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The essential oil of Melaleuca alternifolia is increasingly popular for its naturally occurring pharmacological properties, which is widely used in daily necessities and cosmetics. Understanding the genetic basis of M. alternifolia can also provide useful molecular information that can improve the potential for essential oil yield in breeding. Here, we first reported the genome of M. alternifolia at the chromosome level to anchor the 331.11 Mb sequences into 11 pseudochromosomes with a scaffold N50 of 31.72 Mb. Comparative genomic analysis showed that several genes from the M. alternifolia genome may have evolved toward more terpenoids metabolites by natural selection, including MaSE , MaSDR1 , MaKAO , MaGA20ox , MaISPF , MaDXS , MaHMGS , and MaIDI. Metabolomics data showed that sesquiterpenoids and monoterpenoids were the main categories of volatile organic compounds (VOCs), the contents of most of which were significantly higher in leaves than in roots and stems, suggesting that they are important bioactive constituents of essential oils in the leaves of M. alternifolia. Coexpression and ceRNA network results indicated that the identified class of miR156 may affect the biosynthesis of terpenoids by regulating the expression of related genes. Integrated whole-transcriptome and metabolome analyses showed that the members of the CYP450 and terpene synthase (TPS) gene families exhibited a high correlation with terpenoids accumulation, which can be responsible for terpenoids biosynthesis via complex regulatory networks, including MaCYP76F14 , MaCYP76B10 , MaCYP76A26 , MaCYP82G1 , MaTPS2 , and MaTPS4. These results provide a good insight into the molecular mechanisms of terpenoids biosynthesis in M. alternifolia and will provide basic research and technical support for high yields of essential oils in crop molecular breeding. [Display omitted] • This is the first report of a chromosome-level genome o f Melaleuca alternifolia. • Terpenoids are important bioactive constituents of essential oils. • miR156 may play key role in the biosynthesis of terpenoids. • CYP450 and TPS exhibited a highly correlation with terpenoids accumulation. [ABSTRACT FROM AUTHOR]

• This is the first report of a chromosome-level genome of Cyclocarya paliurus. • Whole-genome duplication event of Cyclocarya paliurus occurred at 3.22–4.86 Mya. • Metabolites accumulation has a strong correlation with genes expression. Cyclocarya paliurus is an endangered medicinal plant of the genus Cyclocarya within the family Juglandaceae, and its leaves have been widely used for the development of healthy tea and medicine with a variety of pharmacologically bioactive components. This is the first report of an ∼634.90 Mb chromosome-level haploid genome assembly of heterozygous autotetraploid C. paliurus (2n = 4x = 64 chromosomes) with 46,292 protein-coding genes. The phylogenetic tree showed that C. paliurus had a close relationship to J. sigillata , J. regia and C. illinoinensis and phylogenetically diverged from the common ancestor (Juglandales) approximately 24 million years ago (Mya). Comparative genome analysis indicated that only one recent WGD event before the autopolyploidization in C. paliurus was distinct from the juglandoid WGD event and occurred from 3.22 to 4.86 Mya. A total of 626 differentially accumulated metabolites (DAMs) and 6,138 differentially expressed genes (DEGs) were identified and mainly involved in steroid, flavonoid and polysaccharide biosynthesis in C. paliurus leaves at different stages. Metabolomics and transcriptomics data showed that most of the genes related to hypoglycemic metabolite biosynthesis in the 10M-YL and 10M-ML groups were significantly higher than those in the 10M-OL group, including CpHMGS , CpMVK , CpMVD , CpCMK , CpDXS , CpC4Hs , CpCHIs , CpF3Hs , CpF 3′5′ H , CpDFRs , CpANS , CpFK , CpmanA , CpmanB , CpRHM , and CpUXE. The results showed that these DEGs have a strong correlation with DAMs in hypoglycemic metabolite biosynthesis, including d -glyceraldehyde-3-phosphate, 1-deoxy- d -xylulose-5′-phosphate, cinnamic acid, fructose, mannose-6-phosphate and UDP-glucose. These findings can help improve the understanding of the molecular mechanism of hypoglycemic metabolites in leaves with different maturities in C. paliurus and provide a theoretical basis and technical support for the development and utilization of C. paliurus. [ABSTRACT FROM AUTHOR]