Dataset of full-length transcriptome assembly and annotation of a two-year-old Bupleurum chinense DC

Transcriptome sequencing has become an important tool for gene discovery in medicinal plants. Compared with next-generation sequencing (NGS), third-generation sequencing, also known as single-molecule real-time (SMRT) sequencing, provides longer reads and avoids PCR amplification, making it particularly suitable for full-length transcriptome analysis. Bupleurum chinense DC. is an important medicinal herb in China. However, genome information for B. chinense remains limited. In this study, total RNA was separately extracted from the root, stem, and leaf of a two-year-old B. chinense plant, and equal amounts of RNA from the three tissues were pooled for PacBio SMRT full-length transcriptome sequencing. This study generated the first full-length transcriptome dataset for B. chinense. The dataset includes 11,448 annotated unigenes, 690 transcription factors, and 6178 SSR markers, with many unigenes associated with terpenoid biosynthesis and other secondary metabolism pathways. The raw data were deposited in the SRA database under BioProject accession number PRJNA1494021. This dataset will facilitate gene discovery, functional characterization, saikosaponin biosynthesis research, marker development, and molecular breeding in B. chinense and related species.