Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis.
Danshen, Salvia miltiorrhiza Bunge, is one of the most widely used herbs in traditional Chinese medicine, wherein its rhizome/roots are particularly valued. The corresponding bioactive components include the tanshinone diterpenoids, the biosynthesis of which is a subject of considerable interest. Previous investigations of the S. miltiorrhiza transcriptome have relied on short-read next-generation sequencing (NGS) technology, and the vast majority of the resulting isotigs do not represent full-length cDNA sequences. Moreover, these efforts have been targeted at either whole plants or hairy root cultures. Here, we demonstrate that the tanshinone pigments are produced and accumulate in the root periderm, and apply a combination of NGS and single-molecule real-time (SMRT) sequencing to various root tissues, particularly including the periderm, to provide a more complete view of the S. miltiorrhiza transcriptome, with further insight into tanshinone biosynthesis as well. In addition, the use of SMRT long-read sequencing offered the ability to examine alternative splicing, which was found to occur in approximately 40% of the detected gene loci, including several involved in isoprenoid/terpenoid metabolism.
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
Zhichao
Z
Xu
Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
Reuben J
RJ
Peters
Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA.
Jason
J
Weirather
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
Hongmei
H
Luo
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
Baosheng
B
Liao
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
Xin
X
Zhang
Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China.
Yingjie
Y
Zhu
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
Aijia
A
Ji
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
Bing
B
Zhang
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
Songnian
S
Hu
Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA.
Kin Fai
KF
Au
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
Jingyuan
J
Song
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.|Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China.
Shilin
S
Chen
D045784:Abietanes / Q000096:biosynthesis* / Q000378:metabolism; D017398:Alternative Splicing; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D027561:Salvia miltiorrhiza / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods; D059467:Transcriptome
D045784:Abietanes; D010940:Plant Proteins; C021751:tanshinone
Salvia miltiorrhiza; alternative splicing; next-generation sequencing; single-molecule real-time sequencing; tanshinone biosynthesis