已有 3677 次阅读 2015-1-23 13:28 |系统分类:论文交流



A chloroplast genomic strategy for designing taxonspecific DNA mini-barcodes: a case study on ginsengs

Wenpan Dong1, Han Liu1, Chao Xu1, Yunjuan Zuo3, Zhongjian Chen2* and Shiliang Zhou1*


最近我们做的人参属DNA条形码的工作在线发表。人参属包括很重要的药材,人参,三七,西洋参等,对于中药材的鉴定,有时候比较困难,很多时候药材都是经过炮制的,用常规的DNA条形码鉴定存在实验技术难题,在本研究中我们利用叶绿体基因组开发了适合人参属鉴定的mini-barcode, 经过验证,这些片段可以很好的鉴定人参属的所有物种。本研究探讨了利用叶绿体基因组开发物种专一、高分辨率的DNA条形码的方法。




Universalconventional DNA barcodes will become more and more popular in biologicalmaterial identifications. However, in many cases such as processed medicines orcanned food, the universal conventional barcodes are unnecessary and/orinapplicable due to DNA degradation. DNA mini-barcode is a solution for suchspecific purposes. Here we exemplify how to develop the best mini-barcodes forspecific taxa using the ginseng genus (Panax) as an example.


Thechloroplast genome of P. notoginseng was sequenced. The genome wascompared with that of P. ginseng. Regions of the highest variabilitywere sought out. The shortest lengths which had the same discrimination powersof conventional lengths were considered the best mini-barcodes. The resultsshowed that the chloroplast genome of P. notoginseng is 156,387 bp.There are only 464 (0.30%) substitutions between the two genomes. The intron ofrps16 and two regions of the coding gene ycf1, ycf1a and ycf1b,evolved the quickest and served as candidate regions. The mini-barcodes of Panaxturned out to be 60 bp for ycf1a at a discrimination power of91.67%, 100 bp for ycf1b at 100%, and 280 bp for rps16at 83.33%.


Thestrategy by searching the whole chloroplast genomes, identifying the mostvariable regions, shortening the focal regions for mini-barcodes are believedto be efficient in developing taxon-specific DNA mini-barcodes. The best DNAmini-barcodes are guaranteed to be found following this strategy.

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