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

Abstract

Background Codonopsis pilosula (Franch.) Nannf. is one of the most widely used medicinal plants. Although chemical and pharmacological studies have shown that codonopsis polysaccharides (CPPs) are bioactive compounds and that their composition is variable, their biosynthetic pathways remain largely unknown. Next-generation sequencing is an efficient and high-throughput technique that allows the identification of candidate genes involved in secondary metabolism.Principal FindingsTo identify the components involved in CPP biosynthesis, a transcriptome library, prepared using root and other tissues, was assembled with the help of Illumina sequencing. A total of 9.2 Gb of clean nucleotides was obtained comprising 91,175,044 clean reads, 102,125 contigs, and 45,511 unigenes. After aligning the sequences to the public protein databases, 76.1% of the unigenes were annotated. Among these annotated unigenes, 26,189 were assigned to Gene Ontology categories, 11,415 to Clusters of Orthologous Groups, and 18,848 to Kyoto Encyclopedia of Genes and Genomes pathways. Analysis of abundance of transcripts in the library showed that genes, including those encoding metallothionein, aquaporin, and cysteine protease that are related to stress responses, were in the top list. Among genes involved in the biosynthesis of CPP, those responsible for the synthesis of UDP-L-arabinose and UDP-xylose were highly expressed.SignificanceTo our knowledge, this is the first study to provide a public transcriptome dataset prepared from C. pilosula and an outline of the biosynthetic pathway of polysaccharides in a medicinal plant. Identified candidate genes involved in CPP biosynthesis provide understanding of the biosynthesis and regulation of CPP at the molecular level.

Whole-transcriptome sequencing of Pinellia ternata using the Illumina platform

“…The sequencing produced 193,032,910 clean reads and 53,544 unigenes after assembly. 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).…”

Response of Bioactive Metabolite and Biosynthesis Related Genes to Methyl Jasmonate Elicitation in Codonopsis pilosula

“…In general, polysaccharide ingredients are known for their activity in strengthening the human body’s immunity, i.e., ganoderma polysaccharides and ginseng polysaccharides. In addition, codonopsis polysaccharides (CPPs) are capable of preventing tumor growth, improving memory, curing diabetes, and increasing hemoglobin [24]. Yang et al [44] demonstrated that CPPs are an acidic hetero-polysaccharide composed of arabinose, glucose, rhamnose, galactose, mannose, glucuronic acid, and galacturonic acid.…”

“…are traditionally used in Chinese medicine for replenishing qi (vital energy) deficiency, strengthening the immune system, improving poor gastrointestinal function, curing gastric ulcers, and appetite [21]. The bioactive constituents are mainly composed of alkaloids [22], phenylpropanoids, polyacetylenes [23], polysaccharides [24], and terpenoids [25]. Lobetyolinin and lobetyolin, which is effective in protecting the gastric mucosa, are the major ingredients of polyacetylenes in C. pilosula [26], while the most common terpenoid is atractylenolide III, which has anti-inflammatory activity [27].…”

Comparative Transcriptome Analysis Uncovers Genes and Pathways Relating to Downy Mildew Resistance in Isabgol (Plantago ovata Forsk.)

“…Raphanus sativus (773bp) [45], Camelia sinensis (521bp) [47] and Codonopsis pilosula (1,243bp) [48] infers fairly good assembly of transcriptome of the study. We predicted, 26569, 18605, 28588 and 22599 CDS respectively in SI, SU, RI and RU of Isabgol transcriptome of which more than 90% have blast hits in 'nr' database of NCBI which is comparatively higher than reported in Isabgol [34] and grapes [23][24] and pearl millet [27].…”