Ability of rbcL and matK DNA barcodes to discriminate between montane forest orchids

Orchidaceae is among the largest plant families in the world; that is why it is notoriously difficult to identify species using traditional taxonomic methods. This problem is especially apparent in the Andean region of South America, a global hotspot for orchid diversity. Plant DNA barcoding has been proposed to help with orchid species discrimination. However, the utility of the rbcL and matK DNA barcode markers to discriminate between orchid species still needs investigating. The goal of this study is to determine the utility of the rbcL and matK DNA barcode markers to discriminate orchid species from a localized Andean montane forest in Ecuador. A total of 174 samples from the Siempre Verde Preserve, Ecuador, were sequenced, returning 51 unique rbcL and 81 unique matK barcode gene region sequences. Similar rates of sequencing success, rbcL (76%) and matK (75%), were found for both gene regions. Sequences were then queried to GenBank, where top matches were compared to the taxonomic identification of samples. Analysis of 132 unique orchid sequences indicated that, overall, the matK gene region was more robust for species (63%) and genus level (78%) discrimination compared to the rbcL gene region (species: 29%; genus: 36%). However, for 11 of 29 genera, rbcL and matK had similar success at genus level discrimination. Collectively, results emphasize the utility of the matK DNA barcode for the discrimination of orchid taxa and the importance of incorporating taxonomic and genetic methods when investigating the identity of plant species from complex groups.