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

Abstract

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.

Figure 1

Representative map of the chloroplast genome of Panax notoginseng. The annotation of the genome was performed using DOGMA. The genes that are drawn outside of the circle are transcribed clockwise, while those inside are counterclockwise. Small single copy (SSC), large single copy (LSC), and inverted repeats (IRa, IRb) are indicated.

Figure 2

The patterns of nucleotide substitutions among the two Panax chloroplast genomes. The patterns were divided into 6 types as indicated by the six non-strand-specific base-substitution types (i.e., numbers of considered G to A and C to T sites for each respective set of associated mutation types). The chloroplast genome of P. notoginseng was used as a standard.

Figure 3

Sliding window plots of nucleotide diversity (π) across the complete chloroplast genome of the two Panax species (window length: 600 bp, step size: 25 bp). Y-axes: nucleotide diversity (π) of each window; X-axes: position of the midpoint of a window.

Figure 4

Genetic distance-based discrimination power changes along with the increase of sequence lengths. Pm: maximum percentage of samples discriminated.