Pinellia (Pinellia ternata (Thunb.) Breit.), as important medicinal plant, has been used to treat various ailments for a long time. The sixteen ploid plant (2n = 16 * 13 = 208) Pinellia T2Plus line was obtained from an octoploid (2n = 8 * 13 = 104) T2 line by chromosome-doubling technique. Compared with T2 line, the content of various medicinal components (polysaccharide, guanosine, adenosine and ephedrine) was increased in T2Plus line. In this study, the transcriptome of T2 line and T2Plus line were characterized by RNA sequencing (RNA-seq) technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis on differential expressed unigenes (DEGs) revealed that multiple metabolic pathway were enriched significantly, such as 'Starch and sucrose metabolism', 'Purine metabolism', 'Photosynthesis' and six transcription factors (MYB, WRKY, bHLH, lateral organ boundaries domain (LBD), homeodomain-zipper (HD-ZIP) and Ethylene-responsive factor (ERF)) play a key role in difference of transcriptome between T2 line and T2Plus line. These metabolic pathways and transcription factors may play an important role in the difference of medicinal components and epigenetic features between these two Pinellia cultivars. This conclusion provides a robust theoretical basis for the mechanism of the formation of medicinal ingredients in Pinellia cultivars. Pinellia (Pinellia ternata (Thunb.) Breit.), mainly distributed in Eastern Asia, has been used to treat various ailments for a long time, such as vomiting, inflammation, cough, epilepsy, cervical cancer and traumatic injury, etc 1. A wide range of biological activities in Pinellia was revealed by pharmacological studies and these activities include sedative and hypnotic 2 , anti-tumor 3 , anti-emetic 4 , anti-inflammatory and antitussive 5 , antibacterial and anti-inflammatory 6. Due to the higher medicinal value and longer life cycle of Pinellia, overexploitation of the wild resources of this Pinellia led to the phenomenon of undersupply undersupply. Therefore, it is necessary to obtain high-yield Pinellia cultivar to sustain balance both the market and the abundance of this species. Genomic polyploidization not only produce new phenotypic traits, but also stronger environmental/stress adaptation, thereby enabling diversification and speciation and driving the evolution and divergence in gene function and plant behavior 7. The polyploid genome is affected the gene expression in response to stress and hormones, thus polyploids tend to exhibit greater tolerance in salt, heat and drought 8-12 ,. In addition, the yield of polyploid plants is generally increased. For example, polyploid sugar beet is provided with the characteristics of nutrient growth, high root yield and high sugar content 13. Artificially induced plant polyploids showing excellent traits have been widely used in agriculture, providing abundant germplasm resources for agricultural production 14-18. The apparent characteristics of plants are closely related to the expression of...