High-quality chromosome-level genome assembly of Arnebia euchroma reveals insights into ecological adaptability and shikonin biosynthesis

Arnebia euchroma (Royle) I. M. Johnst. is known for producing shikonin, a purplish-red bioactive compound in its roots. This perennial Boraginaceae herb is widely distributed in the frigid Pamir Knot of Asia, and has been extensively utilized in medicine, textile, food and cosmetics industries. Using PacBio and Hi-C technologies, we sequenced and assembled its chromosome-level genome of 2.51 Gb, with Contig N50 at 39.20 Mb and Scaffold N50 at 364.98 Mb. A total of 37,166 protein-coding genes were annotated. Comparative genomic and phylogenomic analyses were performed to explore the molecular basis of its ecological adaptability and evolutionary history. An exceptionally high TEs content of 79.51 % was observed, with two LTR-RTs insertion bursts occurring within the past 0–1 million years, suggesting that A. euchroma may still be in a stage of rapid evolution. Compared with phylogenetic ancestors, A. euchroma shows the expansion of stress resistance gene families that partly explains its genetic adaptation to high-altitude environments. Significant CYP76B subfamily expansion was found, and Aeu01G026690 was first identified as potentially encoding enzyme catalyzing GHQ-3"-OH to deoxyshikonin. Integrated transcriptomic and metabolomic analyses show that deoxyshikonin-to-shikonin step is the key in the difference of shikonin and derivatives between bark and xylem. This high-quality genomic resource offers deeper insights into A. euchroma' s mechanisms of adaptive evolution and shikonin biosynthesis and provides a foundation for plant evolutionary biology and synthetic biology research of A. euchroma , facilitating the conservation and breeding of this species as well as other endangered plant resources in the Boraginaceae family. • First chromosome-level genome assembly of Arnebia euchroma was sequenced and assembled. • Elucidated genomic mechanisms of A. euchroma 's ecological adaptation and evolutionary status. • Revealed deeper insights into A. euchroma 's shikonin biosynthesis. • Aeu01G026690 was first identified as potentially encoding enzyme catalyzing GHQ-3"-OH to deoxyshikonin.