Abstract
<em>Dendrobium huoshanense</em> has long been used to treat various diseases in oriental medicine. In order to study its gene expression profile, transcripts involved in the biosynthesis of precursors of polysaccharides, as well as mechanisms underlining morphological differences between wild and cultivated plants, three organs of both wild type and cultivated <em>D. huoshanense</em> were collected and sequenced by Illumina HiSeq4000 platform, yielding 919,409,540 raw reads in FASTQ format. After Trinity de novo assembly and quality control, 241,242 nonredundant contigs with the average length of 967.5 bp were generated. qRT-PCR experiment on the selected transcripts showed the transcriptomic data were reliable. BLASTx was conducted against NR, SwissProt, String, Pfam, and KEGG. Gene ontology annotation revealed more than 40,000 contigs assigned to catalytic activity and metabolic process, suggesting its dynamic physiological activities. By searching KEGG pathway, six genes potentially involved in mannose biosynthetic pathway were retrieved. Gene expression analysis for stems between wild and cultivated <em>D. huoshanense</em> resulted in 956 genes differentially expressed. Simple sequence repeats (SSRs) analysis revealed 143 SSRs with the unit size of 4 and 3,437 SSRs the size of 3. The obtained SSRs are the potential molecular markers for discriminating distinct cultivars of <em>D. huoshanense</em>.
Highlights
Due to its high morphological similarity with species from the same genus Dendrobium, it was often confused with others and researchers made judgments according to its very narrow distribution area which was recorded in ancient books
Commercial cultivation of D. huoshanense began in late twentieth century and the limited time span may explain the reason why gene expression was so similar concerning flower from the cultivar and wild type
This suggests the underling mechanisms of D. huoshanense morphology are complicated
Summary
J. Cheng has been used in traditional Chinese medicine for centuries with the efficacy of curing asthenic symptoms resulted from various diseases as well as treating loss of body fluid due to fever or other causes. Cheng has been used in traditional Chinese medicine for centuries with the efficacy of curing asthenic symptoms resulted from various diseases as well as treating loss of body fluid due to fever or other causes It is embodied in Chinese pharmacopeia as Dendrobii Caulis, along with several other entries that are from the same genus of Dendrobium in Orchidaceae [1]. Metabolic study on D. huoshanense demonstrated that according to accumulating pattern of polysaccharides and related metabolites, its best harvest time should be in the third year [4]. Efforts to tackle the structure of such compounds by anion exchange as well as gel permeation chromatography were
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