title: Genome-wide analysis of the ERF gene family in Arabidopsis and rice.
abstract: Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.
authors.affiliation: Molecular and Cellular Breeding Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan.
authors.forename: Toshitsugu
authors.initials: T
authors.lastname: Nakano
authors.forename: Kaoru
authors.initials: K
authors.lastname: Suzuki
authors.forename: Tatsuhito
authors.initials: T
authors.lastname: Fujimura
authors.forename: Hideaki
authors.initials: H
authors.lastname: Shinshi
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology; D017124:Conserved Sequence; D019143:Evolution, Molecular; D023281:Genomics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000145:classification / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors