Combined analysis of GC-MS, RNA-seq and ATAC-seq elucidates the essential oils variation and terpenes biosynthesis in Citrus grandis ‘Tomentosa’

Citrus grandis 'Tomentosa' (CGT) contain abundant essential oils (EOs), while the variation of them among different varieties is still unclear which hinders the fully utilization of CGT EOs in industry. Besides, the molecular mechanism underlying the accumulation of EOs in Citrus family remains largely unknown. In this study, multi-omics including GC-MS (gas chromatography-mass spectrometry), RNA-seq (ribonucleic acid sequencing), and ATAC-seq (assay for transposase-accessible chromatin using sequencing) were applied for three varieties of CGT ('ZM', 'FM', and 'GQ') to reveal the CGT EOs variation at the chemical, transcriptional and chromatinic levels. CGT EOs mainly consist of monoterpenes and sesquiterpenes, and the total terpenes amounts in three varieties rank as 'ZM' > 'FM' > 'GQ'. The total amount of monoterpenes in 'ZM' is almost triple than that in 'FM' and is septuple than that in 'GQ'. The average contents of sesquiterpenes in the EOs of 'ZM', 'FM', and 'GQ' are 73.9 ug/g, 42.65 ug/g and 1.75 ug/g, respectively. RNA-seq analysis among the three varieties demonstrated that the structural genes of 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE (DXS) and 1-DEOXY-D-XYLYLOSE 5-PHOSPHATE REDUCTOISOMERASE (DXR) are differentially expressed genes (DEGs) in MEP pathway for the biosynthesis of monoterpenes, and 3-HYDROXY-3-METHYLGLUTARYL-COA REDUCTASE (HMGR) is the DEG for sesquiterpenes synthesis in MVA pathway. Integrated GC-MS, RNA-seq and ATAC-seq analysis reveals 9 transcriptional factors were predicted to regulate the terpenes synthesis in the exocarps of CGT. The present investigation provides important information for manufacturers and breeders of CGT who require raw materials and germplasm of CGT in better quality for the production of EOs.