Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis
Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis
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DOI：
10.1038/s41438-020-0301-9
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发表时间：
2020-06-01
影响因子：
8.7
通讯作者：
Wisecaver, Jennifer H.
中科院分区：
文献类型：
--
作者：
Auber, Robert P.;Suttiyut, Thiti;Wisecaver, Jennifer H.
紫草是紫草科紫草科植物，具有重要的药用价值和经济价值。红花紫草根已经被使用了几个世纪，基于生物活性化合物紫草素及其衍生物产生的抗病毒和伤口愈合特性。最近，紫草素及其对映体紫草素和其他几种紫草素/紫草宁衍生物已成为有价值的天然着色剂和新型药物支架。尽管已经从红曲霉中产生了几个转录本和蛋白质组，但仍然没有参考基因组。这限制了对紫草素/紫草素途径的阐明及其进化和生态学意义的研究。在这项研究中，我们使用牛津纳米孔长读测序技术和光敏短读测序技术相结合的方法获得了红曲霉的从头基因组组装。得到的基因组长度与367.41Mb相似，重叠群N50大小为314.31kb，预测了27,720个蛋白质编码基因。利用红曲霉的基因组，我们鉴定了另外几个对羟基苯甲酸香叶转移酶(PGT)同源物，并提供了对它们的进化历史的洞察。对戊烯基转移酶的系统发育分析表明，PGTS起源于现代紫草素/紫草素产生的紫草科物种的共同祖先，可能来自祖先的戊烯基转移酶基因的逆转录转座衍生的重复事件。此外，通过抑制LePGT1在红花毛状根中的表达表明，LePGT1是紫草素产生的主要原因。综上所述，本研究报告的参考基因组和所提供的紫草素/紫草素生物合成进化起源的分析将指导阐明该途径的其余部分。
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 similar to 367.41Mb long, with a contig N50 size of 314.31kb 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.