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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 . [ABSTRACT FROM AUTHOR]