Transcriptome analysis and identification of genes associated with omega-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

Authors: KIM, HYUN UK - Sejong University; LEE, KYONG-RYEOL - Jeonju University; DONGHWAN, SHIM - Seowon University, Korea; LEE, JEONG-HEE - Seeders, Inc; Chen, Grace; HWANG, SEONG BIN - Sejong University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/25/2016
Publication Date: 6/29/2016
Citation: Kim, H., Lee, K., Donghwan, S., Lee, J., Chen, G.Q., Hwang, S. 2016. Transcriptome analysis and identification of genes associated with omega-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens. Biomed Central (BMC) Genomics. 17:474. doi: 10.1186/s12864-016-2805-0.

Interpretive Summary: Perilla frutescens, a high omega-3 fatty acid accumulator, is a cultivated crop of the mint family Lamiaceae. Two distinct varieties, P. frutescens, the oilseed crop for source of perilla oil, and P. crisp for the aromatic leafy herb, are widely used as food ingredients. Perilla oil also has many industrial uses, such as for drying oil in paint, varnish and ink manufacturing, or as a substitute for linseed oil [6]. Perilla seed cakes are used as animal and bird feed. In this study, Illumina HiSeq 2000 platform was used to analyze the seeds and leaf transcriptome which allows a deep coverage of transcripts and detection of differentially expressed gene (DEG) in developing seeds of perilla. A total of 54,079 unique transcripts were identified from 392 mega-base raw sequences, including transcripts for the majority of enzymes involved in lipid biosynthesis and metabolism. We further characterize the expression profiles of 43 key genes involved in fatty acid and oil synthesis using quantitative PCR (qPCR) assays. Our results provide important information for understanding the mechanisms involved in the omega-3 fatty acid accumulation in perilla.

Technical Abstract: Background: Perilla (Perilla frutescens (L.) var frutescens) produces high levels of a-linolenic acid (ALA), an omega-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 to better-understand the mechanisms underlying ALA and seed TAG biosynthesis. Results: 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. Conclusions: This work is the first report on building transcriptomes from perilla seeds and leaves. 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.