Evaluation of DNA barcode candidates for the discrimination of the large plant family Apocynaceae

Abstract

The chloroplast loci matK, rbcL, atpB, rpoC1, plastid spacer region psbA-trnH and nuclear internal transcribed spacer loci ITS sequences were evaluated for its discriminating ability among the closely related medicinal plant species of Apocynaceae. Our main criteria for ranking these barcodes were based on levels of inter and intra-specific divergence. Twenty-one medicinal plants were sequenced for matK, rbcL, atpB, rpoC1, psbA-trnH and ITS. Additionally sequences collected from GenBank were also included in this study. Altogether, 1,876 DNA sequences were used that included 525 sequences belonging to 110 genera of matK, 390 sequences belonging to 68 genera of rbcL, 90 sequences belonging to 13 genera of atpB, 38 sequences belonging to 16 genera of rpoC1, 32 sequences belonging to 27 genera of psbA-trnH and 780 sequences belonging to 70 genera of ITS region. The analyses of inter-specific and intra-specific divergence using the cpDNA spacer region psbA-trnH showed 0.3–0.5 and 0.04–0.2 %, whereas matK showed 0.8–1 and 0.07–0.1 % inter-specific and intra-specific divergence, respectively. Likewise rbcL showed 0.4–0.5 % inter-specific divergence and 0.2–0.1 % intra-specific divergence. The gene rpoC1 showed 0.2–0.3 % inter-specific divergence and 0.02–0.01 % intra-specific divergence, respectively. Similarly atpB showed 0.1–0.4 % inter-specific divergence and 0.09–0.04 % of intra-specific divergence. The nrDNA ITS (ITS1 and ITS2) were analyzed and the results indicated that ITS2 showed better discriminating ability, as it resulted in considerable variation at the generic and species level. The inter-specific divergence in ITS2 ranged from 1 to 9 % with an average of 8 % and the intra-specific divergence ranged from 0.4 to 6 % with an average of 4 %. Thus, ITS2 successfully identified the species and genera at the rate of 91 and 98 %, respectively. The cpDNA spacer psbA-trnH exhibited an identification percentage of 40 and 36 % at the genus and species level, respectively. Additionally ITS2 was also used to authenticate the herbal medicinal species of the genus Caralluma, Rauwolfia and Hoodia. Overall, our data suggest that nuclear ITS2 is the ideal barcode loci to identify/discriminate the large plant family Apocynaceae.