Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao

Abstract

BackgroundAstragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus, family Leguminosae) is one of the most important traditional Chinese herbs. Among many secondary metabolites it produces, the effective bioactive constituents include isoflavonoids and triterpene saponins. The genomic resources regarding the biosynthesis of these metabolites in A. mongolicus are limited. Although roots are the primary material harvested for medical use, the biosynthesis of the bioactive compounds and its regulation in A. mongolicus are not well understood. Therefore, a global transcriptome analysis on A. mongolicus tissues was performed to identify the genes essential for the metabolism and to profile their expression patterns in greater details.ResultsRNA-sequencing was performed for three different A. mongolicus tissues: leaf, stem, and root, using the Illumina Hiseq2000 platform. A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. Among them, 129,966 unigenes (~69.7%) were annotated using four public databases (Swiss-Prot, TrEMBL, CDD, Pfam), and 90,202, 63,946, and 78,326 unigenes were found to express in leaves, roots, and stems, respectively. A total of 8,025 transcription factors (TFs) were identified, in which the four largest families, bHLH, MYB, C3H, and WRKY, were implicated in regulation of tissue development, metabolisms, stress response, etc. Unigenes associated with secondary metabolism, especially those with isolavonoids and triterpene saponins biosynthesis were characterized and profiled. Most genes involved in the isoflavonoids biosynthesis had the lowest expression in the leaves, and the highest in the stems. For triterpene saponin biosynthesis, we found the genes in MVA and non-MVA pathways were differentially expressed among three examined tissues, indicating the parallel but compartmentally separated biosynthesis pathways of IPP and DMAPP in A. mongolicus. The first committed enzyme in triterpene saponin biosynthesis from A. mongolicus, cycloartenol synthase (AmCAS), which belongs to the oxidosqualene cyclase family, was cloned by us to study the astragalosides biosynthesis. Further co-expression analysis indicated the candidate CYP450s and glycosyltransferases (GTs) in the cascade of triterpene saponins biosynthesis. The presence of the large CYP450 families in A. mongolicus was further compared with those from Medicago truncatula and Arabidopsis thaliana, and the diversity and phylegenetic relationships of the CYP450 families were established.ConclusionA transcriptome study was performed for A. mongolicus tissues to construct and profile their metabolic pathways, especially for the important bioactive molecules. The results revealed a comprehensive profile for metabolic activities among tissues, pointing to the equal importance of leaf, stem, and root in A. mongolicus for the production of bioactive compounds. This work provides valuable resources for bioengineering and in vitro synthesis of the natural compounds for medica...

Transcriptome Analysis to Identify the Putative Biosynthesis and Transport Genes Associated with the Medicinal Components of Achyranthes bidentata Bl.

“…In present study, multiple transcripts which encoded some of the known enzymes participated in the MVA pathway and the saponin biosynthesis pathway were found in traditional herbs, e.g., Panax ginseng (Cao et al, 2015), Phyllanthus amarus (Mazumdar and Chattopadhyay, 2016), Panax japonicus (Rai et al, 2016), Astragalus membranaceus Bge (Chen et al, 2015), and Eleutherococcus senticosus (Hwang et al, 2015). Genes involved in the MVA pathway in the A. bidentata transcriptome included 3-hydroxy-3-methylglutaryl CoA synthase (HMGS), HMG-CoA reductase (HMGR), phosphomevalonate kinase (PMK), mevalonate-5-diphosphate decarboxylase (MDD), isopentenyl diphosphate isomerase (IDI), geranyl diphosphate synthase (GPPS), farnesyl diphosphate synthase (FPS), geranylgeranyl diphosphate synthase (GGPPS), squalene synthase (SS), squalene epoxidase(SE), beta-amyrin synthase (β-AS), and CAS.…”

“…Most of the genes involved in triterpene saponins biosynthesis showed higher expression in root tissues compared with leaf tissues ( Figure 8 ). Additionally, more experiments showed that genes involved in pathway of saponion biosynthesis displayed similar expression pattern in Panax japonicus (Rai et al, 2016), and Astragalus membranaceus Bge (Chen et al, 2015). However, the CAS gene was significantly down-regulated in root tissues.…”

“…However, little is known about the modification reaction after cyclization in saponin biosynthesis. More recent studies have shown that some cytochrome P450 monooxygenases (CYP450s) and glycosyl transferases (GTs) are assumed to perform modifications on triterpenoid skeletons, including hydroxylation and glycosidation, which leads to the generation of various triterpenoids (Chen et al, 2015). These enzymes exist as supergene families in the plant genome.…”

De novo Transcriptome Analysis Revealed Genes Involved in Flavonoid and Vitamin C Biosynthesis in Phyllanthus emblica (L.)

“…The high throughput transcriptome sequencing and analyses have become a versatile method for gene discovery and expression profiling in recent years (Kalra et al, 2013; Chen et al, 2015). The Illumina sequencing technology has proven to be an exceptionally successful in a wide variety of whole-transcriptome investigations, particularly for the characterization of non-model organisms where reference genome is not available (Wilhelm et al, 2008; Tang et al, 2011; Chen et al, 2015; Kumar S. et al, 2015).…”

“…The Illumina sequencing technology has proven to be an exceptionally successful in a wide variety of whole-transcriptome investigations, particularly for the characterization of non-model organisms where reference genome is not available (Wilhelm et al, 2008; Tang et al, 2011; Chen et al, 2015; Kumar S. et al, 2015). Several computational tools for de novo assembly of short read sequence data and identification of genes involved in various metabolic pathways have also been demonstrated (Pertea et al, 2003; Zerbino and Birney, 2008; Grabherr et al, 2011; Fu et al, 2012).…”