A haplotype-resolved gap-free genome assembly provides novel insight into monoterpenoid diversification in Mentha suaveolens ‘Variegata’

Abstract

Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, a gap-free assembly with a genome size of 414.3 Mb and 31,251 coding genes was obtained for Mentha suaveolens ‘Variegata’. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, with genome sizes of 401.9 and 405.7 Mb, respectively. The telomeres and centromeres of each haplotype were almost fully annotated. In addition, we detected a total of 41,135 structural variations. Enrichment analysis demonstrated that genes involved in terpenoid biosynthesis were affected by these structural variations. Analysis of volatile metabolites showed that M. suaveolens mainly produces piperitenone oxide rather than menthol. We identified three genes in the M. suaveolens genome which encode isopiperitenone reductase (ISPR), a key rate-limiting enzyme in menthol biosynthesis. However, the transcription levels of ISPR were low. Given that other terpenoid biosynthesis genes were expressed, M. suaveolens ISPRs may account for the accumulation of piperitenone oxide in this species. The findings of this study may provide a valuable resource for improving the detection rate and accuracy of genetic variants, thereby enhancing our understanding of their impact on gene function and expression. Moreover, our haplotype-resolved gap-free genome assembly offers novel insights into molecular marker-assisted breeding of Mentha.

Acknowledgements

This work was supported by introduces the talented person scientific research start funds subsidization project of Chengdu University of Traditional Chinese Medicine (030040015, 030040017) and Hubei science and technology planning project (2020BCB038).

Author Contributions

H.Y., C.S., L.L., C.W., and S.C conceived and supervised the study. H.Y., and G.Z. prepared the materials. Z.W., L.Y., H.T., G. C., and X.K. performed genome assembly and annotation. T.H., H.Z., X.T., and Z.L. analyzed the data. X.T., H.Y., Y.W., and Y.Z. drew the figures. H.Y., S.Z., C.S., L.L., and C.W wrote the manuscript. All authors read and approved the final manuscript.

Data availability statement

The genome data of M. suaveolens were uploaded in 1 K Medicinal Plant Genome Database (http://www.herbgenome.com) [63]. RNA-seq data of different tissues were available in NCBI under Biological Project ID (PRJNA938973, https://dataview.ncbi.nlm.nih.gov/object/PRJNA938973?reviewer=mp56u3u4kcflnb7g3q0gum9qmg).

Conflict of interests

The authors declare that they have no conflict of interest.

Supplementary information

Supplementary data is available at Horticulture Research online.

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