Abstract
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 Syntrichia caninervis, due to its robust and comprehensive stress tolerance, is a promising organism for the identification of stress-related genes. Using S. caninervis 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, ScAP2/ERF genes were classified into three main subfamilies (including 5 AP2 gene members, 72 ERF gene members, and 1 RAV member) and two Soloist members. We found that the ratio for each subfamily was constant between S. caninervis and the model moss Physcomitrella patens, 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 DREB genes in S. caninervis belonged to the A-5 group which play important roles in stress responses and are rarely reported in the literature. Expression profile analysis of ScDREB genes showed different gene expression patterns under dehydration and rehydration; the majority of ScDREB genes demonstrated a stronger response to dehydration relative to rehydration indicating that ScDREB 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 S. caninervis and provide a reference for AP2/ERF gene family classification in other moss species.
Highlights
Syntrichia caninervis is a dominant moss species of biological soil crusts in the Gurbantunggut desert of Northwestern China (Zhang, 2005)
The un-rooted gene tree demonstrated that the 71 S. caninervis AP2/ethyleneresponsive factor (ERF) predicted amino acid sequences can be divided into five main groups: ERF I, ERF II, ERF III, AP2, and related to ABI3/VP1 (RAV) (Supplementary Figure S2)
The APETALA2/Ethylene Responsive Factor (AP2/ERF) genes has been identified in many plant species due to its important roles in development, metabolism, and in response to various stresses (Mizoi et al, 2012; Licausi et al, 2013)
Summary
Syntrichia caninervis is a dominant moss species of biological soil crusts in the Gurbantunggut desert of Northwestern China (Zhang, 2005). According to sequence similarity of the single AP2 domain, DREB family genes are further classified into the groups A1 to A6 and ERF family genes are divided into the groups B1 to B6 (Sakuma et al, 2002). The ERF family was sub-divided into 12 groups in Arabidopsis and fifteen groups in rice according to the structure and similarity of the AP2 domain (Nakano et al, 2006). Both classification schemes have been extensively employed in the literature, and the methods have direct correspondence. The A-1 type of DREB family in Sakuma‘s classification corresponds to the Group III ERF family in Nakano’s classification (Nakano et al, 2006)
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