The chromosome-level Melaleuca alternifolia genome provides insights into the molecular mechanisms underlying terpenoids biosynthesis

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.