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

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 solut...

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Bibliographic Details
Published in:BMC genetics 2014-12, Vol.15 (1), p.138-138, Article 138
Main Authors: Dong, Wenpan, Liu, Han, Xu, Chao, Zuo, Yunjuan, Chen, Zhongjian, Zhou, Shiliang
Format: Article
Language:English
Subjects:
Analysis
Canned foods industry
Case studies
Chloroplasts
Deoxyribonucleic acid
Discrimination
DNA
DNA Barcoding, Taxonomic
Endangered & extinct species
Evolution
Genes
Genes, Plant
Genetic Markers
Genetic research
Genome, Chloroplast
Genomes
International economic relations
Panax
Panax - genetics
Plant sciences
Sequence Analysis, DNA
Success
Wildlife conservation
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Summary: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. 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%. 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.
ISSN:1471-2156
1471-2156
DOI:10.1186/s12863-014-0138-z