**Yingdan Yuan 1,2, Bo Zhang 1,2,3, Xinggang Tang 1,2, Jinchi Zhang 1,2,\* and Jie Lin 1,2,\***


Received: 24 December 2019; Accepted: 27 January 2020; Published: 29 January 2020

**Abstract:** *Dendrobium* is widely used in traditional Chinese medicine, which contains many kinds of active ingredients. In recent years, many *Dendrobium* transcriptomes have been sequenced. Hence, weighted gene co-expression network analysis (WGCNA) was used with the gene expression profiles of active ingredients to identify the modules and genes that may associate with particular species and tissues. Three kinds of Dendrobium species and three tissues were sampled for RNA-seq to generate a high-quality, full-length transcriptome database. Based on significant changes in gene expression, we constructed co-expression networks and revealed 19 gene modules. Among them, four modules with properties correlating to active ingredients regulation and biosynthesis, and several hub genes were selected for further functional investigation. This is the first time the WGCNA method has been used to analyze *Dendrobium* transcriptome data. Further excavation of the gene module information will help us to further study the role and significance of key genes, key signaling pathways, and regulatory mechanisms between genes on the occurrence and development of medicinal components of *Dendrobium*.

**Keywords:** *Dendrobium*; comparative transcriptome; active ingredients; different tissues
