School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
Dingxi Academy of Agricultural Sciences, Dingxi, China.
Sci Rep. 2023 Apr 5;13(1):5602. doi: 10.1038/s41598-023-32493-9.
Scutellaria baicalensis has been one of the most commonly used traditional Chinese medicinal plants in China for more than 2000 years. The three new varieties cultivated could not be distinguished by morphology before flowering. It will hinder the promotion of later varieties. Chloroplast DNA has been widely used in species identification. Moreover, previous studies have shown that complete chloroplast genome sequences have been suggested as super barcodes for identifying plants. Therefore, we sequenced and annotated the complete chloroplast genomes of three cultivated varieties. The chloroplast genomes of SBW, SBR, and SBP were 151,702 bp, 151,799 bp, and 151,876 bp, which contained 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The analysis of the repeat sequences, codon usage, and comparison of chloroplast genomes shared a high degree of conservation. However, the sliding window results show significant differences among the three cultivated varieties in matK-rps16 and petA-psbJ. And we found that the matK-rps16 sequence can be used as a barcode for the identification of three varieties. In addition, the complete chloroplast genome contains more variations and can be used as a super-barcode to identify these three cultivated varieties. Based on the protein-coding genes, the phylogenetic tree demonstrated that SBP was more closely related to SBW, in the three cultivated varieties. Interestingly, we found that S. baicalensis and S. rehderiana are closely related, which provides new ideas for the development of S. baicalensis. The divergence time analysis showed that the three cultivated varieties diverged at about 0.10 Mya. Overall, this study showed that the complete chloroplast genome could be used as a super-barcode to identify three cultivated varieties of S. baicalensis and provide biological information, and it also contributes to bioprospecting.
黄芩是中国使用了 2000 多年的最常用的传统中药植物之一。在开花前，这三个新培育的品种无法通过形态学区分。这将阻碍后期品种的推广。叶绿体 DNA 已广泛用于物种鉴定。此外，先前的研究表明，完整的叶绿体基因组序列已被提议作为鉴定植物的超级条形码。因此，我们对这三个栽培品种的完整叶绿体基因组进行了测序和注释。SBW、SBR 和 SBP 的叶绿体基因组分别为 151702bp、151799bp 和 151876bp，其中包含 85 个蛋白编码基因、36 个 tRNA 基因和 8 个 rRNA 基因。重复序列、密码子使用和叶绿体基因组比较的分析表明它们高度保守。然而，滑动窗口结果显示，在 matK-rps16 和 petA-psbJ 这两个区域，这三个栽培品种之间存在显著差异。我们发现 matK-rps16 序列可作为鉴定这三个品种的条形码。此外，完整的叶绿体基因组包含更多的变异，可作为超级条形码用于鉴定这三个栽培品种。基于蛋白质编码基因，系统发育树表明，在这三个栽培品种中，SBP 与 SBW 的亲缘关系更近。有趣的是，我们发现黄芩和滇黄芩的亲缘关系很近，这为黄芩的开发提供了新的思路。分歧时间分析表明，这三个栽培品种大约在 0.10Mya 时发生分歧。总的来说，本研究表明，完整的叶绿体基因组可作为鉴定黄芩三个栽培品种的超级条形码，提供生物信息，并有助于生物勘探。
