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Article|01 Jun 2020|OPEN
Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis
Robert P. Auber1,2, Thiti Suttiyut2,3, Rachel M. McCoy2,3, Manoj Ghaste2,3, Joseph W. Crook2,3, Amanda L. Pendleton1,2, Joshua R. Widhalm2,1, & Jennifer H. Wisecaver1,2,
1Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
2Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
3Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA

Horticulture Research 7,
Article number: 20082 (2020)
doi: 10.1038/hortres.2020.82
Views: 313

Received: 07 Jan 2020
Revised: 06 Mar 2020
Accepted: 31 Mar 2020
Published online: 01 Jun 2020

Abstract

Lithospermum erythrorhizon (red gromwell; zicao) is a medicinal and economically valuable plant belonging to the Boraginaceae family. Roots from L. erythrorhizon have been used for centuries based on the antiviral and wound-healing properties produced from the bioactive compound shikonin and its derivatives. More recently, shikonin, its enantiomer alkannin, and several other shikonin/alkannin derivatives have collectively emerged as valuable natural colorants and as novel drug scaffolds. Despite several transcriptomes and proteomes having been generated from L. erythrorhizon, a reference genome is still unavailable. This has limited investigations into elucidating the shikonin/alkannin pathway and understanding its evolutionary and ecological significance. In this study, we obtained a de novo genome assembly for L. erythrorhizon using a combination of Oxford Nanopore long-read and Illumina short-read sequencing technologies. The resulting genome is 367.41 Mb long, with a contig N50 size of 314.31 kb and 27,720 predicted protein-coding genes. Using the L. erythrorhizon genome, we identified several additional p-hydroxybenzoate:geranyltransferase (PGT) homologs and provide insight into their evolutionary history. Phylogenetic analysis of prenyltransferases suggests that PGTs originated in a common ancestor of modern shikonin/alkannin-producing Boraginaceous species, likely from a retrotransposition-derived duplication event of an ancestral prenyltransferase gene. Furthermore, knocking down expression of LePGT1 in L. erythrorhizon hairy root lines revealed that LePGT1 is predominantly responsible for shikonin production early in culture establishment. Taken together, the reference genome reported in this study and the provided analysis on the evolutionary origin of shikonin/alkannin biosynthesis will guide elucidation of the remainder of the pathway.