Transcriptome-Wide Identification, Classification, and Characterization of AP2/ERF Family Genes in the Desert Moss Syntrichia caninervis

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.

Identification, Classification, and Functional Analysis of AP2/ERF Family Genes in the Desert Moss Bryum argenteum

“…AP2/ERF genes play central roles during plant stress responses and have been widely identified in both dicotyledonous and monocotyledonous plants using genomic or transcriptomic data [ 20 , 22 ], however, little is known about the functions of AP2/ERF genes in moss species. Several recent studies have demonstrated that AP2/ERF transcription factors play an important role in the stress responses of bryophytes [ 15 , 16 , 19 ]. B. argenteum is extremely tolerant to desiccation stress and is a promising model for the identification of stress related genes [ 8 ], however, no AP2/ERF gene in B. argenteum has been reported until now.…”

“…Additionally, AP2/ERFs also demonstrated to be the most abundant TFs in the DT moss Syntrichia caninervis [ 17 ]. The majority of DREB (Dehydration-Responsive Element-Binding Protein) genes in S. caninervis responded to dehydration and/or rehydration treatments [ 18 , 19 ], indicating that AP2/ERF transcriptional factors also play a central regulatory role during stress responses in moss species.…”

“…High-throughput sequencing has been an effective tool to identify stress-related genes, and transcriptome-based identification and selection of AP2/ERF superfamily genes have been widely used in many non-model plants, such as Hevea brasiliensis [ 23 ], tea [ 24 ], as well as the desiccation tolerant moss S. caninervis [ 19 ]. Previously, we generated a de novo transcriptome for B. argenteum and established a desiccation–rehydration transcriptomic atlas which covered five different hydration stages [ 8 , 25 ].…”

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate inPanax ginsengC.A. Meyer

“…It has been consensus that the conserved motifs of the AP2/ERF transcription factor are crucial to the function of transcription factors, such as nuclear localization and transcriptional activity [7]. The DNA binding domain of AP2/ERF transcription factors, i.e., AP2 domain, was highly conserved in plant species [50],[51]. The AP2 domain of the PgERF genes was also found to be highly conserved.…”

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer

“…It has been the consensus that the conserved motifs of the AP2/ERF transcription factors are crucial to their functions, such as nuclear localization and transcriptional activity [7]. The DNA binding domain of AP2/ERF transcription factors, the AP2 domain, is highly conserved in plant species [50,51]. The AP2 domain of the PgERF genes is also highly conserved.…”