Comparative transcriptome analysis provides novel insights into the seed germination of Panax japonicus, an endangered species in China.

Panax japonicus, an endangered species in China, is usually used as a traditional medicine with functions of hemostasis, pain relief, and detoxify. However, the seeds of P. japonicus are hard to germinate in natural conditions, and the molecular events and systematic changes occurring in seed germination are still largely unknown. In this study, we compared the seeds in different germination stages in terms of morphological features, antioxidant enzyme activities, and transcriptomics. The results indicated that sand storage at 25℃ for 120 d effectively released the seed dormancy of P. japonicus and promoted the seed germination. Moreover, sand storage treatment increased the antioxidant capacity of P. japonicus seeds through increasing the activities of SOD, POD, and CAT. The RNA-seq identified 28,908 differentially expressed genes (DEGs) between different germination stages, of which 1697 DEGs significantly changed throughout the whole germination process. Functional annotations showed that the seed germination of P. japonicus was mainly regulated by the DEGs related to pathways of ROS-scavenging metabolism, plant hormonal signal transduction, starch and sucrose metabolism, energy supply (glycolysis, pyruvate metabolism, and oxidative phosphorylation), and phenylpropanoid biosynthesis, as well as the transcription factors such as bHLHs, MYBs, WRKYs, and bZIPs. This study provides a foundation for unveiling molecular mechanisms underlying the seed germination and is beneficial for accelerating the development of P. japonicus industry.