Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae
- Published
- Accepted
- Subject Areas
- Biochemistry, Biotechnology, Molecular Biology, Plant Science
- Keywords
- DNA barcoding, medicinal plants, ribulose bisphosphate carboxylase large chain (rbcLa), species identification, maturase K (matK), internal transcribed spacer region (ITS2), combination barcodes
- Copyright
- © 2018 Tahir et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae. PeerJ Preprints 6:e26494v1 https://doi.org/10.7287/peerj.preprints.26494v1
Abstract
In pursuit of developing fast and accurate species level molecular identification methods, we tested six DNA barcodes viz. ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa, ITS2+matK+rbcLa for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Metadata, BOLD process IDs and GenBank accession numbers of specimens included in the study
Supporting data for Figure 2
Species level discrimination ability of candidate barcodes by BM and BCM analyses