Genome-wide analysis of AP2/ERF transcription factors in carrot (Daucus carota L.) reveals evolution and expression profiles under abiotic stress

Abstract

AP2/ERF is a large transcription factor family that regulates plant physiological processes, such as plant development and stress response. Carrot (Daucus carota L.) is an important economical crop with a genome size of 480 Mb; the draft genome sequencing of this crop has been completed by our group. However, little is known about the AP2/ERF factors in carrot. In this study, a total of 267 putative AP2/ERF factors were identified from the whole-genome sequence of carrot. These AP2/ERF proteins were phylogenetically clustered into five subfamilies based on their similarity to the amino acid sequences from Arabidopsis. The distribution and comparative genome analysis of the AP2/ERF factors among plants showed the AP2/ERF factors had expansion during the evolutionary process, and the AP2 domain was highly conserved during evolution. The number of AP2/ERF factors in land plants expanded during their evolution. A total of 60 orthologous and 145 coorthologous AP2/ERF gene pairs between carrot and Arabidopsis were identified, and the interaction network of orthologous genes was constructed. The expression patterns of eight AP2/ERF family genes from each subfamily (DREB, ERF, AP2, and RAV) were related to abiotic stresses. Yeast one-hybrid and β-galactosidase activity assays confirmed the DRE and GCC box-binding activities of DREB subfamily genes. This study is the first to identify and characterize the AP2/ERF transcription factors in carrot using whole-genome analysis, and the findings may serve as references for future functional research on the transcription factors in carrot.

Genome-wide identification of cassava R2R3 MYB family genes related to abscission zone separation after environmental-stress-induced abscission

“…Cassava genome sequences suggested to contain a MYB domain were isolated and identified as candidate R2R3 MYB genes by using the Arabidopsis genome as a refs 3,37. R2R3 MYB genes were isolated from the cassava genome (JGI database, version 6.1) using annotations and BLAST analysis with an E-value cutoff set as 0.000013.…”

“…R2R3 MYB genes were isolated from the cassava genome (JGI database, version 6.1) using annotations and BLAST analysis with an E-value cutoff set as 0.000013. The Arabidopsis R2R3 MYB genes were identified using the Arabidopsis Information Resource (TAIR)337. Each putative cassava R2R3 MYB gene was searched against the TAIR database by using BLAST to ensure that no additional related genes were selected337.…”

Hormone dependent survival mechanisms of plants during post-waterlogging stress

“…24,25 AP2/ERFs (Apelata2/ Ethylene response factors) are one of the most important Tf families in plants which control different biotic and abiotic stress responsive pathways. 26,27 Based on DNA binding domain (DBD), AP2/ERFs are further divided into AP2, RAV (Related to Abscisic acid insensitive3/Viviparous1), DREB (subgroup A1-A6), ERF (subgroup B1-B6), and others. 28 The genes responsible for tobacco dehydration stress are expressed by the presence of DREBs.…”

Research Article <i>Bradyrhizobium</i> spp. as attenuators of water deficit stress in runner peanut genotypes based on physiological and gene expression responses

“…In this study, ERF8 presented high expression during water deficit in A. hypogaea cultivars, suggesting its importance in the interaction with the DRE elements and in the tolerance and acclimatization processes of the plant (Dang et al, 2012). Li et al (2015) reported that AP2 and ERF proteins are part of important factors in plant transcription, regulating various development pathways and response to stress. The increase in the expression of genes of the ERF family in Arabidopsis and tobacco provides greater resistance to biotic and abiotic stresses (Park et al, 2001;Berrocal-Lobo et al, 2002;Pan et al, 2010).…”