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Author Rashid M., Guangyuan H., Guangxiao Y., Hussain J., Xu Y.
Title 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.
Journal Evol. Bioinform. Online
Country China
Volume 8
Pages 321-355
Year 2012
PubMed ID 22807623
PubMed Central ID 3396566
DOI -
URL -
Relation
Gene AP2/EREBP101 AP2/EREBP109 AP2/EREBP127 AP2/EREBP129 AP2/EREBP139 AP2/EREBP153 AP2/EREBP22 AP2/EREBP31 AP2/EREBP47 AP2/EREBP59 AP2/EREBP68 AP2/EREBP77 AP2/EREBP79 AP2/EREBP85 AP2/EREBP86 AP2/EREBP92 AP2/EREBP96 DREB1A DREB1B DREB1C DREB1D DREB1E DREB1F DREB1G DREB2A EBP-89 EREBP1 ERF1 ERF100 ERF101 ERF102 ERF103 ERF104 ERF105 ERF106 ERF107 ERF108 ERF109 ERF11 ERF110 ERF112 ERF113 ERF115 ERF117 ERF118 ERF119 ERF12 ERF120 ERF121 ERF122 ERF123 ERF124 ERF125 ERF127 ERF128 ERF129 ERF13 ERF131 ERF132 ERF133 ERF134 ERF136 ERF137 ERF138 ERF14 ERF140 ERF141 ERF15 ERF16 ERF17 ERF18 ERF19 ERF2 ERF20 ERF21 ERF22 ERF23 ERF28 ERF3 ERF3 ERF32 ERF33 ERF34 ERF35 ERF36 ERF37 ERF38 ERF39 ERF4 ERF41 ERF42 ERF43 ERF44 ERF45 ERF47 ERF48 ERF49 ERF5 ERF50 ERF51 ERF53 ERF54 ERF55 ERF56 ERF57 ERF58 ERF59 ERF6 ERF61 ERF62 ERF64 ERF65 ERF66 ERF67 ERF68 ERF69 ERF7 ERF71 ERF72 ERF74 ERF76 ERF77 ERF79 ERF8 ERF80 ERF81 ERF82 ERF83 ERF84 ERF85 ERF86 ERF87 ERF88 ERF89 ERF9 ERF90 ERF91 ERF92 ERF93 ERF94 ERF95 ERF96 ERF97 ERF98 ERF99 FZP IDS1 MFS1 NGR5 PLT1 PLT10 PLT2 PLT3 PLT4 PLT5 PLT6 PLT7 PLT8 PLT9 RPH1 RSR1 SHAT1 SNB SUB1B SUB1C WRI1-1 WRI1-2 WRI3 WRI4
INSD -
Strain Wild Core Collection -
Induced Mutation Lines(NIG Collection) -
Sterile Seed Strain -
Lethal Embryo
Mutantion Strain
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Stages in Each Organ
- Muant Lines (Gene)
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Cultivated Varieties(NIG Collection) -
Stages in Each Organ -
/rice/oryzabase