The Spatial and Temporal Transcriptomic Landscapes of Ginseng, Panax ginseng C. A. Meyer.

Kangyu Wang,Rui Yin,Chunyu Sun,Meiping Zhang,Shicui Jiang,Yanping Lin,Yi Wang

doi:10.1038/srep18283

Abstract

Ginseng, including Asian ginseng (Panax ginseng C. A. Meyer) and American ginseng (P. quinquefolius L.), is one of the most important medicinal herbs in Asia and North America, but significantly understudied. This study sequenced and characterized the transcriptomes and expression profiles of genes expressed in 14 tissues and four different aged roots of Asian ginseng. A total of 265.2 million 100-bp clean reads were generated using the high-throughput sequencing platform HiSeq 2000, representing >8.3x of the 3.2-Gb ginseng genome. From the sequences, 248,993 unigenes were assembled for whole plant, 61,912–113,456 unigenes for each tissue and 54,444–65,412 unigenes for different year-old roots. We comprehensively analyzed the unigene sets and gene expression profiles. We found that the number of genes allocated to each functional category is stable across tissues or developmental stages, while the expression profiles of different genes of a gene family or involved in ginsenoside biosynthesis dramatically diversified spatially and temporally. These results provide an overall insight into the spatial and temporal transcriptome dynamics and landscapes of Asian ginseng, and comprehensive resources for advanced research and breeding of ginseng and related species.

Highlights

Medicinal plants are important to human health and medicine, but most of them are significantly understudied, especially in modern genetics and genomics
We identified the genes involved in triterpenoid biosynthesis that is believed playing an important role in ginsenoside biosynthesis, and analyzed their activities and co-expression networks in different tissues and different year-old roots
Since root systems are major medical products of ginseng and the medical values of ginseng increase rapidly as their ages increase, they were collected from 5, 12, 18- and 25-year old plants

Summary

Introduction

Medicinal plants are important to human health and medicine, but most of them are significantly understudied, especially in modern genetics and genomics. Genome research has been shown in many plants and animals to be significant for enhanced isolation, characterization and utilization of genes of economic importance. We identified the genes involved in triterpenoid biosynthesis that is believed playing an important role in ginsenoside biosynthesis, and analyzed their activities and co-expression networks in different tissues and different year-old roots. The results and findings of this study provide a first overall overview of ginseng gene functions and expression activities in different tissues and at different developmental stages, and resources essential for advanced research and applications of economic genes of ginseng and related species

Methods

Results

Discussion

Conclusion