Weighted Gene Co-expression Network Analysis of the Dioscin Rich Medicinal Plant Dioscorea nipponica.

Wei Sun,Shilin Chen,Jun Yang,Chi Song,Li Xiang,Bo Wang,An Liu,Weihao Wang,Liang Leng

doi:10.3389/fpls.2017.00789

Abstract

Dioscorea contains critically important species which can be used as staple foods or sources of bioactive substances, including Dioscorea nipponica, which has been used to develop highly successful drugs to treat cardiovascular disease. Its major active ingredients are thought to be sterol compounds such as diosgenin, which has been called “medicinal gold” because of its valuable properties. However, reliance on naturally growing plants as a production system limits the potential use of D. nipponica, raising interest in engineering metabolic pathways to enhance the production of secondary metabolites. However, the biosynthetic pathway of diosgenin is still poorly understood, and D. nipponica is poorly characterized at a molecular level, hindering in-depth investigation. In the present work, the RNAs from five organs and seven methyl jasmonate treated D. nipponica rhizomes were sequenced using the Illumina high-throughput sequencing platform, yielding 52 gigabases of data, which were pooled and assembled into a reference transcriptome. Four hundred and eighty two genes were found to be highly expressed in the rhizomes, and these genes are mainly involved in stress response and transcriptional regulation. Based on their expression patterns, 36 genes were selected for further investigation as candidate genes involved in dioscin biosynthesis. Constructing co-expression networks based on significant changes in gene expression revealed 15 gene modules. Of these, four modules with properties correlating to dioscin regulation and biosynthesis, consisting of 4,665 genes in total, were selected for further functional investigation. These results improve our understanding of dioscin biosynthesis in this important medicinal plant and will help guide more intensive investigations.

Highlights

Dioscorea is a large monocot genus of about 450 species of herbaceous vines that are dioecious and rhizomatous or tuberous
D. nipponica has been developed into patent medicine, which is effective in the prevention and treatment of cardiovascular disease and are sold in many countries
All of the plants were cultured in the same conditions (25◦C, humidity 60%, light/dark 16/8 h) with the same volume of sugarfree 1/2 Murashige and Skoog medium in an artificial climate incubator for 30 days, after which the culture medium was replaced with a medium that contained methyl jasmonate (MeJA) (Sigma–Aldrich, America) at a final concentration of 200 μM; samples were collected at 0, 12, 24, 36, 48, 120, and 240 h after treatment

Summary

Introduction

Dioscorea (true yams) is a large monocot genus of about 450 species of herbaceous vines that are dioecious and rhizomatous or tuberous These species have attracted a great deal of attention since they appear similar to dicots (Mignouna et al, 2009) and some are critically important species with edible tubers which serve as a major staple food (Tang et al, 2013) or as a source of bioactive. Recent studies have shown that its extracts exhibit a curative effect toward climacteric syndrome and obesity (Kwon et al, 2003; Dewick, 2011), as well as showing inhibitory effects on many cancers, including melanotic tumors, oral cavity carcinomas and neuroblastomas (Ho et al, 2011; Chien et al, 2012; Rahman et al, 2014) Sterols and their derivatives are suggested to be the major active ingredients in D. nipponica rhizomes. Reliance solely on naturally growing plants as a production system has led to D. nipponica being listed as an endangered species

Objectives

Methods

Results