The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens

Abstract

The palm family (Arecaceae) is of high ecological and economic value, yet identification in the family remains a challenge for both taxonomists and horticulturalists. The family consists of approximately 2600 species across 181 genera and DNA barcoding may be a useful tool for species identification within the group. However, there have been few systematic evaluations of DNA barcodes for the palm family. In the present study, five DNA barcodes (rbcL, matK, trnH-psbA, ITS, ITS2) were evaluated for species identification ability across 669 samples representing 314 species and 100 genera in the Arecaceae, employing four analytical methods. The ITS gene region was found to not be a suitable barcode for the palm family, due in part, to low recovery rates and paralogous gene copies. Among the four analyses used, species resolution for ITS2 was much higher than that achieved with the plastid barcodes alone (rbcL, matK, trnH-psbA), and the barcode combination ITS2 + matK + rbcL gave the highest resolution among all single barcodes and their combinations, followed by ITS2 + matK. Among 669 palm samples analyzed, 110 samples (16.3%) were found to be misidentified. The 2992 DNA barcode sequences generated in this study greatly enriches the existing identification toolbox available to plant taxonomists that are interested in researching genetic relationships among palm taxa as well as for horticulturalists that need to confirm palm collections for botanical garden curation and horticultural applications. Our results indicate that the use of the ITS2 DNA barcode gene region provides a useful and cost-effective tool to confirm the identity of taxa in the Palm family.

Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships

“…Consistent with the diverse patterns found in most angiosperms [ 56 – 58 ], sequence divergence in non-coding regions is higher than that in coding regions. Variable chloroplast sequences have been widely used for plant phylogeny reconstruction [ 58 , 59 ] and for species identification [ 60 , 61 ]. However, among the chloroplast sequences which have most frequently been used in phylogeny reconstruction of tribe Maleae, such as trnH-psbA , trnL - trnF and trnG-trnS, etc .…”

Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants

“…Plant material for most endangered, rare and narrowly distributed species are difficult to gather in the field, whereas botanical gardens and arboretums typically hold a wide diversity of well-documented living plant collections, which are important resources for the purpose of scientific research, conservation, display and education [13]. However, the morphological characters of plants growing in ex situ conditions may change, which may lead to misidentification if the plants lack complete or clear origin information.…”

“…In addition, mislabeling and misidentification before and after introduction into botanical gardens may also be a major cause of species misidentification. Misidentification of species collected from botanical gardens were reported in recent studies [11,13,14], which caused the incorrect inference of phylogenetic relationships and biogeographic history inferences. For instance, Le et al [13] found that 110 out of 669 palm samples (16.4%) collected from botanical gardens were misidentified, which can also be a problem for reintroduction efforts.…”

“…Misidentification of species collected from botanical gardens were reported in recent studies [11,13,14], which caused the incorrect inference of phylogenetic relationships and biogeographic history inferences. For instance, Le et al [13] found that 110 out of 669 palm samples (16.4%) collected from botanical gardens were misidentified, which can also be a problem for reintroduction efforts. De Luca et al [15] confirmed some Erythrina plants introduced or now cultivated in the ancient gardens of Naples were misidentified.…”

“…De Luca et al [15] confirmed some Erythrina plants introduced or now cultivated in the ancient gardens of Naples were misidentified. Therefore, misidentification may spread misleading knowledge and result in the failure of species conservation, whereas verifying the identification of cultivated plant samples using DNA barcodes possibly can avoid misidentification leading to mistakes in biological studies or in conservation-linked reintroduction programs [13].…”