Transcriptome-Wide Identification, Classification, and Characterization of Family Genes in the Desert Moss .

APETALA2/Ethylene Responsive Factor (AP2/ERF) is a large family of plant transcription factors which play important roles in the control of plant metabolism and development as well as responses to various biotic and abiotic stresses. The desert moss , due to its robust and comprehensive stress tolerance, is a promising organism for the identification of stress-related genes. Using transcriptome data, 80 AP2/ERF unigenes were identified by HMM modeling and BLASTP searching. Based on the number of AP2 domains, multiple sequence alignment, motif analysis, and gene tree construction, genes were classified into three main subfamilies (including 5 gene members, 72 gene members, and 1 member) and two Soloist members. We found that the ratio for each subfamily was constant between and the model moss , however, as compared to the angiosperm Arabidopsis, the percentage of ERF subfamily members in both moss species were greatly expanded, while the members of the AP2 and RAV subfamilies were reduced accordingly. The amino acid composition of the AP2 domain of ScAP2/ERFs was conserved as compared with Arabidopsis. Interestingly, most of the identified genes in belonged to the A-5 group which play important roles in stress responses and are rarely reported in the literature. Expression profile analysis of genes showed different gene expression patterns under dehydration and rehydration; the majority of genes demonstrated a stronger response to dehydration relative to rehydration indicating that may play an important role in dehydrated moss tissues. To our knowledge, this is the first study to detail the identification and characterization of the AP2/ERF gene family in a desert moss. Further, this study will lay the foundation for further functional analysis of these genes, provide greater insight to the stress tolerance mechanisms in and provide a reference for AP2/ERF gene family classification in other moss species.