title: A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb.
abstract: Dendrobium officinale is an important traditional Chinese herb. Here, we did a transcriptome-wide, organ-specific study on this valuable plant by combining RNA, small RNA (sRNA) and degradome sequencing. RNA sequencing of four organs (flower, root, leaf and stem) of Dendrobium officinale enabled us to obtain 536,558 assembled transcripts, from which 2,645, 256, 42 and 54 were identified to be highly expressed in the four organs respectively. Based on sRNA sequencing, 2,038, 2, 21 and 24 sRNAs were identified to be specifically accumulated in the four organs respectively. A total of 1,047 mature microRNA (miRNA) candidates were detected. Based on secondary structure predictions and sequencing, tens of potential miRNA precursors were identified from the assembled transcripts. Interestingly, phase-distributed sRNAs with degradome-based processing evidences were discovered on the long-stem structures of two precursors. Target identification was performed for the 1,047 miRNA candidates, resulting in the discovery of 1,257 miRNA--target pairs. Finally, some biological meaningful subnetworks involving hormone signaling, development, secondary metabolism and Argonaute 1-related regulation were established. All of the sequencing data sets are available at NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/). Summarily, our study provides a valuable resource for the in-depth molecular and functional studies on this important Chinese orchid herb.
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.
authors.forename: Dongliang
authors.initials: D
authors.lastname: Yu
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xue
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Jiangjie
authors.initials: J
authors.lastname: Lu
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Shangguo
authors.initials: S
authors.lastname: Feng
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Chenjia
authors.initials: C
authors.lastname: Shen
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Huizhong
authors.initials: H
authors.lastname: Wang
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D031667:Dendrobium / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D009928:Organ Specificity / Q000235:genetics; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger