Journal Article

Testing the effectiveness of rbcLa DNA-barcoding for species discrimination in tropical montane cloud forest vascular plants (Oaxaca, Mexico) using BLAST, genetic distance, and tree-based methods

Trujillo-Argueta, Sonia, del Castillo, Rafael F., Velasco-Murguía, Abril

2022

Overview

DNA-barcoding is a species identification tool that uses a short section of the genome that provides a genetic signature of the species. The main advantage of this novel technique is that it requires a small sample of tissue from the tested organism. In most animal groups, this technique is very effective. However, in plants, the recommended standard markers, such as rbcL a, may not always work, and their efficacy remains to be tested in many plant groups, particularly from the Neotropical region. We examined the discriminating power of rbcL a in 55 tropical cloud forest vascular plant species from 38 families (Oaxaca, Mexico). We followed the CBOL criteria using BLASTn, genetic distance, and monophyly tree-based analyses (neighbor-joining, NJ, maximum likelihood, ML, and Bayesian inference, BI). rbcL a universal primers amplified 69.0% of the samples and yielded 91.3% bi-directional sequences. Sixty-three new rbcL a sequences were established. BLAST discriminates 80.8% of the genus but only 15.4% of the species. There was nil minimum interspecific genetic distances in Quercus, Oreopanax , and Daphnopsis . Contrastingly, Ericaceae (5.6%), Euphorbiaceae (4.6%), and Asteraceae (3.3%) species displayed the highest within-family genetic distances. According to the most recent angiosperm classification, NJ and ML trees successfully resolved (100%) monophyletic species. ML trees showed the highest mean branch support value (87.3%). Only NJ and ML trees could successfully discriminate Quercus species belonging to different subsections: Quercus martinezii (white oaks) from Q. callophylla and Q. laurina (red oaks). The ML topology could distinguish species in the Solanaceae clade with similar BLAST matches. Also, the BI topology showed a polytomy in this clade, and the NJ tree displayed low-support values. We do not recommend genetic-distance approaches for species discrimination. Severe shortages of rbcL a sequences in public databases of neotropical species hindered effective BLAST comparisons. Instead, ML tree-based analysis displays the highest species discrimination among the tree-based analyses. With the ML topology in selected genera, rbcL a helped distinguish infra-generic taxonomic categories, such as subsections, grouping affine species within the same genus, and discriminating species. Since the ML phylogenetic tree could discriminate 48 species out of our 55 studied species, we recommend this approach to resolve tropical montane cloud forest species using rbcL a, as an initial step and improve DNA amplification methods.

• Publisher: PeerJ. Ltd,PeerJ, Inc,PeerJ Inc
• Subject: Analysis / Animals / Bar codes / Bayes Theorem / Bayesian analysis / Bayesian inference phylogenetic tree / Biodiversity / Cloud forests / Clouds / Conservation Biology / Deoxyribonucleic acid / DNA / DNA Barcoding, Taxonomic - methods / Ecological studies / Explosions / Flowers & plants / Genera / Genetic analysis / Genetic distance / Genomes / Genomics / Methods / Mexico / Molecular Biology / Morphology / Neighbor joining phylogenetic tree / Neotropics / Phylogeny / Plant Science / Plants / Quercus / Solanaceae / Species / Taxonomy / Vascular plants / Working groups