Isodon serra and Isodon lophanthoides var. lophanthoides Transcriptome. Isodon

Background: ‘Xihuangcao’ herb has been used as a Chinese herbal medicine for centuries; the difficulty discriminating between the plants that produce this herb hinders its exploration. To facilitate the molecular identification of the original plants, we conducted a transcriptomic analysis of two closely related species: Isodon serra (Maxim.) (IS) and I. lophanthoides (Buch.-Ham. ex D. Don) Hara. Expressed sequence tag (EST)-derived simple sequence repeat (SSR; EST-SSR) markers developed from these transcriptomes are powerful tools for resolving taxonomic problems and standardizing ‘Xihuangcao’-based products in the medicinal market.Results: We obtained 149,650 and 103,221 contigs with N50 values of 1,400 and 1,516 for the IS and I. lophanthoides RNA-Seq datasets, respectively. These contigs were clustered into 107,777 and 68,220 unigenes, which were functionally annotated to identify those genes involved in therapeutic components. A total of 14,138 and 11,756 EST-SSR motifs were identified from the IS and I. lophanthoides unigene datasets, respectively. Of these motifs, 7,453 and 6,428 SSR motifs were used to design primers for IS and I. lophanthoides, respectively. After PCR verification and fluorescence-based genotyping, 24 SSR markers with bright bands, high polymorphism, and single amplification were obtained and used to identify closely related Isodon species/varieties.Conclusion: We characterized the transcriptomic datasets for two ‘Xihuangcao’ herb species, analyzed the function of unigenes generated from these two species, and developed SSR markers. The transcriptomic data will help to determine the mechanism of medicinal component synthesis, help herbal scientists to identify high-quality herbal plants, and provide references for genetic improvement and population genetic and phylogenetic studies in ‘Xihuangcao’ herbs.