Abstract
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 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 ERF-associated 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.
Highlights
Superfamily, located at the end of the ethylene signalling pathway, and has important roles in regulating the ethylene-related response genes
According to differences in conserved domains in their encoding proteins (Supplementary File S2), the other 118 genes were classified into three families: 5 genes belonged to the Related to ABI3/VPs (RAV) family, containing both an AP2 and a B3 domain; 17 genes belonged to the AP2 family, including 15 genes that had two repeated AP2 domains, 2 genes (ZjAP2.5 and ZjAP2.14) that had only one AP2 domain, and 1 gene (ZjAP2.17) that had four repeated AP2 domains; and the remaining 96 genes belonged to the Ethylene response factor (ERF) family, with only one AP2 domain
The deduced amino acid sequences of the AP2 domains in the ERF family were further analysed (Supplementary File S3), and these genes were classified into two subfamilies: 57 members were identified in the ERF subfamily, and 39 members belonged to the dehydration-responsive element-binding (DREB) subfamily
Summary
Superfamily, located at the end of the ethylene signalling pathway, and has important roles in regulating the ethylene-related response genes. Identifying and charactering this transcription factor would be helpful to elucidate ethylene related fruit ripening regulation in Chinese jujube (Ziziphus jujuba Mill.). 119 AP2/ERF genes, including 5 Related to ABI3/VPs (RAV), 17 AP2s, ERFs, 39 dehydration-responsive element-binding (DREB) factors and 1 soloist gene, were identified from the jujube genome sequences. 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. The remaining genes are named soloist, displaying a low similarity with other family members
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