Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

Abstract

A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.land plants | species identification | nuclear ribosomal (nr) DNA T he seed plants account for some 90% of land plant diversity, dominating terrestrial ecosystems and providing food, timber, drugs, fibers, fuels, and ornamentals for human use (1). Identification is an essential step for humans in using and conserving plants. Since the time of Linnaeus, botanists have used a range of character sources as taxonomic evidence for documenting plant biodiversity (2), including gross morphology, anatomy, embryology, palynology, pollination biology, chromosomes, proteins, secondary metabolites, and ad hoc use of DNA sequence data (3). However, it can still be difficult to rapidly and accurately identify plant species. In part, this is because of the huge diversity of plant species and the fact that identifications are often attempted from suboptimal material that lacks the key diagnostic characters. It is especially difficult in the case of closely related species where recent radiation, frequent hybridization, and high intraspecific variation can compound identification problems (4, 5).DNA barcoding, an approach to identify species based on sequences from a short, standardized DNA region, opens up a unique avenue for the identification of organisms (6, 7). Although CO1, a mitochondrial marker, is known to work relatively consistently in animal barcoding, this region has not been adopted for plants because of low substitution rates in the pla...

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

“…Its use has already been shown in Chlorophyta and plants (66,67) as well as in Oomycota (6). The possibility of multikingdom analyses of complex ecosystems like soil using the species-informative, stable, high copy number ITS mirrors the original vision of DNA barcoding, and it already seems feasible, for example, to amplify Fungi and other eukaryotes from soil (23).…”

Impact of pine invasion on the taxonomic and phylogenetic diversity of a relict Mediterranean forest ecosystem

“…This allowed us to assemble the sequence dataset retrieving accessions of most species in our plots from available sources. Second, the (generally) greater discriminatory power of nrITS over plastid regions at low taxonomic levels (species) is well documented in seed plant systematics (e.g., Feliner and Rosselló, 2007;Hollingsworth et al, 2011), supporting this region as a core barcode for spermatophytes (Li et al, 2011). Using these markers allowed us to avoid polytomic groups and to obtain a resolved tree even for those genera with two or more species (e.g., Brachypodium, Cytisus, and others).…”

DNA barcoding of plants: Selection of core markers for taxonomic groups

“…In contrast, plant DNA barcoding is a more complex and it often requires multiple loci. The Consortium for the Barcode of Life (CBOL) plant working group evaluated the efficacy of maturase K (matK) and ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and recommended two-locus based approach with trnH-psbA intergenic spacer as a supplementary marker (3). China Plant Barcode of Life recommended the internal transcribed spacer (ITS) as additional candidate plant DNA barcode.…”