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Article|20 Jan 2022|OPEN
Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis
Thiti Suttiyut1,2 ,† , Robert P. Auber2,3 ,† , Manoj Ghaste1,2 and Cade N. Kane2,4 , Scott A.M. McAdam2,4 , Jennifer H. Wisecaver2,3 , , Joshua R. Widhalm,1,3 ,
1Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
2Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
3Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
4Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
*Corresponding author. E-mail:,
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhab087 (2022)
Views: 361

Received: 30 Jun 2021
Accepted: 07 Dec 2021
Published online: 20 Jan 2022


Plant specialized 1,4-naphthoquinones present a remarkable case of convergent evolution. Species across multiple discrete orders of vascular plants produce diverse 1,4-naphthoquinones via one of several pathways using different metabolic precursors. Evolution of these pathways was preceded by events of metabolic innovation and many appear to share connections with biosynthesis of photosynthetic or respiratory quinones. Here, we sought to shed light on the metabolic connections linking shikonin biosynthesis with its precursor pathways and on the origins of shikonin metabolic genes. Downregulation of Lithospermum erythrorhizon geranyl diphosphate synthase (LeGPPS), recently shown to have been recruited from a cytoplasmic farnesyl diphosphate synthase (FPPS), resulted in reduced shikonin production and a decrease in expression of mevalonic acid and phenylpropanoid pathway genes. Next, we used LeGPPS and other known shikonin pathway genes to build a coexpression network model for identifying new gene connections to shikonin metabolism. Integrative in silico analyses of network genes revealed candidates for biochemical steps in the shikonin pathway arising from Boraginales-specific gene family expansion. Multiple genes in the shikonin coexpression network were also discovered to have originated from duplication of ubiquinone pathway genes. Taken together, our study provides evidence for transcriptional crosstalk between shikonin biosynthesis and its precursor pathways, identifies several shikonin pathway gene candidates and their evolutionary histories, and establishes additional evolutionary links between shikonin and ubiquinone metabolism. Moreover, we demonstrate that global coexpression analysis using limited transcriptomic data obtained from targeted experiments is effective for identifying gene connections within a defined metabolic network.