title: Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens.
abstract: Perilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis.
  
  
  
  Perilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses.
  
  
  
  This work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds.
authors.affiliation: Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea. hukim64@sejong.ac.kr.
authors.forename: Hyun Uk
authors.identifier: 0000-0002-4566-3057
authors.initials: HU
authors.lastname: Kim
authors.affiliation: Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea.
authors.forename: Kyeong-Ryeol
authors.initials: KR
authors.lastname: Lee
authors.affiliation: Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea.
authors.forename: Donghwan
authors.initials: D
authors.lastname: Shim
authors.affiliation: SEEDERS Inc, Daejeon, 34015, Republic of Korea.
authors.forename: Jeong Hee
authors.initials: JH
authors.lastname: Lee
authors.affiliation: U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA, 94710, USA.
authors.forename: Grace Q
authors.initials: GQ
authors.lastname: Chen
authors.affiliation: Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea.
authors.forename: Seongbin
authors.initials: S
authors.lastname: Hwang
mesh_terms: D015525:Fatty Acids, Omega-3 / Q000096:biosynthesis*; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D050356:Lipid Metabolism; D058977:Molecular Sequence Annotation; D031344:Perilla frutescens / Q000235:genetics* / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics*; D012639:Seeds / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D014280:Triglycerides / Q000378:metabolism
chemical_list: D015525:Fatty Acids, Omega-3; D010940:Plant Proteins; D014280:Triglycerides
keywords: Perilla frutescens; Seed; Transcriptome; Triacylglycerol; α-linolenic acid; ω-3 fatty acid