DNA Barcoding Bromeliaceae: Achievements and Pitfalls

Abstract

BackgroundDNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost.Methodology/Principal FindingsIt is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH–psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling.Conclusions/SignificanceOur results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these complex botanical groups.

The Internal Transcribed Spacer (ITS) Region and trnhH-psbA Are Suitable Candidate Loci for DNA Barcoding of Tropical Tree Species of India

“…However, we were able to get high-quality bidirectional sequences with the success rate falling next to rbcL, which is considered the most efficient barcode locus as far as sequence quality is considered. The high quality bidirectional sequence was also obtained by Maia et al in the family Bromeliaceae, where only 2 out of 101 samples failed in generating high quality trnH-psbA bidirectional sequences after the second trial [9]. Except for the low PCR amplification rate of trnH-psbA , our study agrees with the findings of the work reported by Gonzalez et al [6], where they observed that trnH-psbA was the best performing locus for barcoding Amazonian trees.…”

“…In a recent study, it has been predicted that over half of the estimated 11,000 Amazonian tree species may face a direct risk of extinction [1].Thus, there is an urgent need to carry out an inventory and manage diversity using innovative tools, like DNA barcoding. Significant progress has been made in mapping the Neotropical plants during the last decades [2]–[5], including studies on DNA barcoding in tree species [6] and other plant species [7]–[9]. However, such studies on tree species of India are lacking.…”

Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations

“…Other candidates include nuclear ribosomal genes [7]; however, their utility as DNA barcodes may be limited by incomplete concerted evolution, fungal contamination, and amplification failure [3]. Although DNA barcoding using multiple genes has proven successful with high resolution for phylogenetically diverse communities, e.g., Panamian trees (98% species discrimination, [8]), Mesoamerican orchids and Kruger National Park trees (> 90% species identification, [9]), but see Gonzalez et al (< 70% species identification, [10] for Amazonian trees), barcoding studies of single clades have had limited success, e.g., 43.5% species discriminated in Bromeliaceae [11], and 32% in Fraxinus [12]. Alternative candidates for DNA barcodes are low-copy nuclear genes, which have received little attention (i.e., [13]).…”

Molecular and Morphological Diversity of Lithothamnion spp. (Hapalidiales, Rhodophyta) from Deepwater Rhodolith Beds in the Northwestern Gulf of Mexico

“…Taking into account the results of the pairwise distance distribution analysis (Fig. 4), this may be a result of psbA being more conserved than COI, considering that studies in other taxonomic groups have shown conserved genes lead to paraphyletic relationships and unresolved phylogenies (Maia et al 2012).…”