynhg5dkysl2c5esinq