Regulation of transcriptome networks that mediate ginsenoside biosynthesis by essential ecological factors

Zhongce Wang; Zhiguo Chen; You Tang; Meiping Zhang; Meng Huang

doi:10.1371/journal.pone.0290163

Regulation of transcriptome networks that mediate ginsenoside biosynthesis by essential ecological factors

PLoS One. 2023 Aug 17;18(8):e0290163. doi: 10.1371/journal.pone.0290163. eCollection 2023.

Authors

Zhongce Wang¹, Zhiguo Chen², You Tang¹, Meiping Zhang³, Meng Huang¹

Affiliations

¹ College of Electrical and Information Engineering, Jilin Agricultural Science and Technology University, Jilin, Jilin, China.
² College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin, Jilin, China.
³ College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, China.

Abstract

Ginseng, a valuable Chinese medicinal herb, is renowned worldwide for its effectiveness in alleviating certain conditions and promoting overall health. In this study, we performed weighted gene co-expression network analysis (WGCNA) on the accumulation of essential saponins under the influence of 13 essential environmental factors (including air temperature, air bottom temperature, surface mean temperature, soil temperature, surface shortwave radiation, soil moisture, soil water content, rainfall, total precipitation, elevation, soil type, soil pH, and soil water potential). We identified a total of 40 transcript modules associated with typical environmental factors and the accumulation of essential saponins. Among these, 18 modules were closely related to the influence of typical environmental factors, whereas 22 modules were closely related to the accumulation of essential saponins. These results were verified by examining the transcriptome, saponin contents, environmental factor information and the published data and revealed the regulatory basis of saponin accumulation at the transcriptome level under the influence of essential environmental factors. We proposed a working model of saponin accumulation mediated by the transcriptional regulatory network that is affected by typical environmental factors. An isomorphic white-box neural network was constructed based on this model and the predicted results of the white-box neural network correlated with saponin accumulation. The effectiveness of our correlation-directed graph in predicting saponin contents was verified by bioinformatics analysis based on results obtained in this study and transcripts known to affect the biosynthesis of saponin Rb1. The directed graph represents a useful tool for manipulating saponin biosynthesis while considering the influence of essential environmental factors in ginseng and other medicinal plants.

Copyright: © 2023 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ginsenosides*
Panax* / genetics
Saponins*
Soil
Transcriptome
Water

Substances

Ginsenosides
Saponins
Soil
Water

Grants and funding

1)the Education Development Plan Project of Jilin Province (No. JJKH20210415KJ,Zhc W), http://jyt.jl.gov.cn, supports study design, data collection and analysis; 2) the Science and Technology Development Plan Project of Jilin Province (No. YDZJ202201ZYTS692,Y T), http://kjt.jl.gov.cn, supports data collection and analysis, decision to publish.