Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications

Abstract

DNA barcoding, a species identification system based on sequences from a short, standardized DNA region, has emerged recently as a new tool for taxonomists. We investigated the discriminatory power of a subset of highly variable proposed plant barcoding loci (matK, trnH‐psbA, ITS2) in Quercus, a taxonomically complex tree genus of global importance. The research included all currently recognized species and some major variants of the Mediterranean region and Europe (32 taxa) and 17 East Asian and North American species used for comparison. Based on sequence character state, we assigned unique plastid haplotypes to 40.8% of the investigated species; ITS2 increased the resolution up to 87.8% of total taxa. Nevertheless, unsuccessful genetic distance‐based discrimination questioned the potential efficiency of correct species identification for future studies. Most species appeared to be nonmonophyletic in parallel phylogenetic tests. Three subgeneric groups were outlined, with different rates of within‐group variability and geographical differentiation. Members of one of these groups (corresponding to the Eurasian Group Ilex) were paraphyletic to Group Quercus from the New and Old World and the Eurasian Group Cerris. The data gathered indicate that barcoding markers may help to identify closely related species clusters and contribute to the inference of major diversification and evolutionary patterns in oaks, but the methodology per se appears to be of limited efficacy in defining species limits, unless we make a profound revision of traditional Quercus taxonomic categories. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 478–499.

Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding

“…Furthermore, in our study, the overall variation per 100 base pairs in the nuclear regions (17.8%) is nearly three times higher than the variation within the cp genome (6.5%), which is comparable to the findings for oaks [34]. The higher overall variation in nuclear genomes can be explained by the different modes of inheritance for cp (uniparental) and nc (biparental) genomes, and the much higher mutation rates in nuclear genomes [35,36].…”

“…In the research study of the Western China species, where six of the species investigated in this study have also been included, psbK_psbI exposed the highest variations (4.22%), but trnH_psbA also showed a high variation (3.66%) compared with our values [27]. In a recent barcoding study, over 40 species from different sections of the genus Quercus have been analyzed using matK, trnH_psbA, and internal transcribed spacer (ITS) sequences [34]. In this study, matK revealed the lowest sequence variation (5.4%), followed by trnH_psbA (8.1%) and the nuclear ITS region (21.6%).…”

Development of molecular markers for determining continental origin of wood from white oaks (QuercusL. sect.Quercus)

“…Recently, the barcode regions matK and trnH-psbA were evaluated for their power to discriminate select species from oak sections Cerris, Heterobalanus (= "Group Ilex"), Lobatae, and Quercus [34]. In this study, the matK region proved to have too low resolution for the differentiation within the genus; interestingly, for trnH-psbA, the variability was too high to identify fixed interspecific differences [35]. The intergenic linkers trnLF, trnCD and trnDT we found valuable in this work have been widely tested in population and evolutionary genetic studies of plants, and they show wide variation in their ability to discriminate species and lineages [36].…”

A phylogenetic analysis of genus Onobrychis and its relationships within the tribe Hedysareae (Fabaceae)

“…The not "orthodox" position within the section Lophobrychis may be justified by such variability. The difficult phylogenetic reconstruction due to species of hybrid origin is well known in "difficult" genera such as Quercus (Fagaceae) (Simeone et al, 2013) or Rebutia (Cactaceae) (Mosti et al, 2011).…”