Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice

Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice

February 2006 | Toshitsugu Nakano, Kaoru Suzuki, Tatsuhito Fujimura, and Hideaki Shinshi
A comprehensive computational analysis identified 122 ERF family genes in Arabidopsis and 139 in rice. The study provided an overview of the gene family in Arabidopsis, including gene structures, phylogeny, chromosome locations, and conserved motifs. Comparative analysis between Arabidopsis and rice ERF genes revealed that the ERF family in both species was divided into 12 and 15 groups, respectively. Eleven of these groups were present in both species, suggesting that major functional diversification in the ERF family predates the monocot/dicot divergence. Some groups were species-specific. The study discussed the relationship between the structure and function of ERF family proteins, concluding that the expansion of the ERF family in plants may have been due to chromosomal/segmental duplication, tandem duplication, and ancient transposition and homing. The ERF family is part of the AP2/ERF superfamily, which includes the AP2 and RAV families. The AP2/ERF domain is involved in DNA binding and is conserved in various plant transcription factors. The ERF family is further divided into the ERF subfamily and the CBF/DREB subfamily. The study identified 147 genes in the AP2/ERF superfamily in Arabidopsis, including 122 ERF family genes. Phylogenetic analysis of these genes revealed 12 groups, with some further divided into subgroups. The study also identified conserved motifs outside the AP2/ERF domain, which may play roles in transcriptional regulation. The results of the study will be useful for future functional analyses of ERF family genes. The study also compared the ERF family genes in Arabidopsis and rice, revealing that the classification of the ERF family in Arabidopsis is applicable to the rice ERF family with some exceptions. The rice ERF family has a larger number of genes in group VII compared to Arabidopsis. The study identified additional conserved motifs in the rice ERF family, including CMVII-6, -7, and -8. The study also identified seven rice ERF genes that could not be assigned to any of the groups designated in Arabidopsis, which were divided into three additional groups. The study also discussed the evolution and divergence of the ERF family genes, suggesting that the expansion of the ERF family in plants may have been due to chromosomal/segmental duplication, tandem duplication, and ancient transposition and homing. The study concluded that the ERF family genes play important roles in various biological processes and responses to environmental stimuli. The results of the study will be useful for future functional analyses of the ERF family genes.A comprehensive computational analysis identified 122 ERF family genes in Arabidopsis and 139 in rice. The study provided an overview of the gene family in Arabidopsis, including gene structures, phylogeny, chromosome locations, and conserved motifs. Comparative analysis between Arabidopsis and rice ERF genes revealed that the ERF family in both species was divided into 12 and 15 groups, respectively. Eleven of these groups were present in both species, suggesting that major functional diversification in the ERF family predates the monocot/dicot divergence. Some groups were species-specific. The study discussed the relationship between the structure and function of ERF family proteins, concluding that the expansion of the ERF family in plants may have been due to chromosomal/segmental duplication, tandem duplication, and ancient transposition and homing. The ERF family is part of the AP2/ERF superfamily, which includes the AP2 and RAV families. The AP2/ERF domain is involved in DNA binding and is conserved in various plant transcription factors. The ERF family is further divided into the ERF subfamily and the CBF/DREB subfamily. The study identified 147 genes in the AP2/ERF superfamily in Arabidopsis, including 122 ERF family genes. Phylogenetic analysis of these genes revealed 12 groups, with some further divided into subgroups. The study also identified conserved motifs outside the AP2/ERF domain, which may play roles in transcriptional regulation. The results of the study will be useful for future functional analyses of ERF family genes. The study also compared the ERF family genes in Arabidopsis and rice, revealing that the classification of the ERF family in Arabidopsis is applicable to the rice ERF family with some exceptions. The rice ERF family has a larger number of genes in group VII compared to Arabidopsis. The study identified additional conserved motifs in the rice ERF family, including CMVII-6, -7, and -8. The study also identified seven rice ERF genes that could not be assigned to any of the groups designated in Arabidopsis, which were divided into three additional groups. The study also discussed the evolution and divergence of the ERF family genes, suggesting that the expansion of the ERF family in plants may have been due to chromosomal/segmental duplication, tandem duplication, and ancient transposition and homing. The study concluded that the ERF family genes play important roles in various biological processes and responses to environmental stimuli. The results of the study will be useful for future functional analyses of the ERF family genes.
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