Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis

BMC Genomics. 2015 Mar 14;16(1):180. doi: 10.1186/s12864-015-1357-z.

Abstract

Background: Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant.

Result: In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes involved in the saponin biosynthetic pathway.

Conclusions: The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Gene Expression Profiling*
  • High-Throughput Nucleotide Sequencing
  • Intramolecular Transferases / genetics
  • Mevalonic Acid / metabolism
  • Molecular Sequence Annotation
  • Panax / classification
  • Panax / genetics*
  • Panax / metabolism*
  • Phylogeny
  • Plant Proteins / genetics
  • Saponins / biosynthesis*
  • Transcriptome*

Substances

  • Plant Proteins
  • Saponins
  • Intramolecular Transferases
  • lanosterol synthase
  • Mevalonic Acid