Send to

Choose Destination
BMC Genomics. 2016 Jun 24;17:474. doi: 10.1186/s12864-016-2805-0.

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

Author information

Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea.
Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea.
Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea.
SEEDERS Inc, Daejeon, 34015, Republic of Korea.
U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA, 94710, USA.
Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea.



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.


Perilla frutescens; Seed; Transcriptome; Triacylglycerol; α-linolenic acid; ω-3 fatty acid

[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center