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

Abstract

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.

Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

“…Although the average values were not much different between plastomic and matK data, the minimum value of matK (0.005) was much lower than that of the plastome (0.012). While some previous studies showed that matK was not able to identify all species in some close taxonomic groups [65,66], our result suggests that the entire cp genome could do better than matK in identifying closely related species. The chloroplast genome was proposed to be used as meta-barcode by some previous studies [61][62][63][64].…”

Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera

“…[3]), protecting endangered species (e.g. [4]), controlling agricultural pests (e.g. [5]), and identifying diseases (e.g.…”

“…Many papers on barcoding methodology choose to focus on issues other than the species concept, e.g., on the quality of primer annealing to DNA, the different strategies for matching an unknown query sequence with sequences in a reference database, the use of BLAST scores, etc. [4], but the species definition lies at the heart of DNA barcoding. For general reference sets of sequence data, however, investigators often turn to GenBank [9], where non-experts may have submitted the species annotations (e.g., [10]).…”

In vitro propagation and DNA barcode analysis of the endangered Silene schimperiana in Saint Katherine protectorate

“…The results of the present study show a successful identification of Silene schimperiana on the species and genus levels. The success of species identification using DNA barcoding is contributing to the availability of nucleotide data of the corresponding taxa in the DNA sequences database [37]. However, additional experiments with other markers to entirely identify the plant more accurately are required.…”