Transcriptome Analysis of Dendrobium officinale and its Application to the Identification of Genes Associated with Polysaccharide Synthesis

Abstract

Dendrobium officinale is one of the most important Chinese medicinal herbs. Polysaccharides are one of the main active ingredients of D. officinale. To identify the genes that maybe related to polysaccharides synthesis, two cDNA libraries were prepared from juvenile and adult D. officinale, and were named Dendrobium-1 and Dendrobium-2, respectively. Illumina sequencing for Dendrobium-1 generated 102 million high quality reads that were assembled into 93,881 unigenes with an average sequence length of 790 base pairs. The sequencing for Dendrobium-2 generated 86 million reads that were assembled into 114,098 unigenes with an average sequence length of 695 base pairs. Two transcriptome databases were integrated and assembled into a total of 145,791 unigenes. Among them, 17,281 unigenes were assigned to 126 KEGG pathways while 135 unigenes were involved in fructose and mannose metabolism. Gene Ontology analysis revealed that the majority of genes were associated with metabolic and cellular processes. Furthermore, 430 glycosyltransferase and 89 cellulose synthase genes were identified. Comparative analysis of both transcriptome databases revealed a total of 32,794 differential expression genes (DEGs), including 22,051 up-regulated and 10,743 down-regulated genes in Dendrobium-2 compared to Dendrobium-1. Furthermore, a total of 1142 and 7918 unigenes showed unique expression in Dendrobium-1 and Dendrobium-2, respectively. These DEGs were mainly correlated with metabolic pathways and the biosynthesis of secondary metabolites. In addition, 170 DEGs belonged to glycosyltransferase genes, 37 DEGs were related to cellulose synthase genes and 627 DEGs encoded transcription factors. This study substantially expands the transcriptome information for D. officinale and provides valuable clues for identifying candidate genes involved in polysaccharide biosynthesis and elucidating the mechanism of polysaccharide biosynthesis.

Transcriptomic analyses reveal putative genes associated with bibenzyl biosynthesis in the traditional Chinese herb Dendrobium officinale

“…Although several generated transcriptomic data have been available for Dendrobium [9,48,53,50], in our study, based on the root tissues 23,131 unigenes were annotated, and this number was smaller when compared to previous data, but it is comparable to the identified unigenes using transcriptomic data of root tissues generated by . In total, 1,324 DEGs, including 912 up-regulated and 430 down-regulated DEGs, were identified through the comparison of expression changes between our two libraries.…”

“…Polysaccharides perform immunomodulatory and hepatoprotective activities while bibenzyl compounds exhibit antioxidant, anticancer and immunomodulatory activities [18,19,45,16,46,47]. Several studies have been conducted on the identification of putative genes involved in polysaccharide biosynthesis [9,41,48]. However, little is known regarding the physiological and molecular bases of bibenzyl biosynthesis in planta.…”

“…The active medicinal ingredients in D. officinale include: polysaccharides, alkaloids, phenols, terpenes, flavonoids and bibenzyl [9][10]. In Dendrobium plants, the content of sesquiterpene alkaloid is the main measure of its quality and medicinal efficacy [11][12].…”

Putative Genes Identified in Alkaloids Biosynthesis in Dendrobium officinale by Correlating the Contents of Main Bioactive Metabolites with Genes Expression between Protocorm-like Bodies and Leaves

“…Finally, all of the NDP-sugars are extended into macromolecular polysaccharides by successive catalysis of glycosyltransferases (GTs) [15]. Searches against KEGG database enabled prediction of the biosynthesis pathway of DOPs as shown in Additional le 1 [16,17]. The conversion of NDP-sugars into many types of DOPs in Golgi Complex was catalyzed by different kinds of glycosyltransferases such as glucosyltransferases, fucosyltransferases, mannosytransferases and xylosyltransferases in D. o cinale [12,18].…”

Comparative Analysis and Expression Patterns of the PLP_deC Genes in Dendrobium officinale

“…Dendrobium officinale Kimura et Migo (also known as D. catenatum) is a perennial herb that is commonly used as a valuable Chinese herbal medicine and has a long evolutionary history among orchids. D. officinale is rich in alkaloids [1,2], and its genome, transcriptome, and metabolome indicate that D. officinale may also contain terpenoid indole alkaloids (TIAs) [3][4][5]. The common precursor of TIAs is strictosidine, which is formed by the combination of tryptamine and secologanin [6,7].…”