title: De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration.
abstract: BACKGROUND
  The desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employed RNA-Seq and digital gene expression (DGE) technologies to study the genome-wide expression profiles of the dehydration and rehydration processes in this important desert plant.
  
  
  RESULTS
  We applied a two-step approach to investigate the gene expression profile upon rehydration in the moss Bryum argenteum using Illumina HiSeq2000 sequencing platform. First, a total of 57,247 transcript assembly contigs (TACs) were obtained from 54.79 million reads by de novo assembly, with an average length of 863 bp and N50 of 1,372 bp. Among the reconstructed TACs, 36,916 (64.5%) revealed similarity with existing protein sequences in the public databases. 23,509 and 21,607 TACs were assigned GO and KEGG annotation information, respectively. Second, samples were taken from 3 hydration stages: desiccated (Dry), rehydrated 2 h (R2) and rehydrated 24 h (R24), and DEG libraries were constructed for Differentially Expressed Genes (DEGs) discovery. 4,081 and 6,709 DEGs were identified in R2 and R24, compared with Dry, respectively. Compared to the desiccated sample, up-regulated genes after two hours of hydration are primarily related to stress responses. GO function enrichment network, EKGG metabolic pathway and MapMan analysis supports the idea of the rapid recovery of photosynthesis after 24 h of rehydration. We identified 770 transcription factors (TFs) which were classified into 50 TF families. 142 TF transcripts were up-regulated upon rehydration including 23 members of the ERF family.
  
  
  CONCLUSIONS
  In this study, we constructed a pioneering, high-quality reference transcriptome in B. argenteum and generated three DGE libraries to elucidate the changes of gene expression upon rehydration. Expression profiles consistent with the rapid recovery of photosynthesis (at R2) and the re-establishment of a positive carbon balance following rehydration (at R24) were observed. Our study will extend our knowledge of bryophyte transcriptomes and provide further insight into the molecular mechanisms related to rehydration and desiccation-tolerance.
authors.affiliation: Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. gaobei11@mails.ucas.ac.cn.|University of Chinese Academy of Sciences, Beijing, 100049, China. gaobei11@mails.ucas.ac.cn.
authors.forename: Bei
authors.initials: B
authors.lastname: Gao
authors.affiliation: Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. zhangdy@ms.xjb.ac.cn.
authors.forename: Daoyuan
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. xiaoshuangliok@sina.com.
authors.forename: Xiaoshuang
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. yanghonglan@ms.xjb.ac.cn.
authors.forename: Honglan
authors.initials: H
authors.lastname: Yang
authors.affiliation: Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. zhangym@ms.xjb.ac.cn.
authors.forename: Yuanming
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Plant Biology, Southern Illinois University-Carbondale, Carbondale, IL, 62901-6509, USA. wood@plant.siu.edu.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Wood
mesh_terms: D019068:Bryopsida / Q000235:genetics* / Q000502:physiology; D003890:Desiccation; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D010788:Photosynthesis; D010940:Plant Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome
chemical_list: D010940:Plant Proteins