Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera

The nucleotide sequence of the entire grapevine genome has been obtained and its draft sequence has served as the model for fruit crops. Many transcription factors involved in stress-resistance pathways have been identified, among which the AP2/ERF is a large, and one of the most important families of transcription factors in plants. In this study, 132 putative transcription factor genes in the AP2/ERF family were identified from the database of the Vitis vinifera (grapevine) genome, and were compared with those from three other completely sequenced genomes, Arabidopsis thaliana, Populus trichocarpa (poplar), and Oryza sativa (rice). The grapevine AP2/ERF genes were classified into four subfamilies, AP2, DREB, ERF, RAV, and a soloist, and there were considerable variations among the subfamily members comparing with those in other species. The amino acid sequence, composition, physical and chemical characterization, phylogenetic tree, conserved domain sequences, function domain, and locations on chromosomes were predicted and analyzed. In silico mapping of the gene loci showed that AP2/ERF family genes of grapevine were localized oil 19 linkage groups. The extant AP2/ERF gene family in grapevine apparently resulted from whole genome, segmental and tandem duplications. Several grapevine AP2/ERF genes have been identified which are orthologous to those characterized in Arabidopsis with known functions. (C) 2009 Elsevier B.V. All rights reserved.