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Background   Cinnamomum camphora  has been cultivated as an economically important tree for its medicinal and aromatic properties. Selective breeding has produced  Cinnamomum  plants for special uses, including spice strains with characteristic flavors and aromas and high-potency medicinal cultivars. The molecular biology underlying terpenoid biosynthesis is still unexplored.    Results  Gas chromatography-mass spectrometry was used to analyze the differences in contents and compositions of essential oil terpenoids in linalool- and borneol-type chemotypes of  C. camphora . The data revealed that the essential oils consist primarily of monoterpenes with only very minor quantities of sesquiterpenes and diterpenes and that the essential oil differs in different chemotypes of  C. camphora , with higher yields of (−)-borneol from the borneol-type than from the linalool-type. To study the terpenoid biosynthesis of signature compounds of the major monoterpenes, we performed RNA sequencing to profile the leaf transcriptomes of the two chemotypes of  C. camphora . A total of 23.76 Gb clean data was generated from two chemotypes and assembled into 156,184 unigenes. The total length, average length, N50 and GC content of unigenes were 155,645,929 bp, 997 bp, 1430 bp, and 46.5%, respectively. Among them, 76,421 unigenes were annotated by publicly available databases, of which 67 candidate unigenes were identified to be involved in terpenoid biosynthesis in  C. camphora . A total of 2863 unigenes were identified to be differentially expression between borneol-type and linalool-type, including 1714 up-regulated and 1149 down-regulated unigenes. Most genes encoding proteins involved in terpenoid precursor MVA and MEP pathways were expressed in similar levels in both chemotypes of  C. camphora . In addition, 10 and 17 DEGs were significantly enriched in the terpene synthase activity and oxidoreductase activity terms of their directed acyclic graphs (DAG), respectively. Three monoterpene synthase genes,  TPS14-like1, TPS14-like2  and  TPS14-like3  were up-regulated in the borneol-type compared to the linalool-type, and their expression levels were further verified using quantitative real-time PCR.    Conclusions  This study provides a global overview of gene expression patterns related to terpenoid biosynthesis in  C. camphora , and could contribute to a better understanding of the differential accumulation of terpenoids in different  C. camphora  chemotypes.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4941-1) contains supplementary material, which is available to authorized users.

Transcriptome analysis and identification of genes related to terpenoid biosynthesis in Cinnamomum camphora