De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum

Abstract

Various active components have been extracted from the root of Polygonum cuspidatum. However, the genetic basis for their activity is virtually unknown. In this study, 25600002 short reads (2.3 Gb) of P. cuspidatum root transcriptome were obtained via Illumina HiSeq 2000 sequencing. A total of 86418 unigenes were assembled de novo and annotated. Twelve, 18, 60 and 54 unigenes were respectively mapped to the mevalonic acid (MVA), methyl-D-erythritol 4-phosphate (MEP), shikimate and resveratrol biosynthesis pathways, suggesting that they are involved in the biosynthesis of pharmaceutically important anthraquinone and resveratrol. Eighteen potential UDP-glycosyltransferase unigenes were identified as the candidates most likely to be involved in the biosynthesis of glycosides of secondary metabolites. Identification of relevant genes could be important in eventually increasing the yields of the medicinally useful constituents of the P. cuspidatum root. From the previously published transcriptome data of 19 non-model plant taxa, 1127 shared orthologs were identified and characterized. This information will be very useful for future functional, phylogenetic and evolutionary studies of these plants.

Transcriptome Sequencing of Codonopsis pilosula and Identification of Candidate Genes Involved in Polysaccharide Biosynthesis

“…Compared to datasets published on medicinal plants, the number of unigenes obtained from C . pilosula was lower than that obtained from Polygonum cuspidatum (86,418), Dimocarpus longan (68,925), and Hypericum perforatum (59,184), but was higher than that from Siraitia grosvenorii (43,891) [21, 24, 52, 53]. However, the average length of unigenes obtained here was 728 bp, which was longer than that from other medicinal plants, including P .…”

“…To date, a large volume of sequences relevant to the biosynthesis of a number of natural products has been identified using this technique [19–24]. However, these efforts focused primarily on the biosynthesis of flavonoids, unsaturated fatty acids, triterpenoid sapogenins, and saponins.…”

Whole-transcriptome sequencing of Pinellia ternata using the Illumina platform

“…The number of unigenes obtained from P. ternata was lower than that obtained from Carthamus tinctorius (120,778) (Lulin et al, 2012), Polygonum cuspidatum (86,418) (Hao et al, 2012), and Salvia miltiorrhiza (64,139) , However, the number of unigenes obtained from P. ternata was higher than that from Codonopsis pilosula (45,511) (Gao et al, 2015), and Isatis indigotica (36,367) (Chen et al, 2013). The average unigene length (611 bp) was slightly greater than that of other medicinal plants, including C. tinctorius (446 bp) (Lulin et al, 2012), S. miltiorrhiza (413 bp) , and P. cuspidatum (365 bp) (Hao et al, 2012). The unigene annotation rate observed in the present study (79.72%) was relatively higher.…”

Chemical and biological research of Clematis medicinal resources

“…the biosynthetic pathway of secondary metabolites has not been studied; the regulation of Clematis biological processes at genomic level, epigenomic level [63], transcriptional and post-transcriptional levels, and translational and post-translational levels is totally unknown, although it is essential for the conservation, sustainable development and utilization of the Clematis medicinal resources. The biological and chemical studies of Taxus [57] and Polygonum [58] with the use of omics technologies provide a paradigm of the active integration of various state-of-the-art methodologies into the early stage of the drug research and development. Systems biology and omics techniques will play an increasingly significant role in future medical research involving bioactive compounds of Clematis.…”