中国中医科学院中药研究所所长陈士林团队开展的中草药DNA条形码生物鉴定体系研究，引发国际广泛关注。具有百年历史的植物学顶级期刊《新植物学家》以及五年平均影响因子超过10的两个国际著名期刊《生物技术前沿》和《生物学评述》分别刊登了其几项最近研究成果。这标志着中药鉴定学迈入通用和标准化的基因鉴定时代。

中草药DNA条形码技术在鉴定领域被公认为一次技术革命：中药材从主观的眼观口尝升级到客观的基因判定，这一革命改变了生药鉴定学科被动追赶其他学科的局面，在鉴定学领域已处于国际学科前沿领先水平。

《生物技术前沿》以“草药鉴定从形态到DNA的文艺复兴”为题，介绍了陈士林团队创建的中草药DNA条形码鉴定体系和鉴定数据库。该数据库收载了包括中、日、韩、美、欧洲和印度药典几乎所有药材品种在内的23262个物种，共计78847条DNA条形码序列。

“该体系可以实现对中药材及其原植物、中药材种子种苗、粉末以及细胞、组织等来源材料的物种准确鉴定，并为中药企业定制中药材DNA条形码鉴定系统，以保障中药生产投料安全。”陈士林介绍，“在这个中药材DNA条形码鉴定系统中，包含序列、条形码、二维码等多种输出格式，可以实现移动客户端查询，一步操作即可实现准确鉴定。”

该鉴定系统收集了各主产区冬虫夏草及其13种混伪品和近缘种共236份，能准确鉴定冬虫夏草和其混伪品与近缘种。

针对亲缘关系很近且难以鉴定的物种，陈士林及其团队提出利用叶绿体基因组作为“超级条形码”鉴定近缘中药材的设想。（来源：科技日报讯  杨朝晖）

High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy

Abstract  A circular consensus sequencing (CCS) strategy involving single molecule, real-time (SMRT) DNA sequencing technology was applied to de novo assembly and single nucleotide polymorphism (SNP) detection of chloroplast genomes.Chloroplast DNA was purified from enriched chloroplasts of pooled individuals to construct a shotgun library for each species. The sequencing reactions were performed on a PacBio RS platform. CCS sub-reads were generated from polymerase reads that passed the native dumbbell-shaped DNA templates multiple times. The complete chloroplast genome sequence was generated by mapping all reads to the draft sequence constructed in a step-by-step manner.The full-chain, PCR-free approach eliminates the possible context-specific biases in library construction and sequencing reaction. The chloroplast genome was easily and completely assembled using the data generated from one SMRT Cell without requiring a reference genome. Comparisons of the three assembled Fritillaria genomes to 34.1 kb of validation Sanger sequences revealed 100% concordance, and the detected intraspecies SNPs at a minimum variant frequency of 15% were all confirmed.This simple approach with potential for parallel sequencing yields high-quality chloroplast genomes for sensitive SNP detection and comparative analyses. We recommend this approach for its powerful applicability for evolutionary genetics and genomics studies in plants based on the sequences of chloroplast genomes.

原文链接：http://onlinelibrary.wiley.com/doi/10.1111/nph.12966/pdf