3 years ago

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad
Winston Johnson, Sephra N. Rampersad, Amanda C. Ramdass, Fazeeda N. Hosein, Luke Rostant, Shobha Maharaj, Nigel Austin
The islands of the Caribbean are considered to be a “biodiversity hotspot.” Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology-based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within “best match” and “best close match” criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor-joining tree-based comparisons. The performance of both markers seemed to be species-specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the utility of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad, at least to the genus level, was assessed based on three approved barcodes (matK, rbcL and rpoC1). The Trinidad sequences were accurately identified to the genus level for all plant species successfully amplified and sequenced by the matK and rbcL markers.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/ece3.3220

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