title: Temporal transcriptome changes induced by methyl jasmonate in Salvia sclarea.
abstract: Salvia sclarea is a traditional medicinal and aromatic plant that grows in Europe and produces various economically important compounds, including phenylpropanoid derivatives and terpenoids. Methyl jasmonate (MeJA) is commonly used to elicit plant stress responses. However, how MeJA enhances production of secondary metabolites in S. sclarea is not well understood. We performed a genome-wide analysis of temporal gene expression in S. sclarea leaves and roots. The transcriptome profiles 0, 10 and 26 h after MeJA treatment were analyzed by Illumina RNA-Seq. A total of 16,142 isogenes (average length 866bp; N50 1035bp) were obtained by de novo assembly of 35,757,567 raw sequencing reads. When these sequencing reads were mapped onto the assembled Unigenes, 3236, 2792 and 798 Unigenes were found to be expressed differentially between 0 and 10h, 0 and 26 h, and 10 and 26h, respectively. These included many secondary metabolite biosynthesis, stress and defense-related genes. A qRT-PCR analysis confirmed the expression profiles of selected differentially expressed genes (DEGs) revealed by RNA-Seq data, and also extended our analysis of differential gene expression to 73 h. Our investigations revealed temporal differences in the responses of S. sclarea to MeJA treatment. MeJA treatment induced the expression of a large number of genes involved in phenylpropanoid biosynthesis, especially between 0 and 10h, and 0 and 26 h. Additionally, many genes encoding transcription factors, cytochrome P450s, glycosyltransferases, methyltransferases and transporters were shown to respond to MeJA elicitation. DEGs related to structural molecule activity and cell death showed a significant temporal variation. A chromatographic analysis of metabolites at 26h, 73h and six days after MeJA treatment indicated that these transcriptomic changes precede MeJA-induced changes in secondary metabolite content. This study sheds light on the molecular mechanisms of MeJA elicitation and is helpful in understanding how exogenous MeJA treatment mediates extensive plant transcriptome reprogramming/remodeling. Our results can be utilized to characterize genes related to secondary metabolism and their regulation, and in breeding S. sclarea for desirable chemotypes.
authors.affiliation: Biotechnology Institute, School of Environment, Dalian Jiaotong University, Dalian 116028, China. Electronic address: haodc@126.com.
authors.forename: Da Cheng
authors.initials: da C
authors.lastname: Hao
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Shi Lin
authors.initials: SL
authors.lastname: Chen
authors.affiliation: Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK. Electronic address: anne.osbourn@jic.ac.cn.
authors.forename: Anne
authors.initials: A
authors.lastname: Osbourn
authors.affiliation: Department of Chemistry, University of Ioannina, Ioannina GR-45110, Greece.
authors.forename: Vassiliki G
authors.initials: VG
authors.lastname: Kontogianni
authors.affiliation: Department of Mathematics, School of Science, Dalian Jiaotong University, Dalian 116028, China.
authors.forename: Li Wei
authors.initials: LW
authors.lastname: Liu
authors.affiliation: Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), Departamento de Recursos Naturales y Desarrollo Rural, C./Mayor s/n, 30150 La Alberca, Murcia, Spain.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Jordán
mesh_terms: D000085:Acetates / Q000494:pharmacology*; D003517:Cyclopentanes / Q000494:pharmacology*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D053858:Metabolic Networks and Pathways; D054883:Oxylipins / Q000494:pharmacology*; D010937:Plant Growth Regulators / Q000494:pharmacology*; D018515:Plant Leaves / Q000235:genetics; D018517:Plant Roots / Q000235:genetics; D027544:Salvia / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D000085:Acetates; D003517:Cyclopentanes; D054883:Oxylipins; D010937:Plant Growth Regulators; C072239:methyl jasmonate
keywords: De novo assembly; Growth; Metabolism; Methyl jasmonate; Salvia sclarea; Transcriptome sequencing