Abstract
DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication of hawthorn materials in natural health products.
Highlights
The main aim of DNA barcoding is to identify an unknown organism by comparing a DNA sequence from the unknown with records in a database of identified sequences, based on some measure of genetic similarity (Hebert et al 2003a; Chase et al 2005; Ross et al 2008; Seberg and Petersen 2009; Hollingsworth et al 2011; Dong et al 2012) or combination of diagnostic sequence characters (Reid et al 2011; Weitschek et al 2013)
We will comment on the additional information that our DNA barcode data provide and on the serious limitations that our results place on using DNA barcodes to identify hawthorn species and authenticate hawthorn natural health products (NHPs)
We have examined the utility of DNA barcoding in a sample of 355 accessions representing 93 mostly specieslevel taxa from all major clades known to date, in a moderately large plant genus, Crataegus
Summary
The main aim of DNA barcoding is to identify an unknown organism by comparing a DNA sequence from the unknown with records in a database of identified sequences, based on some measure of genetic similarity (Hebert et al 2003a; Chase et al 2005; Ross et al 2008; Seberg and Petersen 2009; Hollingsworth et al 2011; Dong et al 2012) or combination of diagnostic sequence characters (Reid et al 2011; Weitschek et al 2013). The Barcode of Life Data Systems (BOLD) database (Ratnasingham and Hebert 2007) plays an important role as a centralized and curated depository for DNA barcode sequences that is effective in archiving and making accessible detailed voucher information for each organism from which the sequence was obtained. It remains to be seen to what extent these markers can assist identification in closely related plant taxa that are difficult to identify because, for example, there is a limited number of characters, not all of which are necessarily present at the phenological stage of a given specimen
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