Transcriptome Analysis of Methyl Jasmonate-Elicited Panax ginseng Adventitious Roots to Discover Putative Ginsenoside Biosynthesis and Transport Genes

Abstract

The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of a few expressed sequence tags (ESTs) using the traditional Sanger method. Here, approximately 53 million clean reads of adventitious root transcriptome were separately filtered via Illumina HiSeq™2000 from two samples treated with MeJA (Pg-MeJA) and equal volumes of solvent, ethanol (Pg-Con). Jointly, a total of 71,095 all-unigenes from both samples were assembled and annotated, and based on sequence similarity search with known proteins, a total of 56,668 unigenes was obtained. Out of these annotated unigenes, 54,920 were assigned to the NCBI non-redundant protein (Nr) database, 35,448 to the Swiss-prot database, 43,051 to gene ontology (GO), and 19,986 to clusters of orthologous groups (COG). Searching in the Kyoto encyclopedia of genes and genomes (KEGG) pathway database indicated that 32,200 unigenes were mapped to 128 KEGG pathways. Moreover, we obtained several genes showing a wide range of expression levels. We also identified a total of 749 ginsenoside biosynthetic enzyme genes and 12 promising pleiotropic drug resistance (PDR) genes related to ginsenoside transport.

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.…”

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

“…Transcriptome sequencing/analysis is very effective tool for gene identi cation [53][54][55][56] and to identify gene expression at different developmental stages or physiological conditions of a cell [47]. Illumina HiSeq™ 4000 technology is effective, timeless, affordable, trusty tool for transcriptome description and gene detection in non-model plants as well.…”

“…fuscidiscus and P. ginseng in the National Center for Biotechnology Information (NCBI) database are available (August 2019), while no ESTs are available in GenBank for P. vietnamensis. Previous studies investigated the genetic variation and veri ed the taxonomic status of the Panax species at the molecular level [40][41][42][43][44][45][46][47][48][49]. However, few researchers studied the P. vietnamensis in Vietnam [50][51][52].…”

Identification of effective membrane efflux transporters against β‐amyrin through molecular docking approach

“…However, it was difficult and time‐consuming to select hundreds and thousands of transporters for some specific compound to know whether it will efflux the target compound or not as there are thousands of transport proteins in different organisms . In the present study, integral membrane proteins were selected, previously, PgPDR3 an integral membrane protein was identified to be responsible in the ginsenoside accumulation and might be responsible for its efflux from cell . The purine permease (PUP) transporter is also an integral membrane protein showing high affinity to purine, cytosine and adenine derivatives .…”

“…27 In the present study, integral membrane proteins were selected, previously, PgPDR3 an integral membrane protein was identified to be responsible in the ginsenoside accumulation and might be responsible for its efflux from cell. 29,30 The purine permease (PUP) transporter is also an integral membrane protein showing high affinity to purine, cytosine and adenine derivatives. 31 Moreover, it was also important to explore the localization of the membrane protein.…”