Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae
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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.
Cite this as
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 PeerJ Preprints 6:e26494v1 https://doi.org/10.7287/peerj.preprints.26494v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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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
ITS2+matK+rbcLa combination barcode in FASTA format
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Aisha Tahir conceived and designed the experiments, performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Fatma Hussain conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft, collection of plant specimens.
Nisar Ahmed conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.
Abdolbaset Ghorbani conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.
Amer Jamil conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
Barcode of Life Data System:
DBMPP090-14
DBMPP091-14
DBMPP092-14
DBMPP089-14
DBMPP102-14
DBMPP103-14
DBMPP099-14
DBMPP100-14
DBMPP101-14
DBMPP109-14
DBMPP110-14
DBMPP111-14
DBMPP116-14
DBMPP117-14
DBMPP118-14
DBMPP180-14
DBMPP298-16
DBMPP299-16
DBMPP096-14
DBMPP097-14
DBMPP098-14
DBMPP106-14
DBMPP107-14
DBMPP108-14
DBMPP104-14
DBMPP105-14
DBMPP119-14
DBMPP113-14
DBMPP114-14
DBMPP115-14
Funding
This work was supported by Higher Education Commission Pakistan and International Food Policy Research Institute (IFPRI). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
