Genome-wide Analysis of the Distribution of AP2/ERF Transcription Factors Reveals Duplication and Elucidates their Potential Function in Chinese Cabbage (Brassica rapa ssp. pekinensis)

Abstract

The AP2/ERF family is one of the largest groups of transcription factors in plants. Members of this family are involved in various biological processes, such as plant development, pathogen defense and stress responses. Here, we identified a total of 289 AP2/ERF transcription factors from Chinese cabbage based on the genome sequence. According to sequence similarity and the number of AP2/ERF domains, the 289 AP2/ERF proteins were classified into five groups (DREB, ERF, AP2, RAV and Soloist). The amino acid sequence, composition, physical and chemical characterization, phylogenetic tree and conserved domain were predicted and analyzed. The analysis results showed that AP2/ERF transcription factors from Chinese cabbage and Arabidopsis share high similarity. The sequences of 286 AP2/ERF genes were distributed unevenly among the ten chromosomes of the Chinese cabbage genome. Three genes could not be assigned to any specific chromosome, and were located on scaffold sequences. Gene duplication events of AP2/ERF family genes exist on Chinese cabbage chromosomes. Eight AP2/ERF genes, chosen from five subfamilies, respectively, were further investigated for their stress response by quantitative RT-PCR analysis. In total, eight genes were expressed differentially during cold or heat stress conditions.