Dong Li-Na, Liu Zhi-Fang, Xu Wei-Bin, Yang Jun-Bo, Kidner Catherine A, Hughes Mark, Yan Hai-Fei, Wang Hong, Li De-Zhu
Guangxi Key Laboratory of Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, Guangxi, 541006, China.
Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, Shandong, 250100, China.
BMC Plant Biol. 2025 Jul 24;25(1):953. doi: 10.1186/s12870-025-06948-2.
The accurate identification of herbal medicine is a prerequisite for safe and effective use. DNA barcoding has been widely used for the identification of herbal medicine. However, choosing and refining a suitable barcode is complex in plants. The genus Lysimachia includes over 180 species and is widely used as herbal medicine in China and elsewhere. Species identification within this genus based on morphological, microscopic, or chemical characters is often challenging. In this study, 44 accessions representing 17 putative species of Lysimachia from southern China were sequenced using genome skimming. Whole plastome and nrDNA sequences were successfully recovered from these data. Combining 13 published plastomes of Lysimachia, the discrimination power of standard barcodes, along with plastome and hypervariable sequences from the plastome were compared across 57 plastomes from 22 putative species.
Standard barcodes have limitation in providing accurate species level identification; however, they can facilitate the rapid classification of unknown samples at the generic level. The plastomes exhibit a highly degree of conservation in the structure and gene content, yet they successfully identify all studied taxa. Five highly variable loci from plastomes were identified: petN-psbM, ycf1, rpl22, trnK-rps16, and ndhC-trnV. While these regions improved the discrimination power compared to standard barcodes, they still could not yield accurate identification of all taxa studied. However, when combined with ITS, ycf1 provides 100% successful species identification.
We recommend that the use of whole plastome and the combination of ycf1 + ITS as accurate and effective barcodes for species identification in Lysimachia. This study also highlights the potential for effective use of genome skimming data.
准确鉴定草药是安全有效使用的前提。DNA条形码已广泛用于草药鉴定。然而，在植物中选择和优化合适的条形码很复杂。珍珠菜属包括180多种，在中国和其他地方被广泛用作草药。基于形态、微观或化学特征对该属内的物种进行鉴定往往具有挑战性。在本研究中，对代表中国南方17种假定珍珠菜属物种的44份材料进行了基因组浅层测序。从这些数据中成功获得了完整的叶绿体基因组和nrDNA序列。结合已发表的13个珍珠菜属叶绿体基因组，比较了标准条形码以及来自叶绿体基因组的叶绿体基因组和高变序列在22种假定物种的57个叶绿体基因组中的鉴别能力。
标准条形码在提供准确的物种水平鉴定方面存在局限性；然而，它们可以促进未知样品在属水平上的快速分类。叶绿体基因组在结构和基因含量上表现出高度的保守性，但它们成功地鉴定了所有研究的分类群。从叶绿体基因组中鉴定出五个高变位点：petN-psbM、ycf1、rpl22、trnK-rps16和ndhC-trnV。虽然这些区域与标准条形码相比提高了鉴别能力，但它们仍然不能准确鉴定所有研究的分类群。然而，当与ITS结合时，ycf1能实现100%成功的物种鉴定。
我们建议使用完整的叶绿体基因组以及ycf1 + ITS的组合作为珍珠菜属物种鉴定的准确有效条形码。本研究还强调了有效利用基因组浅层测序数据的潜力。
