Genome assembly and multi-omics analyses of Isodon lophanthodies provide insights into the distribution of medicinal metabolites induced by exogenous methyl jasmonate.

Background: Isodon lophanthodies is a perennial herb and the whole plant has medicinal value distributed in southern China and southeast Asia. The absence of a reference genome has hindered evolution and genomic breeding research of this species.

Results: In this study, we present a high-quality, chromosome-level genome assembly of I. lophanthodies with integrating PacBio and Hi-C sequencing data. We assembled a genome of 412.78 Mb with a scaffold N50 of ~ 33.43 Mb, organized into 12 pseudochromosomes. This assembly includes 36,324 genes and 209.51 Mb of repetitive sequences. Phylogenetic analysis revealed that I. lophanthodies and its sister species Isodon rubescens diverged approximately 9.99 million years ago (MYA), and shared a recent whole-genome duplication (WGD) event. Combined with the gene expression profile and metabolite fluctuation in response to methyl jasmonate, two key enzymes involved in salicin synthesis pathway were further identified.

Conclusions: This genome assembly provides an essential reference for future research on I. lophanthodies, and enhances our understanding of salicin synthesis and medicinal metabolite profiles in response to exogenous methyl jasmonate.