A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs
文献类型：期刊论文
| 作者 | Dong, Wenpan; Liu, Han; Xu, Chao; Zuo, Yunjuan2; Chen, Zhongjian1; Zhou, Shiliang |
| 刊名 | BMC GENETICS
 |
| 出版日期 | 2014 |
| 卷号 | 15 |
| 关键词 | Panax Chloroplast genome DNA mini-barcode ycf1 |
| ISSN号 | 1471-2156 |
| DOI | 10.1186/s12863-014-0138-z |
| 文献子类 | Article |
| 英文摘要 | Background: Universal conventional DNA barcodes will become more and more popular in biological material identifications. However, in many cases such as processed medicines or canned food, the universal conventional barcodes are unnecessary and/or inapplicable due to DNA degradation. DNA mini-barcode is a solution for such specific purposes. Here we exemplify how to develop the best mini-barcodes for specific taxa using the ginseng genus (Panax) as an example. Results: The chloroplast genome of P. notoginseng was sequenced. The genome was compared with that of P. ginseng. Regions of the highest variability were sought out. The shortest lengths which had the same discrimination powers of conventional lengths were considered the best mini-barcodes. The results showed that the chloroplast genome of P. notoginseng is 156,387 bp. There are only 464 (0.30%) substitutions between the two genomes. The intron of rps16 and two regions of the coding gene ycf1, ycf1a and ycf1b, evolved the quickest and served as candidate regions. The mini-barcodes of Panax turned out to be 60 bp for ycf1a at a discrimination power of 91.67%, 100 bp for ycf1b at 100%, and 280 bp for rps16 at 83.33%. Conclusions: The strategy by searching the whole chloroplast genomes, identifying the most variable regions, shortening the focal regions for mini-barcodes are believed to be efficient in developing taxon-specific DNA mini-barcodes. The best DNA mini-barcodes are guaranteed to be found following this strategy. |
| 学科主题 | Genetics & Heredity |
| 出版地 | LONDON |
| WOS关键词 | SEQUENCE ; IDENTIFICATION ; PRIMERS ; MARKERS |
| WOS研究方向 | Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:000348227800001 |
| 出版者 | BMC |
| 资助机构 | Ministry of Science and Technology of China [2011FY120200, 2012BAC01B05, 2012AA021602] ; NSFC [30370154] |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/27321]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 作者单位 | 1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 2.Wenshan Coll, Inst Sanqi Res, Wenshan 663000, Yunnan, Peoples R China 3.Chinese Acad Sci, Shanghai Chenshan Plant Sci Res Ctr, Shanghai Chenshan Bot Garden, Shanghai 201602, Peoples R China |
| 推荐引用方式 GB/T 7714 | Dong, Wenpan,Liu, Han,Xu, Chao,et al. A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs[J]. BMC GENETICS,2014,15. |
| APA | Dong, Wenpan,Liu, Han,Xu, Chao,Zuo, Yunjuan,Chen, Zhongjian,&Zhou, Shiliang.(2014).A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs.BMC GENETICS,15. |
| MLA | Dong, Wenpan,et al."A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs".BMC GENETICS 15(2014). |
入库方式： OAI收割
来源：植物研究所
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