Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways

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.

Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit

“…Compared with many other analysis methods, WGCNA has the advantages of summarizing and standardizing the methods and functions of integrated R packages [35]. Moreover, combining the WGCNA method and RNA-Seq data can be used to better mine the genes and transcription factors related to the traits [36]. In this study, the WGCNA method was used for the first time in pitaya fruit, and the modules related to pigmentation traits were identified.…”

Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor

“…In plant breeding and horticulture, transcriptome sequencing is highly employed for predicting novel genes, gene function, and genome evolution [ 11 ]. Here, we performed whole-transcriptome sequencing to study the mechanism of purple color development in D. nestor petals, which is the first report, as compared to other Dendrobium species [ 13 , 69 , 70 , 71 , 72 ]. H and B samples might have relatively similar anthocyanins accumulation and synthesis, hence the high similarity as evident in Figure 1 a,b and Figure 4 b.…”

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)

“…Traditional biological research on factors affecting life activities is usually based on exploring the molecular mechanisms of DNA, mRNA, or proteins [ 15 ]. The limitations of traditional biological research were exposed with the rapid development of sequencing technology, namely, it only has importance in revealing the genetic mechanism of specific traits, but it cannot fully and effectively mine biological significance contained in massive data [ 38 , 39 , 40 , 41 ].…”

“…With the advent of high-throughput technology, methods such as a single gene differential expression analysis or cluster analysis often miss a lot of useful information when faced with a complex network composed of a large amount of DNA, RNA or protein. Therefore, a biological network analysis method emerged on the basis of global gene expression patterns [ 14 , 15 , 16 , 17 ]. One of the most useful methods is weighted gene coexpression network analysis (WGCNA), which can be used in unweighted correlation networks to alleviate multiple detection problems from big data analysis.…”