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      Transcriptome Analysis of Secondary Metabolism Pathway, Transcription Factors, and Transporters in Response to Methyl Jasmonate in Lycoris aurea

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          Abstract

          Lycoris aurea, a medicinal species of the Amaryllidaceae family, is used in the practice of traditional Chinese medicine (TCM) because of its broad pharmacological activities of Amaryllidaceae alkaloids. Despite the officinal and economic importance of Lycoris species, the secondary mechanism for this species is relatively deficient. In this study, we attempted to characterize the transcriptome profiling of L. aurea seedlings with the methyl jasmonate (MeJA) treatment to uncover the molecular mechanisms regulating plant secondary metabolite pathway. By using short reads sequencing technology (Illumina), two sequencing cDNA libraries prepared from control (Con) and 100 μM MeJA-treated (MJ100) samples were sequenced. A total of 26,809,842 and 25,874,478 clean reads in the Con and MJ100 libraries, respectively, were obtained and assembled into 59,643 unigenes. Among them, 41,585 (69.72%) unigenes were annotated by basic local alignment search tool similarity searches against public sequence databases. These included 55 Gene Ontology (GO) terms, 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 25 Clusters of Orthologous Groups (COG) families. Additionally, 4,175 differentially expressed genes (DEGs; false discovery rate ≤ 0.001 and |log 2 Ratio| ≥ 1) with 2,291 up-regulated and 1,884 down-regulated, were found to be affected significantly under MeJA treatment. Subsequently, the DEGs encoding key enzymes involving in the secondary metabolite biosynthetic pathways, transcription factors, and transporter proteins were also analyzed and summarized. Meanwhile, we confirmed the altered expression levels of the unigenes that encode transporters and transcription factors using quantitative real-time PCR (qRT-PCR). With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of L. aurea may be improved. Additionally, the genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of L. aurea.

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          Most cited references50

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          TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

          TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP and PVM.
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            Elicitor signal transduction leading to production of plant secondary metabolites.

            Plant secondary metabolites are unique sources for pharmaceuticals, food additives, flavors, and other industrial materials. Accumulation of such metabolites often occurs in plants subjected to stresses including various elicitors or signal molecules. Understanding signal transduction paths underlying elicitor-induced production of secondary metabolites is important for optimizing their commercial production. This paper summarizes progress made on several aspects of elicitor signal transduction leading to production of plant secondary metabolites, including: elicitor signal perception by various receptors of plants; avirulence determinants and corresponding plant R proteins; heterotrimeric and small GTP binding proteins; ion fluxes, especially Ca2+ influx, and Ca2+ signaling; medium alkalinization and cytoplasmic acidification; oxidative burst and reactive oxygen species; inositol trisphosphates and cyclic nucleotides (cAMP and cGMP); salicylic acid and nitric oxide; jasmonate, ethylene, and abscisic acid signaling; oxylipin signals such as allene oxide synthase-dependent jasmonate and hydroperoxide lyase-dependent C12 and C6 volatiles; as well as other lipid messengers such as lysophosphatidylcholine, phosphatidic acid, and diacylglycerol. All these signal components are employed directly or indirectly by elicitors for induction of plant secondary metabolite accumulation. Cross-talk between different signaling pathways is very common in plant defense response, thus the cross-talk amongst these signaling pathways, such as elicitor and jasmonate, jasmonate and ethylene, and each of these with reactive oxygen species, is discussed separately. This review also highlights the integration of multiple signaling pathways into or by transcription factors, as well as the linkage of the above signal components in elicitor signaling network through protein phosphorylation and dephosphorylation. Some perspectives on elicitor signal transduction and plant secondary metabolism at the transcriptome and metabolome levels are also presented.
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              R Dixon (2001)
              Plants elaborate a vast array of natural products, many of which have evolved to confer selective advantage against microbial attack. Recent advances in molecular technology, aided by the enormous power of large-scale genomics initiatives, are leading to a more complete understanding of the enzymatic machinery that underlies the often complex pathways of plant natural product biosynthesis. Meanwhile, genetic and reverse genetic approaches are providing evidence for the importance of natural products in host defence. Metabolic engineering of natural product pathways is now a feasible strategy for enhancement of plant disease resistance.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                05 January 2017
                2016
                : 7
                : 1971
                Affiliations
                [1] 1Institute of Botany, Jiangsu Province and Chinese Academy of Sciences Nanjing, China
                [2] 2The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm Nanjing, China
                [3] 3Key Laboratory of Biology and Genetic Improvement of Soybean, National Center for Soybean Improvement, Ministry of Agriculture, Nanjing Agricultural University Nanjing, China
                Author notes

                Edited by: Ping Ma, University of Georgia, USA

                Reviewed by: Jingyi Zhang, University of Georgia, USA; Ziyang Ma, University of Georgia, USA

                *Correspondence: Ren Wang jswangren@ 123456aliyun.com

                This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Plant Science

                †These authors have contributed equally to this work.

                Article
                10.3389/fpls.2016.01971
                5217099
                28111578
                3a9b034e-f6eb-4491-9d0c-65baeab83559
                Copyright © 2017 Wang, Xu, Wang, Xia, Jiang and Wang.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 01 October 2016
                : 12 December 2016
                Page count
                Figures: 9, Tables: 3, Equations: 0, References: 61, Pages: 13, Words: 7095
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31270339
                Award ID: 31301798
                Award ID: 31572151
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                amaryllidaceae alkaloids,lycoris aurea,methyl jasmonate,transcriptome sequencing,secondary metabolite

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