Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, 54538, Republic of Korea.
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
Sci Rep. 2022 Mar 23;12(1):5001. doi: 10.1038/s41598-022-09032-z.
Solanum nigrum, known as black nightshade, is a medicinal plant that contains many beneficial metabolites in its fruit. The molecular mechanisms underlying the synthesis of these metabolites remain uninvestigated due to limited genetic information. Here, we identified 47,470 unigenes of S. nigrum from three different tissues by de novo transcriptome assembly, and 78.4% of these genes were functionally annotated. Moreover, gene ontology (GO) analysis using 18,860 differentially expressed genes (DEGs) revealed tissue-specific gene expression regulation. We compared gene expression patterns between S. nigrum and tomato (S. lycopersicum) in three tissue types. The expression patterns of carotenoid biosynthetic genes were different between the two species. Comparison of the expression patterns of flavonoid biosynthetic genes showed that 9 out of 14 enzyme-coding genes were highly upregulated in the fruit of S. nigrum. Using CRISPR-Cas9-mediated gene editing, we knocked out the R2R3-MYB transcription factor SnAN2 gene, an ortholog of S. lycopersicum ANTHOCYANIN 2. The mutants showed yellow/green fruits, suggesting that SnAN2 plays a major role in anthocyanin synthesis in S. nigrum. This study revealed the connection between gene expression regulation and corresponding phenotypic differences through comparative analysis between two closely related species and provided genetic resources for S. nigrum.
龙葵，又称黑茄，是一种药用植物，其果实中含有许多有益的代谢物。由于遗传信息有限，这些代谢物合成的分子机制尚未得到研究。在这里，我们通过从头转录组组装从三个不同组织中鉴定出 47470 个龙葵的 unigenes，其中 78.4%的基因具有功能注释。此外，使用 18860 个差异表达基因（DEGs）进行基因本体论（GO）分析表明，基因表达受到组织特异性的调控。我们比较了三个组织类型中龙葵和番茄（Solanum lycopersicum）之间的基因表达模式。两种物种的类胡萝卜素生物合成基因的表达模式不同。比较类黄酮生物合成基因的表达模式表明，14 个酶编码基因中有 9 个在龙葵果实中高度上调。通过 CRISPR-Cas9 介导的基因编辑，我们敲除了 R2R3-MYB 转录因子 SnAN2 基因，该基因是番茄 ANTHOCYANIN 2 的同源基因。突变体表现出黄色/绿色果实，表明 SnAN2 在龙葵中花青素合成中起主要作用。本研究通过对两个密切相关的物种进行比较分析，揭示了基因表达调控与相应表型差异之间的联系，并为龙葵提供了遗传资源。
