Thymus , a perennial plant in the Lamiaceae family, is one of the most important medicinal herbs due to its essential oil and major monoterpenes components such as Thymol and Carvacrol. The similarities in morphology, growth pattern, and chemical compounds between some species and Thymus , such as Z. multiflora often leads to incorrect identification and use of Thymus . There are many studies investigating and analyzing the essential oil of Thymus species and Z. multiflora in Iran and worldwide. Despite the recent developments, our knowledge about genomic information, transcriptomics, and key genes involved in the biosynthesis of secondary metabolites in Thymus species is very limited. To date, the majority of molecular studies have been focused on phylogenic relationships between different species by using the limited available genetic information. RNA sequencing can facilitate and accelerate the identification of key genes involved in the biosynthesis pathways of secondary metabolites and investigation of the relationship among species. The present study was aimed to investigate the transcriptomes of T. daenensis، T. vulgaris، T. lancifolius، T. persicus، T. pubescens، T. armeniacus و Z. multiflora , to identify key genes in the biosynthesis of monoterpenoids, and study similarities and differences among these species. To this end, total RNAs extracted from vegetative growth were sent to Macrogene, Korea to be sequenced by Illumina HiSeqTM2500 After assembling the reads using various tools, the best outcome/output was selected and transcripts were annotated in databases including KEGG, Uniport, and Terzyme. Then, key genes responsible in the synthesis of terpenoids were identified based on annotation results. In addition, phylogenetic relationships among species was investigated based on the key genes and single copy orthologs. According to the evaluation criteria/index, the best assembly was a product of Trinity tools. Based on the results from the T identification, most of the contigs were Key Words: Sequencing, transcriptom, phylogenetics, single copy orthologies
