title: Gene set by de novo assembly of Perilla species and expression profiling between P. frutescens (L.) var. frutescens and var. crispa.
abstract: Perilla frutescens (L.) Britt. is a self-pollinating annual species and is widely cultivated in China, Korea and Japan as an economic crop and a source of medicine and spices. In this study, we sequenced one cultivar variety (PF98095) of P. frutescens (L.) var. frutescens Britt., which was assembled as reference and other three varieties (PF11109, weedy of var. frutescens, PF06336 and PF06353, cultivars of varieties crispa) in order to carry out comparative expression profiling within cultivar and weedy in varieties frutescens and between varieties frutescens and varieties crispa of cultivar type in P. frutescens. Assembly of PF98095, annotation mapping, DEG (differentially expressed gene) profiling, and comparative analysis were performed. We found that more than 65% of the reads were mapped to the reference of P. frutescens gene set. Moreover, we detected 22,962 DEGs in the weedy variety compared to the cultivar, and also, 22,138 and 23,845 DEGs were identified in two cultivars according to the reference, respectively. The DEGs and functional classification were developed to analyze the differences between weedy and cultivar and between varieties frutescens and varieties crispa of Perilla. Furthermore, candidate genes for the different color and seed size of Perilla were identified that could be further investigated in future study. The herein results may play a significant role, and contribute in functional transcriptome studies of Perilla.
authors.affiliation: Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 340-702, Republic of Korea.
authors.forename: Wei
authors.initials: W
authors.lastname: Tong
authors.affiliation: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea.
authors.forename: Soon-Jae
authors.initials: SJ
authors.lastname: Kwon
authors.affiliation: National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Jeongsoo
authors.initials: J
authors.lastname: Lee
authors.affiliation: National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.affiliation: Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 340-702, Republic of Korea.
authors.forename: Yong-Jin
authors.initials: YJ
authors.lastname: Park
authors.affiliation: Department of Applied Plant Sciences, Oriental Bio-herb Research Institute, Kangwon National University, Chuncheon 200-701, Republic of Korea.
authors.forename: Seung Hun
authors.initials: SH
authors.lastname: Choi
authors.affiliation: Department of Applied Plant Sciences, Oriental Bio-herb Research Institute, Kangwon National University, Chuncheon 200-701, Republic of Korea.
authors.forename: Kyu Jin
authors.initials: KJ
authors.lastname: Sa
authors.affiliation: Department of Applied Plant Sciences, Oriental Bio-herb Research Institute, Kangwon National University, Chuncheon 200-701, Republic of Korea.
authors.forename: Byeong Wan
authors.initials: BW
authors.lastname: Kim
authors.affiliation: Department of Applied Plant Sciences, Oriental Bio-herb Research Institute, Kangwon National University, Chuncheon 200-701, Republic of Korea. Electronic address: jukyonglee@kangwon.ac.kr.
authors.forename: Ju Kyong
authors.initials: JK
authors.lastname: Lee
mesh_terms: D020451:Contig Mapping; D018506:Gene Expression Regulation, Plant; D058977:Molecular Sequence Annotation; D031344:Perilla frutescens / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant
keywords: DEG profiling; Leaf color; Perilla; Transcriptome; Weedy and cultivar