AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots

Abstract

The transcription factor family intimately regulates gene expression in response to hormones, biotic and abiotic factors, symbiotic interactions, cell differentiation, and stress signalling pathways in plants. In this study, 170 AP2/ERF family genes are identified by phylogenetic analysis of the rice genome (Oryza sativa l. japonica) and they are divided into a total of 11 groups, including four major groups (AP2, ERF, DREB, and RAV), 10 subgroups, and two soloists. Gene structure analysis revealed that, at position-6, the amino acid threonine (Thr-6) is conserved in the double domain AP2 proteins compared to the amino acid arginine (Arg-6), which is preserved in the single domain of ERF proteins. In addition, the histidine (His) amino acid is found in both domains of the double domain AP2 protein, which is missing in single domain ERF proteins. Motif analysis indicates that most of the conserved motifs, apart from the AP2/ERF domain, are exclusively distributed among the specific clades in the phylogenetic tree and regulate plausible functions. Expression analysis reveals a widespread distribution of the rice AP2/ERF family genes within plant tissues. In the vegetative organs, the transcripts of these genes are found most abundant in the roots followed by the leaf and stem; whereas, in reproductive tissues, the gene expression of this family is observed high in the embryo and lemma. From chromosomal localization, it appears that repetition and tandem-duplication may contribute to the evolution of new genes in the rice genome. In this study, interspecies comparisons between rice and wheat reveal 34 rice loci and unveil the extent of collinearity between the two genomes. It was subsequently ascertained that chromosome-9 has more orthologous loci for CRT/DRE genes whereas chromosome-2 exhibits orthologs for ERF subfamily members. Maximum conserved synteny is found in chromosome-3 for AP2 double domain subfamily genes. Macrosynteny between rice and Arabidopsis, a distant, related genome, uncovered 11 homologs/orthologs loci in both genomes. The distribution of AP2/ERF family gene paralogs in Arabidopsis was most frequent in chromosome-1 followed by chromosome-5. In Arabidopsis, ERF subfamily gene orthologs are found on chromosome-1, chromosome-3, and chromosome-5, whereas DRE subfamily genes are found on chromosome-2 and chromosome-5. Orthologs for RAV and AP2 with double domains in Arabidopsis are located on chromosome-1 and chromosome-3, respectively. In conclusion, the data generated in this survey will be useful for conducting genomic research to determine the precise role of the AP2/ERF gene during stress responses with the ultimate goal of improving crops.

Genome-wide identification and phylogenetic analysis of the AP2/ERF gene superfamily in sweet orange (Citrus sinensis)

“…Although C. sinensis has a much larger genome (367-396 Mbp) (Arumuganathan and Earle, 1991) than Arabidopsis (145 Mbp), the structure and phylogenic arrangements are quite similar. Indeed, other studies have shown that the AP2/ERF superfamily in soybeans (with a genome size of 1115 Mbp) (Zhang et al, 2008) appeared to be quite similar to that found in rice (430 Mbp) (Rashid et al, 2012), grape (475 Mbp) (Licausi et al, 2010), and cucumber (367 Mbp) (Hu and Liu, 2011). In fact, any irregular distribution of genes in the AP2/ERF superfamily among different plant species may have evolved from genomic losses or duplication events of a common ancestor, contributing to the expansion or restriction of the number of these genes (Hu and Liu, 2011;Rashid et al, 2012;Zhang et al, 2012).…”

“…It participates in the pathways that respond to hormones and biotic and abiotic stresses, such as jasmonate (JA), abscisic acid (ABA), drought (Liu et al, 1998;Golldack et al, 2011), salinity (Golldack et al, 2011), low temperature (Carvallo et al, 2011), and diseases . Proteins of the ERF family were found in several plant species including Arabidopsis (Sakuma et al, 2002), rice (Nakano et al, 2006;Sharoni et al, 2011;Rashid et al, 2012), cotton (Champion et al, 2009), tomato (Sharma et al, 2010), grape (Licausi et al, 2010), and apple (Zhuang et al, 2011). The understanding of the ERF family in C. sinensis is still incipient, and only a few studies are found in the literature .…”

“…Plants have evolved to overcome several environmental changes associated with drought, waterlogging, air temperatures, plagues, grazing, and soil-borne diseases by developing a complex network of cellular, molecular, and biochemical signaling (Sharma et al, 2010;Rashid et al, 2012). Signaling and biological control of tolerance to environmental stresses are governed by genetic regulation at the transcriptional level and are mainly induced by transcript factors (Jofuku et al, 1994;Sharma et al, 2010).…”

Overexpression of the OsERF71 Transcription Factor Alters Rice Root Structure and Drought Resistance

“…Transcription factors that contain a highly conserved AP2/ERF DNA-binding domain are widespread in the plant kingdom (Rashid et al, 2012). Since AP2 was first identified and studied in the context of Arabidopsis flower development (Jofuku et al, 1994), 122 and 170 AP2/ERF genes have been predicted in the Arabidopsis (Nakano et al, 2006) and rice (Rashid et al, 2012) genomes, respectively.…”

“…Since AP2 was first identified and studied in the context of Arabidopsis flower development (Jofuku et al, 1994), 122 and 170 AP2/ERF genes have been predicted in the Arabidopsis (Nakano et al, 2006) and rice (Rashid et al, 2012) genomes, respectively. This family of transcription factors has been implicated in regulating plant growth and development (Elliott et al, 1996;Chuck et al, 1998;Boutilier et al, 2002), but members also are known to be components of mechanisms that provide protection from abiotic stresses, including drought (Stockinger et al, 1997;Jaglo-Ottosen et al, 1998;Liu et al, 1998).…”