Identification and characterization of AP2/ERF transcription factors in moso bamboo (Phyllostachys edulis)

Аннотация

Bamboo belongs to subfamily Bambusoideae of the grass family and is one of the most important non-timber forest resources in the world. The AP2/ERF superfamily is a group of plant specific transcription factors and plays important roles in the regulation of plant growth and responses to biotic and abiotic stress. By comprehensively analyzing the recently uncovered whole genome sequence and full length cDNA of moso bamboo (Phyllostachys edulis), 142 AP2/ERF transcription factors were identified and 53 among them are supported by full length cDNA. Compared with a recent report on the identification of 116 AP2/ERF transcription factors from the P. edulis genome, our study identified ~22% more AP2/ERF transcription factors. Phylogenetic analysis based on the sequence of the AP2/ERF domain assigned 23 genes to the AP2 family, 7 to the RAV family, 64 genes to the ERF subfamily, and 47 to the DREB subfamily, respectively. A soloist divergent from others was also found. The further multiple sequence alignment of the AP2/ERF domain, phylogenetic analysis and motif recognition were performed and revealed conserved residues, similarities and evolution relationship of members in each family or subfamily. The ortholog relationship and colinearity between P. edulis and O. sativa were analyzed. Additionally, 36 duplicates of orthologs in O. sativa genome were identified, which may originate from the whole genome duplication. Despite of the ortholog duplication, the gene numbers in groups A5, B3, and B6 are significantly lower than those in O. sativa and A. thaliana, and the A3 group is missing, suggesting potential gene loss of these groups during species divergence. This study provides more knowledge of AP/ERF genes in P. edulis.