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.

Figure 1

Comparison of unigene length between hit and no-hit unigenes in Nr database.

Figure 2

Searching characterization of the assembled unigenes against Nr and Swiss-prot databases. (A) E-value distribution of Blast hits in Nr database; (B) E-value distribution of Blast hits in Swiss-prot database; (C) Distribution of assembled unigene similarities based on the top Blast hits in Nr database; (D) Distribution of assembled unigene similarities based on the top Blast hits in Swiss-prot database; and (E) Homology distribution among other plant species based on the top Blast hits in Nr database.

Figure 3

Histogram presentation of gene ontology (GO) functional classification. The results are summarized in three GO ontologies: biological process, cellular component and molecular function. The right y-axis indicates the number of unigenes in a category and the left y-axis indicates the percentage in the same category.

Figure 4

Histogram presentation of clusters of orthologous groups (COG) functional classification.

Figure 5

(A) Unigenes of 11 sub-categories under “metabolism” category; (B) Unigenes of 13 pathways under “other secondary metabolites biosynthesis” sub-category.

Figure 6

FPKM values of all-unigenes expressed in Pg-Con and Pg-MeJA. Each dot indicates one unigene. The dots above the yellow line indicate up-regulated genes and below this line are down-regulated genes. The horizontal coordinates represent the FPKM values of Pg-Con and the vertical coordinates the Pg-MeJA FPKM values. The X and Y-axis are in log-scale.

Figure 7

Putative ginsenoside biosynthesis pathway in P. ginseng. Enzymes encoded by unigenes found in this study are circled. MVA, mevalonate; MVAP, mevalonate phosphate; MVAPP, mevalonate diphosphate; IPP, isopentenyl diphosphate; DMAPP, dimethylallyl diphosphate; GPP, geranyl diphosphate; FPP, farnesyl diphosphate.

Figure 8

Phylogenetic analysis of 10 identified SS unigenes from our dataset and other plant SSs. Phylogenetic tree was generated using the neighbor-joining (NJ) method in MEGA4. $▲$ indicates the unigenes from our current study. The box in red outline indicates one group of genes that are more similar with each other.

Figure 9

Phylogenetic analysis of 12 potential PDR unigenes of our dataset and other plant PDRs. Among two kinds of unigenes, some having 70% similarity among them, are under one cluster (CL) initiated with “CL” along with the same number such as “CL1490”, followed by different number of contigs, whereas others start directly with “Unigene” such as “Unigene12975”. $▲$ indicates the unigenes from our current study. The box in red outline indicates one group of genes that are more similar with each other.