Identification of species in the angiosperm family Apiaceae using DNA barcodes

Abstract

Apiaceae (Umbelliferae) is a large angiosperm family that includes many medicinally important species. The ability to identify these species and their adulterants is important, yet difficult to do so because of their subtle fruit morphological differences and often lack of diagnostic features in preserved specimens. Moreover, dried roots are often the official medical organs, making visual identification to species almost impossible. DNA barcoding has been proposed as a powerful taxonomic tool for species identification. The Consortium for the Barcode of Life (CBOL) Plant Working Group has recommended the combination of rbcL+matK as the core plant barcode. Recently, the China Plant BOL Group proposed that the nuclear ribosomal DNA internal transcribed spacer (ITS), as well as a subset of this marker (ITS2), be incorporated alongside rbcL+matK into the core barcode for seed plants, particularly angiosperms. In this study, we assess the effectiveness of these four markers plus psbA-trnH as Apiaceae barcodes. A total of 6032 sequences representing 1957 species in 385 diverse genera were sampled, of which 211 sequences from 50 individuals (representing seven species) were newly obtained. Of these five markers, ITS and ITS2 showed superior results in intra- and interspecific divergence and DNA barcoding gap assessments. For the matched data set (173 samples representing 45 species in five genera), the ITS locus had the highest identification efficiency (73.3%), yet ITS2 also performed relatively well with 66.7% identification efficiency. The identification efficiency increased to 82.2% when using an ITS+psbA-trnH marker combination (ITS2+psbA-trnH was 80%), which was significantly higher than that of rbcL+matK (40%). For the full sample data set (3052 ITS sequences, 3732 ITS2 sequences, 1011 psbA-trnH sequences, 567 matK sequences and 566 rbcL sequences), ITS, ITS2, psbA-trnH, matK and rbcL had 70.0%, 64.3%, 49.5%, 38.6% and 32.1% discrimination abilities, respectively. These results confirm that ITS or its subset ITS2 be incorporated into the core barcode for Apiaceae and that the combination of ITS/ITS2+psbA-trnH has much potential value as a powerful, standard DNA barcode for Apiaceae identification.

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

“…In conclusion, we support the use of the ITS marker as a supplementary barcode in plants, while the performance of ITS should be evaluated in extensive trials in different plant groups (Liu et al, 2013; Liu J. et al, 2014; Wirta et al, 2016). The pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost, is the combination of T+I (90.5% species resolution), the most efficient and economical marker among single or combined DNA barcodes when identifying tree species in Aceraceae.…”

“…In the past, biologists identified phylogenetic relationships and positions of biological specimens mainly based on morphological features, such as leaves, flower shape, size, and color. However, traditional taxonomy has at least two drawbacks: first, if the specimens are damaged or lack sufficient diagnostic characters, the specialists may be unable to make accurate identifications (Yan et al, 2015); second, morphologically and taxonomically difficult groups sometimes require an experienced professional taxonomist to address species identification (Li et al, 2011; Liu J. et al, 2014). Such taxonomists need training and experience, which require much time, effort and money.…”

“…DNA barcoding is one method that uses standard molecular techniques to achieve rapid and accurate species identification by a short DNA sequence (Hebert et al, 2003; Hebert and Gregory, 2005; Liu et al, 2013; Krawczyk et al, 2014). This method to remedy the limitations of a traditional morphology-based identification system will allow for more rapid progress in traditional taxonomic work (Kress et al, 2005; Liu J. et al, 2014; Nigro et al, 2016). …”

Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes

“…The ITS region was proposed as one of the core and powerful barcodes for seed plants (China Plant BOL Group, 2011), and its utility has also been supported in several barcoding studies (Liu et al, 2011, 2014; Muellner et al, 2011; Pang et al, 2011; Zhang et al, 2012; Chen et al, 2014; Zhang J. Q. et al, 2015). In a barcoding study of Euro-Mediterranean oaks, ITS2 increased the species resolution when combined with two plastid barcoding loci (Simeone et al, 2013); however, by itself, the ITS region showed no species identification when the genetic distance method was applied.…”

Patterns of Genetic Diversity in the Globally Invasive Species Wild Parsnip (Pastinaca sativa)

“…ITS is also useful as a species barcode for angiosperms , and adequate intraspecific and interspecific variation exists at this locus to delineate species within the family Apiaceae (Liu et al 2014). Although ITS has been useful at infrageneric-level analyses, it can also be effective in providing information about population genetic structure (e.g., Besnard et al 2007;Gao et al 2012;Lorenz-Lemke et al 2005).…”