Comparative transcriptome analysis reveals a gene expression profile that contributes to rhizome swelling in Panax japonicus var. major

Panax japonicus var. major is a rare and endangered Chinese traditional medicinal plant that simultaneously forms two types of rhizomes (Swp: Swollen part and Slp: Slender part). However, the mechanism controlling rhizome enlargement in P. japonicus var. major is poorly understood. In this study, the mechanism of rhizome enlargement was investigated by comparing the differences of internal anatomy, hormone contents, starch content and molecular transcription levels between Swp and Slp of in P. japonicus var. major. Illumina sequencing generated 1,333 differentially expressed genes (DEGs) that were differentially expressed between the two samples. Pathway enrichment analysis revealed that DEGs involved in starch and sucrose metabolism, diterpenoid biosynthesis and plant hormone signal transduction pathway were significantly enriched. Additionally, starch determination results showed that starch content in the swollen part was significantly higher than that in the slender part. Furthermore, hormone determination results showed that gibberellin A1 (GA1), gibberellin A53 (GA53), indole-3-acetic acid (IAA) and jasmonic acid (JA) contents were negatively correlated, while cis-zeatin (cZ) content was positively correlated with rhizome enlargement. The results of this research screened out several DEGs and potential candidate genes for rhizome enlargement, which lays the foundation for the identification of expanded genes in Panax species.