Objective   Base on transcriptome sequencing, the molecular mechanisms that caused the secondary metabolic differences between the leaves and roots of Sarcandra glabra were studied for clinic applications of the two parts, as well as for determination of the effective components in the medicinal herb.

  Method   Specimens of S. glabra were collected from Fuzhou, Fujian for a transcriptome analysis on the leaves and roots using the Illumina HiSeq platform. After filtration and the Trinity assembly, the unigenes were compared with Nr, Nt, Pfam, KOG, Swiss-Prot, KEGG, and GO by BLAST, and the differentially expressed genes analyzed. A special attention was paid on the differentially enriched genes in the KEGG metabolic pathway.

  Result   More than 40 million clean reads were obtained from the sequencing. The Trinity assembly yielded 508 271 unigenes with an average length of 740 bp. Based on BLAST, 148 561 unigenes, accounting for 58.80% of the total, were successfully annotated using 7 functional annotation databases. There were 29 732 unigenes identified with differential gene expressions between the leaves and the roots. Of which, 12 511 were up-regulated and 17 221 down-regulated. Dozens of significantly different KEGG metabolic pathways were found that associated with functions such as starch/sucrose metabolism, phenylpropanoid biosynthesis, glyoxylate/dicarboxylate metabolism, carbon fixation in photosynthetic organisms, phagosome/glutathione metabolism, photosynthesis, alanine/aspartate/glutamate metabolism, sesquiterpenoid/triterpenoid biosynthesis, porphyrin/chlorophyll metabolism, nitrogen metabolism, circadian rhythm-plant/photosynthesis-antenna proteins, stilbenoid/diarylheptanoid/gingerol biosynthesis, unsaturated fatty acids biosynthesis, limonene/pinene degradation, carotenoid biosynthesis, diterpenoid biosynthesis, flavonoid biosynthesis, fatty acid elongation, etc. Insofar as pharmacodynamics is concerned, the secondary metabolic pathway of the phenylpropanoid biosynthesis had 193 differentially expressed genes between the leaves and the roots, that of the sesquiterpene/triterpene biosynthesis 82, that of the diterpene biosynthesis 40, and that of the flavonoid biosynthesis 35. In addition, the up-regulated genes of sesquiterpene synthase, ent-kaur-16-ene synthase, and flavonol synthase/flavanone 3-hydroxylase, as well as the down-regulated genes of 8-hydroxygeraniol dehydrogenase, vinornine synthase, and squalene synthase were found significantly different between the two parts.

  Conclusion   The genes related to the secondary metabolic pathways of phenylalanine sesquiterpenoid and triterpenoid, diterpenes, and flavonoids most significantly differed in leaves and roots of S. glabra. The significantly differentiated genes associated with the key enzymes provided important information for analyzing the molecular mechanisms of the medicinal herb.