Transcriptome analysis of the differences between two kinds of Cassia nomame germplasm resources

Cassia nomame belongs to the genus Cassia of the leguminous Cassia subfamily. It is used as a traditional wild Chinese herbal medicine with a long history and rich medicinal use. However, owing to limited germplasm resources and research methods, there is still a lack of understanding of C. nomame at the molecular level, especially the differences between various cultivars and secondary metabolic regulatory genes. In this study, we performed de novo transcriptome assembly of two C. nomame cultivars with different characteristics using transcriptome method. A total of 56,136 unigenes were obtained, of which 34,783 genes were annotated, including 7,309 candidate transcription factors (TFs) of 57 TF families. Through differential expression analysis, we identified 4,696 differentially expressed genes (DEGs). The results of Gene Ontology (GO) and KEGG functional enrichment analysis revealed that the DEGs were mainly involved in secondary metabolite biosynthetic process, transcriptional regulation, response to hormone, growth, and development. TF family analysis and verification experiments showed that these TFs were significantly different expressed in the two C. nomame germplasm resources, which suggested that they might be important genes affecting the traits of C. nomame. In conclusion, the results of this study are significant for mining C. nomame germplasm resources and enhancing our understanding of the formation of different germplasm resources and medicinal ingredients mining.