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.

Identification and Expression Profiling of the Auxin Response Factors in Dendrobium officinale under Abiotic Stresses

“…The partial sequences of the ARF family genes were screened from four transcriptome data sets that were previously published [56]. All of the sequencing data sets are available at NCBI Sequence Read Archive () under accession IDs SRR2014227, SRR2014230, SRR2014236, SRR2014246, SRR2014297, SRR2014325, SRR2014396, and SRR2014476.…”

Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway

“…Dendrobium, a large genus in Orchidaceae, is well-known in East Asia due to its high economic and medicinal values [ 35 , 41 – 43 ]. Several transcriptomes of D. officinale have been sequenced to validate genes related to alkaloid and polysaccharide biosynthesis [ 29 , 44 , 45 ].…”

“…The resulting MS/MS data was identified using MaxQuant with the integrated Andromeda search engine (version 1.4.1.2). Tandem mass spectra were queried against the D. officinale genome, and the transcriptome data were concatenated using the reverse decoy database [ 29 , 34 , 35 ]. Trypsin/P was specified as the cleavage enzyme, allowing up to four missing cleavage sites.…”

NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes

“…To verify the utility of NATpipe for NAT and nat-siRNA discovery, we performed a case study by using RNA sequencing (RNA-seq) data of Dendrobium officinale , a non-model plant species. In our recent study, eight RNA-seq data sets [two biological replicates for each of four organs including root, stem, leaf and flower; NCBI SRA ( http://www.ncbi.nlm.nih.gov/sra ) accession IDs: SRR2014227, SRR2014230, SRR2014236, SRR2014246, SRR2014297, SRR2014325, SRR2014396 and SRR2014476] were generated, providing 445,430,002 valid reads 35 . Although the draft genome of Dendrobium officinale has been reported 36 , the genome assembly and the gene annotations are still far from a satisfied status.…”