Deep sequencing reveals transcriptome re-programming of Polygonum multiflorum thunb. roots to the elicitation with methyl jasmonate

Abstract

The phytohormone methyl jasmonate (MeJA) has been successfully used as an effective elicitor to enhance production of stilbenoid which is induced in plants as a secondary metabolite possibly in defense against herbivores and pathogens. However, the mechanism of MeJA-mediated stilbenoid biosynthesis remains unclear. Genomic information for Polygonum multiflorum Thunb. (P. multiflorum) is currently unavailable. To obtain insight into the global regulation mechanism of MeJA in the steady state of stilbene glucoside production (26 h after MeJA elicitation), especially on stilbene glucoside biosynthesis, we sequenced the transcriptomes of MeJA-treated and untreated P. multiflorum roots and obtained more than 51 million clean reads, from which 79,565 unigenes were obtained by de novo assembly. 56,972 unigenes were annotated against databases including Nr, Nt, Swiss-Prot, KEGG and COG. 18,677 genes expressed differentially between untreated and treated roots. Expression level analysis indicated that a large number of genes were associated with plant-pathogen interaction, plant hormone signal transduction, stilbenoid backbone biosynthesis, and phenylpropanoid biosynthesis. 15 known genes involved in the biosynthesis of stilbenoid backbone were found with 7 genes showing increased transcript abundance following elicitation of MeJA. The significantly up (down)-regulated changes of 70 genes in stilbenoid biosynthesis were validated by qRT-PCR assays and PCR product sequencing. According to the expression changes and the previously proposed enzyme functions, multiple candidates for the unknown steps in stilbene glucoside biosynthesis were identified. We also found some genes putatively involved in the transcription factors. This comprehensive description of gene expression information could greatly facilitate our understanding of the molecular mechanisms of MeJA-mediated stilbenoid biosynthesis in P. multiflorum roots. Our results shed new light on the global regulation mechanism by which MeJA regulates the physiology of P. multiflorum roots and is helpful to understand how MeJA elicits other plant species besides P. multiflorum.

Keywords: Methyl jasmonate; Polygonum multiflorum thunb.; Real-time fluorescence quantitative PCR; Transcriptional profile.

Fig. 1

Functional annotation of assembled unigenes based on gene ontology (GO) categorization

Fig. 2

Clusters of orthologous groups (COG) classification of unigenes in non-elicited and elicited samples. A RNA processing and modification, B chromatin structure and dynamics, C energy production and conversion, D cell cycle control, cell division, chromosome partitioning, E amino acid transport and metabolism, F nucleotide transport and metabolism, G carbohydrate transport and metabolism, H coenzyme transport and metabolism, I lipid transport and metabolism, J translation, ribosomal structure and biogenesis, K transcription, L replication, recombination and repair, M cell wall/membrane/envelope biogenesis, N cell motility, O posttranslational modification, protein turnover, chaperones, P inorganic ion transport and metabolism, Q secondary metabolism biosynthesis, transport and catabolism, R general function prediction only, S function unknown, T signal transduction mechanisms, U intracellular trafficking, secretion, and vesicular transport, V defense mechanisms, W extracellular structures, Y nuclear structure, Z cytoskeleton

Fig. 3

Histogram presentation of clusters of orthologous groups (COG) classification of unigenes in control vs treatment

Fig. 4

Plant–pathogen interaction elicited by MeJA in P. multiflorum roots

Fig. 5

“Phenylpropanoid biosynthesis” induced by MeJA in P. multiflorum roots

Fig. 6

“Stilbenoid, diarylheptanoid and gingerol biosynthesis” induced by MeJA in P. multiflorum roots