A high-quality reference genome sequences of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizome

Authors: SONG, ZHENQIAO - Shandong Agricultural University; LIN, CAICAI - Shandong Agricultural University; XING, PIYI - Shandong Agricultural University; FEN, YUANYUAN - Shandong Agricultural University; JIN, HUA - Shandong Agricultural University; ZHOU, CHANGHAO - Shandong Agricultural University; Gu, Yong; WANG, JIANHUA - Shandong Agricultural University; LI, XINGFENG - Shandong Agricultural University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/26/2020
Publication Date: 9/17/2020
Citation: Song, Z., Lin, C., Xing, P., Fen, Y., Jin, H., Zhou, C., Gu, Y.Q., Wang, J., Li, X. 2020. A high-quality reference genome sequences of salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizome. The Plant Genome. 13(3). Article e20041. https://doi.org/10.1002/tpg2.20041.
DOI: https://doi.org/10.1002/tpg2.20041

Interpretive Summary: The PacBio single molecular sequencing technology was employed to generate long sequence reads to assemble the genome of Salvia miltiorrhiza, a plant species with important value in traditional Chinese medicine. Sequence analyses on the assembled sequences revealed that the S. miltiorrhiza genome contains 32,483 protein-coding genes. Approximate 64.84% of the sequences belong to repetitive DNAs that can be further divided into different categories including long terminal repeat (LTR) transposable elements (LTR TEs). The high percentage of young LTR TEs suggests that multiple TE transposition bursts occurred recently in S. miltiorrhiza, resulting in a rapid evolutionary change of its genome structure. We found that genes involved in secondary metabolism pathways have been expanded and that these genes often have high expression levels in root tissues, providing an explanation of active biosynthesis of chemical components in a tissue-specific manner. The reference genome sequence generated in this work provides a value resource for future studies on elucidation of secondary metabolism synthesis pathway in S. miltiorrhiza and for genetic improvement of important traits.

Technical Abstract: Salvia miltiorrhiza Bunge, also known as red sage or Danshen, is an important traditional Chinese medicine to treat cardiovascular and other diseases. Here, a high-quality reference genome of S. miltiorrhiza was generated by combining PacBio long read sequencing and chromatin interaction mapping (Hi-C) technologies, resulting in the chromosome-scale assembly of a 594.75-Mb genome sequence with a contig N50 of 2.70 Mb. The S. miltiorrhiza genome contained 32,483 protein-coding genes with repetitive DNA content about 64.84%. The high percentage of young LTRs suggests that multiple TE transposition bursts occurred recently in S. miltiorrhiza. Genes unique to secondary metabolism pathways were expanded in the S. miltiorrhiza genome. Based on a novel experiment design and transcriptomic analyses, we revealed high expressions of many tanshinone biosynthesis genes and gene clusters in the phloem of red roots where active components are synthesized. This reference genome sequence will facilitate future studies on elucidation of secondary metabolism synthesis pathway and genetic improvement of S. miltiorrhiza.