standardDNAWith the advantages of strong universal primer adaptability and low sequencing cost, barcodes are widely used in fields such as biodiversity protection and traceability. For complex taxa with closely related species, frequent hybridization and recent radiation evolution, the standardDNADue to limited sequence variation and insufficient resolution, barcodes are difficult to meet the needs for accurate identification. Although the strategy of shallow genome sequencing to obtain the complete plastid genome (super barcoding) has improved the identification rate of some difficult taxa, the uniparental inheritance characteristics of the plastid genome make it limited in the analysis of introgressed taxa.
近日，中国科学院昆明植物研究所等团队在维管植物物种鉴定领域取得进展。该研究系统评估了基因组浅层测序数据，特别是基于k-mer分析在维管植物物种鉴定中的应用潜力，提出了一套可推广的标准分析流程。
研究选取石松类、蕨类、裸子植物和被子植物代表性类群，覆盖32属、475种共1969份样本进行系统分析。结果表明，标准条形码仅能区分约49.3%的物种，组装质体全基因组可将鉴别率提升至57.6%。进一步应用浅层测序数据的k-mer分析，物种鉴别率显著提高至66.8%，较标准条形码整体提升17.5%。该技术流程兼容现有标准条形码数据库，可有效应对近缘种鉴定难题。研究还明确了基因组大小对k-mer分析的影响，对于基因组大小≤5Gb的类群，在约0.5X测序深度下即可取得良好鉴定效果；对于基因组大小＞5Gb的类群，需对测序数据进行均一化处理后再开展分析。
The study clarified that the use of shallow genome sequencing can significantly improve species identification capabilities, providing a replicable solution for improving the plant DNA barcode reference database and supporting global biodiversity research.
Relevant research results were published in "New Phytologist" (New Phytologist)superior. The research work is supported by the Ministry of Science and Technology’s Science and Technology Basic Resources Survey Project, the Yunnan Province “Prosperous Yunnan Talent Support Plan” Young Talent Project, and the Chinese Academy of Sciences International Talent Plan.
Source: https://www.cas.cn/syky/202608/t20260818_5118524.shtml