Arnebia tschimganica is a vulnerable species within the Boraginaceae (Boraginales), which has long been taxonomically debated due to inconsistent molecular and morphological characteristics. Shikonin and its derivatives, which are found in the roots of Boraginaceae species, possess significant pharmacological and industrial potential; however, the regulatory mechanisms underlying their biosynthesis are not yet fully comprehended. The lack of reference genomes for Arnebia species has hindered further research in these fields. Here, this study sequenced and assembled the chromosome-level genome of A. tschimganica, revealing that Boraginales is sister to Lamiales within the lamiids and suggesting that the taxonomic status of A. tschimganica should be regressed from Arnebia to Lithospermum. Arnebia tschimganica has undergone a recent whole-genome duplication that is shared with other Boraginaceae species, and this event has driven the evolution of shikonin biosynthesis. Multi-omics analysis revealed significant differences in shikonin production between A. tschimganica and Lithospermum erythrorhizon, attributing reduced shikonin productions in A. tschimganica to low transcript levels of key biosynthetic genes postdivergence. Furthermore, AtsDSH1, the enzyme responsible for catalyzing the hydroxylation of deoxyshikonin to shikonin in A. tschimganica, was identified and functionally characterized. Two ERF transcription factors were identified as conserved regulators of the dehydroshikonin hydroxylase gene DSH1, potentially regulating shikonin biosynthesis. These findings provide a chromosome-level genomic perspective to clarify the taxonomy of this controversial swing species and advance valuable insights for shikonin biosynthesis regulation.

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