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. 2012:8:321-55.
doi: 10.4137/EBO.S9369. Epub 2012 Jun 21.

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

Affiliations

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

Muhammad Rashid et al. Evol Bioinform Online. 2012.

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.

Keywords: AP2/ERF; Arabidopsis; CBF/DREB; RAV; phylogenetic analysis; rice; wheat.

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Figures

Figure 1
Figure 1
The conserved amino acid residues found in ERF (A) and CBF/DREB (B).
Figure 2
Figure 2
Alignment of the AP2/ERF domains from Rice (O. sativa) cv. japonica ERF proteins. (A and B) displayed the alignment of single AP2/ERF and double AP2/ERF double domain proteins respectively. Notes: The arrows represent the predicted helix and sheets. Asterisks exhibited the conserved amino acid residues among the AP2/ERF domain proteins.
Figure 3
Figure 3
An unrooted phylogenetic tree of Rice AP2/ERF proteins is constructed using NJ method. Notes: The line marked distinction between ERF and CRT/DREB protein sub families. Scale bar represents 0.01 amino acid substitution per site.
Figure 4A
Figure 4A
The phylogenetic relationship in the AP2/ERF family genes. Group-Ia, Ib and group-Ic represent the AP2/ERF double domain proteins with their conserved motifs. Group-II exhibited the RAV family genes with one B3 domain. Their conserved motifs determined by the MEME online tools are given the Supplementary File 1.
Figure 4B
Figure 4B
The phylogenetic relationship among the AP2/ERF family genes in rice. Group-IIIa, IIIb and IIIc corresponds to the AP2/ERF single domain proteins. Group-IIIa, IIIb and IIIc falls in the ERF. Their conserved motifs determined by the MEME online tools are given the Supplementary File 1.
Figure 4B
Figure 4B
The phylogenetic relationship among the AP2/ERF family genes in rice. Group-IIIa, IIIb and IIIc corresponds to the AP2/ERF single domain proteins. Group-IIIa, IIIb and IIIc falls in the ERF. Their conserved motifs determined by the MEME online tools are given the Supplementary File 1.
Figure 4C
Figure 4C
The phylogenetic relationship among the AP2/ERF family genes in rice. Group-IV symbolises the AP2/ERF single domain proteins. Group-IVa, IVb, IVc and IVd are predicted to relate CBF/DREB genes. Their conserved motifs determined by the MEME online tools are given the Supplementary File 1.
Figure 5
Figure 5
RAV like motif sequences conserved in the C-terminal region of group-II in rice. Notes: The conserved sequences are under lined calculated by MEME programme. Consensus amino acid sequences are given below the line.
Figure 6
Figure 6
The conserved motif amino acid sequences in group-III are identified in the N-terminal region. Note: The consensus sequences are given under the line.
Figure 7
Figure 7
The conserved motif amino acid sequences in group-IVc and group-IVd respectively are identified in the C-terminal region. Note: The consensus sequences are given under the line.
Figure 8
Figure 8
The conserved motif amino acid sequences in group-IVa are identified in the C-terminal region. Note: The consensus sequences are given under the line.
Figure 9
Figure 9
Distribution of AP2/ERF family genes with full cDNA information. (A) Distribution of gene length in 2000 bp mapping hits. (B) Exon size distribution in gene length.
Figure 10
Figure 10
Distribution of rice AP2/ERF family genes in vegetative (root, stem, leaf and sheath) and reproductive tissues (inflorescence, ovary, anther, embryo, pistil, lemma, palea and endosperm). Note: The expression profile is determined by using the RiceXPro database.
Figure 11
Figure 11
Gene’s classification according to their expression level in each tissue.
Figure 12
Figure 12
Tissue specific expression of the AP2/ERF family genes in each group.
Figure 13
Figure 13
The physical location of the AP2/ERF genes on rice chromosomes. Notes: The chromosome number is indicated at the top of each chromosome. The genes are indicated on the locus by their generic names and function.
Figure 14
Figure 14
Comparative mapping of wheat AP2/ERF genes on rice chromosomes.
Figure 15
Figure 15
Comparative mapping of rice and Arabidopsis AP2/ERF family.

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